To list the DataSHIELD profiles:
-dsadmin.profiles(o)dsadmin.profiles(o)
To create a new DataSHIELD profile, to initialize it the DataSHIELD settings as declared by the installed packages and to enable it, use the following.
-# ensure the profile does not exist
-if (dsadmin.profile_exists(o, "demo"))
- dsadmin.profile_delete(o, "demo")
-# create a profile, disabled
-dsadmin.profile_create(o, "demo", cluster = "default")
-# make only dsBase and resourcer packages visible
-dsadmin.profile_init(o, "demo", packages = c("dsBase", "resourcer"))
-# ready to be used
-dsadmin.profile_enable(o, "demo")# ensure the profile does not exist
+if (dsadmin.profile_exists(o, "demo"))
+ dsadmin.profile_delete(o, "demo")
+# create a profile, disabled
+dsadmin.profile_create(o, "demo", cluster = "default")
+# make only dsBase and resourcer packages visible
+dsadmin.profile_init(o, "demo", packages = c("dsBase", "resourcer"))
+# ready to be used
+dsadmin.profile_enable(o, "demo")
When a DataSHIELD R package is installed but should be used only by a restricted group of users, proceed as follow:
-dsadmin.profile_perm_add(o, "demo", subject = "testers", type = "group")
-# verify permissions
-dsadmin.profile_perm(o, "demo")dsadmin.profile_perm_add(o, "demo", subject = "testers", type = "group")
+# verify permissions
+dsadmin.profile_perm(o, "demo")
Settings
@@ -199,25 +199,25 @@ Methods
To list the aggregation functions:
-dsadmin.get_methods(o, type = "aggregate", profile = "demo")
+dsadmin.get_methods(o, type = "aggregate", profile = "demo")
To list the aggregation functions:
-dsadmin.get_methods(o, type = "aggregate", profile = "demo")dsadmin.get_methods(o, type = "aggregate", profile = "demo")Fully custom settings can be defined (useful for developers).
-dsadmin.set_method(o, "hello", func = function(x) { paste0("Hello ", x, "!") }, type = "aggregate", profile = "demo")
-# verfiy custom method
-dsadmin.get_method(o, "hello", type = "aggregate", profile = "demo")dsadmin.set_method(o, "hello", func = function(x) { paste0("Hello ", x, "!") }, type = "aggregate", profile = "demo")
+# verfiy custom method
+dsadmin.get_method(o, "hello", type = "aggregate", profile = "demo")
A simple test of our custom hello() function would
be:
-library(DSOpal)
-builder <- DSI::newDSLoginBuilder()
-builder$append(server = "study1", url = "https://opal-demo.obiba.org",
- user = "administrator", password = "password",
- profile = "demo")
-logindata <- builder$build()
-conns <- DSI::datashield.login(logins = logindata)
-# call the hello() function on the R server
-datashield.aggregate(conns, expr = quote(hello('friends')))
-datashield.logout(conns)library(DSOpal)
+builder <- DSI::newDSLoginBuilder()
+builder$append(server = "study1", url = "https://opal-demo.obiba.org",
+ user = "administrator", password = "password",
+ profile = "demo")
+logindata <- builder$build()
+conns <- DSI::datashield.login(logins = logindata)
+# call the hello() function on the R server
+datashield.aggregate(conns, expr = quote(hello('friends')))
+datashield.logout(conns)
Options
@@ -225,9 +225,9 @@ OptionsThe DataSHIELD R options affects the behaviour of some methods.
To modify an R option:
-dsadmin.set_option(o, "datashield.privacyLevel", "10", profile = "demo")
-# verify options
-dsadmin.get_options(o, profile = "demo")
+dsadmin.set_option(o, "datashield.privacyLevel", "10", profile = "demo")
+# verify options
+dsadmin.get_options(o, profile = "demo")
To modify an R option:
-dsadmin.set_option(o, "datashield.privacyLevel", "10", profile = "demo")
-# verify options
-dsadmin.get_options(o, profile = "demo")dsadmin.set_option(o, "datashield.privacyLevel", "10", profile = "demo")
+# verify options
+dsadmin.get_options(o, profile = "demo")R Parser
@@ -239,7 +239,7 @@ R Parser for possible values.
To set the legacy R parser:
-dsadmin.profile_rparser(o, "demo", rParser = "v1")
+dsadmin.profile_rparser(o, "demo", rParser = "v1")
To set the legacy R parser:
-dsadmin.profile_rparser(o, "demo", rParser = "v1")dsadmin.profile_rparser(o, "demo", rParser = "v1")
@@ -255,12 +255,12 @@ Users
group(s). Groups can represent data access and DataSHIELD service
access.
Users
group(s). Groups can represent data access and DataSHIELD service
access.
-if (oadmin.user_exists(o, "userx"))
- oadmin.user_delete(o, "userx")
-# generated password
-password <- oadmin.user_add(o, "userx", groups = c("demo", "datashield"))
-# verify user
-subset(oadmin.users(o), name == "userx")
+if (oadmin.user_exists(o, "userx"))
+ oadmin.user_delete(o, "userx")
+# generated password
+password <- oadmin.user_add(o, "userx", groups = c("demo", "datashield"))
+# verify user
+subset(oadmin.users(o), name == "userx")
-if (oadmin.user_exists(o, "userx"))
- oadmin.user_delete(o, "userx")
-# generated password
-password <- oadmin.user_add(o, "userx", groups = c("demo", "datashield"))
-# verify user
-subset(oadmin.users(o), name == "userx")Permissions
@@ -269,23 +269,23 @@ Permissions
-lapply(opal.tables(o, "CNSIM")$name, function(table) {
- opal.table_perm_add(o, "CNSIM", table, subject = "demo", type = "group", permission = "view")
-})
-# verify table permissions
-opal.table_perm(o, "CNSIM", "CNSIM1")
-lapply(opal.tables(o, "CNSIM")$name, function(table) {
- opal.table_perm_add(o, "CNSIM", table, subject = "demo", type = "group", permission = "view")
-})
-# verify table permissions
-opal.table_perm(o, "CNSIM", "CNSIM1")lapply(opal.tables(o, "CNSIM")$name, function(table) {
+ opal.table_perm_add(o, "CNSIM", table, subject = "demo", type = "group", permission = "view")
+})
+# verify table permissions
+opal.table_perm(o, "CNSIM", "CNSIM1")
Similarly, permissions to use all the resources of a project in a DataSHIELD context is even simpler:
-opal.resources_perm_add(o, "RSRC", subject = "demo", type = "group", permission = "view")
-# verify permissions
-opal.resources_perm(o, "RSRC")opal.resources_perm_add(o, "RSRC", subject = "demo", type = "group", permission = "view")
+# verify permissions
+opal.resources_perm(o, "RSRC")
Then grant permission to use the DataSHIELD service to a group of users:
-dsadmin.perm_add(o, subject = "datashield", type = "group", permission = "use")
-# verify permissions
-dsadmin.perm(o)dsadmin.perm_add(o, subject = "datashield", type = "group", permission = "use")
+# verify permissions
+dsadmin.perm(o)
Note that it is also possible to grant permission to access a specific DataSHIELD profile (see Profiles section).
@@ -296,7 +296,7 @@TeardownGood practice is to free server resources by sending a logout
request:
-opal.logout(o)
+opal.logout(o)
@@ -317,7 +317,7 @@ Teardown
-Site built with pkgdown 2.0.6.
+Site built with pkgdown 2.0.7.
diff --git a/docs/articles/index.html b/docs/articles/index.html
index ab9919fd..501db9f7 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -84,7 +84,7 @@ All vignettes
diff --git a/docs/articles/opal-files.html b/docs/articles/opal-files.html
index 31d37924..f34618c3 100644
--- a/docs/articles/opal-files.html
+++ b/docs/articles/opal-files.html
@@ -88,7 +88,7 @@ Opal Files
Yannick
Marcon
- 2023-02-03
+ 2023-12-20
Source: vignettes/opal-files.Rmd
opal-files.Rmd
@@ -112,56 +112,56 @@ 2023-02-03
Setup the connection with Opal:
-library(opalr)
-o <- opal.login("administrator", "password", "https://opal-demo.obiba.org")
+library(opalr)
+o <- opal.login("administrator", "password", "https://opal-demo.obiba.org")
Download a file:
-opal.file_download(o, "/home/administrator/CNSIM.zip")
+opal.file_download(o, "/home/administrator/CNSIM.zip")
Download a file, protected by a password:
-opal.file_download(o, "/home/administrator/CNSIM.zip", "CNSIM-encrypted.zip", key="ABCDEFGHIJKL")
+opal.file_download(o, "/home/administrator/CNSIM.zip", "CNSIM-encrypted.zip", key="ABCDEFGHIJKL")
Upload the file at another location:
-opal.file_upload(o, "CNSIM.zip", "/projects/CNSIM")
+opal.file_upload(o, "CNSIM.zip", "/projects/CNSIM")
Create a folder and list folder content:
-fooDir <- paste0("/projects/CNSIM/foo-", sample(10000:99999, 1))
-opal.file_mkdir(o, fooDir)
-opal.file_ls(o, "/projects/CNSIM")
+fooDir <- paste0("/projects/CNSIM/foo-", sample(10000:99999, 1))
+opal.file_mkdir(o, fooDir)
+opal.file_ls(o, "/projects/CNSIM")
Move file to the new folder and list folder content:
-opal.file_mv(o, "/projects/CNSIM/CNSIM.zip", fooDir)
-opal.file_ls(o, fooDir)
+opal.file_mv(o, "/projects/CNSIM/CNSIM.zip", fooDir)
+opal.file_ls(o, fooDir)
Rename the new folder and list folder content:
-barDir <- paste0("/projects/CNSIM/bar-", sample(10000:99999, 1))
-opal.file_mv(o, fooDir, barDir)
-opal.file_ls(o, "/projects/CNSIM")
+barDir <- paste0("/projects/CNSIM/bar-", sample(10000:99999, 1))
+opal.file_mv(o, fooDir, barDir)
+opal.file_ls(o, "/projects/CNSIM")
Extract the content of the archive file into a folder:
-out <- opal.file_unzip(o, paste0(barDir, "/CNSIM.zip"), barDir)
-opal.file_ls(o, out)
+out <- opal.file_unzip(o, paste0(barDir, "/CNSIM.zip"), barDir)
+opal.file_ls(o, out)
Write a file from the Opal file system into the R server session
workspace:
-opal.file_write(o, paste0(barDir, "/CNSIM.zip"))
-opal.execute(o, "list.files()")
+opal.file_write(o, paste0(barDir, "/CNSIM.zip"))
+opal.execute(o, "list.files()")
Read back the file into the Opal file system:
-opal.file_read(o, "CNSIM.zip", paste0(barDir, "/ds.zip"))
-opal.file_ls(o, barDir)
+opal.file_read(o, "CNSIM.zip", paste0(barDir, "/ds.zip"))
+opal.file_ls(o, barDir)
Remove created folder and list folder content:
-opal.file_rm(o, barDir)
-opal.file_ls(o, "/projects/CNSIM")
+opal.file_rm(o, barDir)
+opal.file_ls(o, "/projects/CNSIM")
Good practice is to free server resources by sending a logout
request:
-# clean server side
-opal.logout(o)
-# clean client side
-unlink("CNSIM-encrypted.zip")
-unlink("CNSIM.zip")
+# clean server side
+opal.logout(o)
+# clean client side
+unlink("CNSIM-encrypted.zip")
+unlink("CNSIM.zip")
Create a project, linked to a database (default or first one):
-if (opal.project_exists(o, "dummy"))
- opal.project_delete(o, "dummy")
-opal.project_create(o, "dummy", database = TRUE)
-opal.project(o, "dummy")
+if (opal.project_exists(o, "dummy"))
+ opal.project_delete(o, "dummy")
+opal.project_create(o, "dummy", database = TRUE)
+opal.project(o, "dummy")
Backup and Restore
Backup a project and download the backup archive (encrypted):
-opal.project_backup(o, 'CNSIM', '/home/administrator/backup/CNSIM')
-opal.file_download(o, '/home/administrator/backup/CNSIM', '/tmp/CNSIM.zip', key = "12345abcdef")
+opal.project_backup(o, 'CNSIM', '/home/administrator/backup/CNSIM')
+opal.file_download(o, '/home/administrator/backup/CNSIM', '/tmp/CNSIM.zip', key = "12345abcdef")
Restore a project from an uploaded (and encrypted) archive:
-opal.file_upload(o, '/tmp/CNSIM.zip', '/home/administrator')
-opal.project_restore(o, 'dummy', '/home/administrator/CNSIM.zip', key = "12345abcdef")
-# verify tables
-opal.tables(o, "CNSIM")
+opal.file_upload(o, '/tmp/CNSIM.zip', '/home/administrator')
+opal.project_restore(o, 'dummy', '/home/administrator/CNSIM.zip', key = "12345abcdef")
+# verify tables
+opal.tables(o, "CNSIM")
@@ -162,23 +162,23 @@ Tables
List the tables in a project, with their count of variables and
entities:
-opal.tables(o, "CNSIM", counts = TRUE)
+opal.tables(o, "CNSIM", counts = TRUE)
The table object can be retrieved as follow:
-opal.table(o, "CNSIM", "CNSIM1", counts = TRUE)
+opal.table(o, "CNSIM", "CNSIM1", counts = TRUE)
The existence of a table can be checked:
-opal.table_exists(o, "CNSIM", "CNSIM1")
+opal.table_exists(o, "CNSIM", "CNSIM1")
And more specifically, verify whether a table is a view or not:
-opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
+opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
A table can be created, either as a raw table or a view. To create a
view, specify which tables are referred:
-# drop table if it exists
-opal.table_delete(o, "CNSIM", "CNSIM123")
-# then create a view, no variables
-opal.table_create(o, "CNSIM", "CNSIM123", tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+# drop table if it exists
+opal.table_delete(o, "CNSIM", "CNSIM123")
+# then create a view, no variables
+opal.table_create(o, "CNSIM", "CNSIM123", tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
Dictionaries
@@ -187,68 +187,68 @@ Dictionaries
-opal.variables(o, "CNSIM", "CNSIM1")
+opal.variables(o, "CNSIM", "CNSIM1")
It is also possible to get the full data dictionary of a table, as
separate data frames of variables and categories. This is the
recommended format for working with a data dictionary:
-dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
-dico$variables
-dico$categories
+dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
+dico$variables
+dico$categories
Here we modify the data dictionary by appending a derivation script
to each of the variables:
-dico$variables$script <- paste0("$('", dico$variables$name, "')")
-dico$variables
+dico$variables$script <- paste0("$('", dico$variables$name, "')")
+dico$variables
Then we apply this derived variables dictionary to the view we have
previously created and verify the counts of columns (variables) and rows
(entities) in this table:
-opal.table_dictionary_update(o, "CNSIM", "CNSIM123", variables = dico$variables, categories = dico$categories)
-opal.table(o, "CNSIM", "CNSIM123", counts = TRUE)
+opal.table_dictionary_update(o, "CNSIM", "CNSIM123", variables = dico$variables, categories = dico$categories)
+opal.table(o, "CNSIM", "CNSIM123", counts = TRUE)
Assign this view to a symbol in the R server, and get the summary
statics:
-opal.assign(o, "D", "CNSIM.CNSIM123")
-opal.execute(o, "summary(D)")
+opal.assign(o, "D", "CNSIM.CNSIM123")
+opal.execute(o, "summary(D)")
Values
Get the values in a table for a specific Participant entity:
-opal.valueset(o, "CNSIM", "CNSIM123", identifier = "1454")
+opal.valueset(o, "CNSIM", "CNSIM123", identifier = "1454")
Get all the values of a table in our local R session as a data.frame
(tibble) object:
-cnsim1 <- opal.table_get(o, "CNSIM", "CNSIM1")
-cnsim2 <- opal.table_get(o, "CNSIM", "CNSIM2")
-cnsim3 <- opal.table_get(o, "CNSIM", "CNSIM3")
+cnsim1 <- opal.table_get(o, "CNSIM", "CNSIM1")
+cnsim2 <- opal.table_get(o, "CNSIM", "CNSIM2")
+cnsim3 <- opal.table_get(o, "CNSIM", "CNSIM3")
Then do some alterations on this data.frame and save it back as a raw
table:
-# make sure IDs are unique
-cnsim1$id <- paste0(cnsim1$id, "-1")
-cnsim2$id <- paste0(cnsim2$id, "-2")
-cnsim3$id <- paste0(cnsim3$id, "-3")
-# bind tables
-cnsim123 <- rbind(cnsim1, cnsim2, cnsim3)
-# remove some columns
-cnsim123$DIS_AMI <- NULL
-cnsim123$DIS_CVA <- NULL
-cnsim123$DIS_DIAB <- NULL
-# save as a raw table
-opal.table_save(o, cnsim123, "CNSIM", "CNSIM", overwrite = TRUE, force = TRUE)
-opal.table(o, "CNSIM", "CNSIM", counts = TRUE)
+# make sure IDs are unique
+cnsim1$id <- paste0(cnsim1$id, "-1")
+cnsim2$id <- paste0(cnsim2$id, "-2")
+cnsim3$id <- paste0(cnsim3$id, "-3")
+# bind tables
+cnsim123 <- rbind(cnsim1, cnsim2, cnsim3)
+# remove some columns
+cnsim123$DIS_AMI <- NULL
+cnsim123$DIS_CVA <- NULL
+cnsim123$DIS_DIAB <- NULL
+# save as a raw table
+opal.table_save(o, cnsim123, "CNSIM", "CNSIM", overwrite = TRUE, force = TRUE)
+opal.table(o, "CNSIM", "CNSIM", counts = TRUE)
Verify that this raw table resulting from the merge of the other
tables as same values for a given Participant:
-opal.valueset(o, "CNSIM", "CNSIM", identifier = "1454-1")
+opal.valueset(o, "CNSIM", "CNSIM", identifier = "1454-1")
It is possible to truncate a table, i.e. delete ALL the values of a
table (which must not be a view), without modifying the dictionary:
-opal.table_truncate(o, "CNSIM", "CNSIM")
-opal.table(o, "CNSIM", "CNSIM", counts = TRUE)
+opal.table_truncate(o, "CNSIM", "CNSIM")
+opal.table(o, "CNSIM", "CNSIM", counts = TRUE)
Annotations
@@ -257,27 +257,27 @@ Annotations
-opal.taxonomies(o)
+opal.taxonomies(o)
List the vocabularies of a taxonomy:
-opal.vocabularies(o, taxonomy = "Mlstr_area")
+opal.vocabularies(o, taxonomy = "Mlstr_area")
List the terms of a vocabulary:
-opal.terms(o, taxonomy = "Mlstr_area", vocabulary = "Lifestyle_behaviours")
+opal.terms(o, taxonomy = "Mlstr_area", vocabulary = "Lifestyle_behaviours")
To apply a taxonomy term to a table dictionary, use the following for
batch annotation:
-annotations <- tibble::tribble(
- ~variable, ~taxonomy, ~vocabulary, ~term,
- "LAB_TSC", "Mlstr_area", "Physical_measures", "Physical_characteristics",
- "LAB_TRIG", "Mlstr_area", "Physical_measures", "Physical_characteristics",
- "LAB_HDL", "Mlstr_area", "Physical_measures", "Physical_characteristics",
- "LAB_GLUC_ADJUSTED", "Mlstr_area", "Physical_measures", "Physical_characteristics"
-)
-opal.annotate(o, "CNSIM", "CNSIM123", annotations = annotations)
+annotations <- tibble::tribble(
+ ~variable, ~taxonomy, ~vocabulary, ~term,
+ "LAB_TSC", "Mlstr_area", "Physical_measures", "Physical_characteristics",
+ "LAB_TRIG", "Mlstr_area", "Physical_measures", "Physical_characteristics",
+ "LAB_HDL", "Mlstr_area", "Physical_measures", "Physical_characteristics",
+ "LAB_GLUC_ADJUSTED", "Mlstr_area", "Physical_measures", "Physical_characteristics"
+)
+opal.annotate(o, "CNSIM", "CNSIM123", annotations = annotations)
To list the variable annotations:
-opal.annotations(o, "CNSIM", "CNSIM123")
+opal.annotations(o, "CNSIM", "CNSIM123")
@@ -289,34 +289,34 @@ Resources
-opal.resources(o, "RSRC")
+opal.resources(o, "RSRC")
To create a reference to a resource (a compressed CSV file, stored in
a Opal file system, authorized by a personal access token):
-if (opal.resource_exists(o, "RSRC", "CNSIM4"))
- opal.resource_delete(o, "RSRC", "CNSIM4")
-opal.resource_create(o, "RSRC", "CNSIM4",
- url = "opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip",
- format = "csv", secret = "EeTtQGIob6haio5bx6FUfVvIGkeZJfGq")
-# verify the resource reference object
-opal.resource(o, "RSRC", "CNSIM4")
+if (opal.resource_exists(o, "RSRC", "CNSIM4"))
+ opal.resource_delete(o, "RSRC", "CNSIM4")
+opal.resource_create(o, "RSRC", "CNSIM4",
+ url = "opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip",
+ format = "csv", secret = "EeTtQGIob6haio5bx6FUfVvIGkeZJfGq")
+# verify the resource reference object
+opal.resource(o, "RSRC", "CNSIM4")
From a resource reference, it is possible to build and get the
resource object in the local R session:
-opal.resource_get(o, "RSRC", "CNSIM4")
+opal.resource_get(o, "RSRC", "CNSIM4")
Depending on the nature of the resource, it may be possible to coerce
it to a data.frame in the client side:
-library(resourcer)
-as.data.frame(opal.resource_get(o, "RSRC", "CNSIM4"))
+library(resourcer)
+as.data.frame(opal.resource_get(o, "RSRC", "CNSIM4"))
The same operation can be done on the R server side:
-# assign the resource object
-opal.assign.resource(o, "rsrc", "RSRC.CNSIM4")
-# coerce it to a data.frame
-opal.assign.script(o, "D", quote(as.data.frame(rsrc)))
-# get some summary statistics
-opal.execute(o, "summary(as.factor(D$GENDER))")
+# assign the resource object
+opal.assign.resource(o, "rsrc", "RSRC.CNSIM4")
+# coerce it to a data.frame
+opal.assign.script(o, "D", quote(as.data.frame(rsrc)))
+# get some summary statistics
+opal.execute(o, "summary(as.factor(D$GENDER))")
Permissions
@@ -337,7 +337,7 @@ TeardownGood practice is to free server resources by sending a logout
request:
-opal.logout(o)
+opal.logout(o)
@@ -358,7 +358,7 @@ Teardown
-Site built with pkgdown 2.0.6.
+Site built with pkgdown 2.0.7.
diff --git a/docs/articles/opal-rsession.html b/docs/articles/opal-rsession.html
index 7a892618..17bece90 100644
--- a/docs/articles/opal-rsession.html
+++ b/docs/articles/opal-rsession.html
@@ -88,7 +88,7 @@ Opal R Session
Yannick
Marcon
- 2023-02-03
+ 2023-12-20
Source: vignettes/opal-rsession.Rmd
opal-rsession.Rmd
@@ -118,8 +118,8 @@ Setup
must be created with the “default” profile, i.e. in the “default” R
servers cluster (note that the profile parameter is optional):
-library(opalr)
-o <- opal.login("administrator", "password", "https://opal-demo.obiba.org", profile = "default")
+library(opalr)
+o <- opal.login("administrator", "password", "https://opal-demo.obiba.org", profile = "default")
Assign
@@ -127,42 +127,42 @@ Assign
Assign a Opal table to a data.frame (if user has permission
to see values of the Opal table):
-opal.assign.table(o, symbol = "df", value = "CNSIM.CNSIM1")
+opal.assign.table(o, symbol = "df", value = "CNSIM.CNSIM1")
In place of a standard data.frame, Opal can assign data into
a tibble:
-opal.assign.table.tibble(o, symbol = "tbl", value = "CNSIM.CNSIM1")
+opal.assign.table.tibble(o, symbol = "tbl", value = "CNSIM.CNSIM1")
Resource objects can be assigned to the R server session:
-opal.assign.resource(o, symbol = "rsrc", value = "RSRC.CNSIM3")
+opal.assign.resource(o, symbol = "rsrc", value = "RSRC.CNSIM3")
An R expression can also be assigned to a symbol (use
quote() to not interpret the expression in the client side
R session). As an example assign a function body:
-opal.assign.script(o, symbol = "hello", value = quote(function(x) { paste0("Hello ", x, "!") }))
+opal.assign.script(o, symbol = "hello", value = quote(function(x) { paste0("Hello ", x, "!") }))
List the R symbols that lives in the remote R session:
-opal.symbols(o)
+opal.symbols(o)
Execute
R expressions can be executed on the server side:
-# column names
-opal.execute(o, script = "names(tbl)")
-# get variable description from column attributes
-opal.execute(o, script = "attributes(tbl$GENDER)")
-# coerce resource to a data.frame and plot histogram of one column
-plot(opal.execute(o, script = "hist(as.data.frame(rsrc)$LAB_HDL)"))
-# execute the custom function
-opal.execute(o, script = "hello('friends')")
+# column names
+opal.execute(o, script = "names(tbl)")
+# get variable description from column attributes
+opal.execute(o, script = "attributes(tbl$GENDER)")
+# coerce resource to a data.frame and plot histogram of one column
+plot(opal.execute(o, script = "hist(as.data.frame(rsrc)$LAB_HDL)"))
+# execute the custom function
+opal.execute(o, script = "hello('friends')")
The remote data can be downloaded into the client side R session:
-GENDER <- opal.execute(o, script = "tbl$GENDER")
+GENDER <- opal.execute(o, script = "tbl$GENDER")
To execute more complex R code, use a local source file:
-opal.execute.source(o, path = "/path/to/some_code.R")
+opal.execute.source(o, path = "/path/to/some_code.R")
Files
@@ -170,11 +170,11 @@ Files
Files can be written from the Opal file system to the R server
session folder:
-opal.file_write(o, source = "/projects/CNSIM/CNSIM3.zip", "test.zip")
+opal.file_write(o, source = "/projects/CNSIM/CNSIM3.zip", "test.zip")
Similarly, files can be read from the R server session folder into
the Opal file system:
-opal.file_read(o, source = "test.zip", destination = "/tmp")
+opal.file_read(o, source = "test.zip", destination = "/tmp")
+opal.workspace_save(o, save="demo")
+opal.workspaces(o)
Teardown
@@ -191,7 +191,7 @@ TeardownGood practice is to free server resources by sending a logout
request:
-opal.logout(o)
+opal.logout(o)
@@ -212,7 +212,7 @@ Teardown
-Site built with pkgdown 2.0.6.
+Site built with pkgdown 2.0.7.
diff --git a/docs/authors.html b/docs/authors.html
index e777bdac..a50c4cbc 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -117,7 +117,7 @@ Citation
diff --git a/docs/index.html b/docs/index.html
index c90832dc..05f8608f 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -95,27 +95,27 @@
-
+
Opal R Client for the Opal data warehouse. Most of the web services of Opal can be reached by an opalr function: import/export, data dictionaries, projects, tables, resources, permissions, users, DataSHIELD profiles etc.
See opalr documentation.
Installation:
-# install from CRAN
-install.packages("opalr")
-
-# or install latest development version
-remotes::install_github("obiba/opalr")
+# install from CRAN
+install.packages("opalr")
+
+# or install latest development version
+remotes::install_github("obiba/opalr")
Basic usage:
-library(opalr)
-o <- opal.login('administrator', 'password', url = 'https://opal-demo.obiba.org')
-
-# assign a table (as a data.frame) to a R symbol
-opal.assign(o, 'D', 'CNSIM.CNSIM1')
-
-# perform R operations on the server side
-opal.execute(o, 'summary(D$GENDER)')
-opal.execute(o, 'summary(D$LAB_GLUC)')
-
-opal.logout(o)
+library(opalr)
+o <- opal.login('administrator', 'password', url = 'https://opal-demo.obiba.org')
+
+# assign a table (as a data.frame) to a R symbol
+opal.assign(o, 'D', 'CNSIM.CNSIM1')
+
+# perform R operations on the server side
+opal.execute(o, 'summary(D$GENDER)')
+opal.execute(o, 'summary(D$LAB_GLUC)')
+
+opal.logout(o)
-
-Dev status
-
-
-
+
@@ -190,7 +184,7 @@ Dev status
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 384d3091..5adc2f4d 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,10 +1,10 @@
-pandoc: 2.19.2
-pkgdown: 2.0.6
+pandoc: 3.1.1
+pkgdown: 2.0.7
pkgdown_sha: ~
articles:
datashield-admin: datashield-admin.html
opal-files: opal-files.html
opal-projects: opal-projects.html
opal-rsession: opal-rsession.html
-last_built: 2023-02-03T12:50Z
+last_built: 2023-12-20T07:25Z
diff --git a/docs/reference/dictionary.annotate.harmo_status.html b/docs/reference/dictionary.annotate.harmo_status.html
index ff50a785..90a2c2bd 100644
--- a/docs/reference/dictionary.annotate.harmo_status.html
+++ b/docs/reference/dictionary.annotate.harmo_status.html
@@ -71,7 +71,7 @@ Set variable annotation with Harmonization Status term
- dictionary.annotate.harmo_status(tibble, variables = NULL, status)
+ dictionary.annotate.harmo_status(tibble, variables = NULL, status)
@@ -98,14 +98,14 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-cqx <- dictionary.annotate.harmo_status(cqx,
- variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"),
- status = "complete")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+cqx <- dictionary.annotate.harmo_status(cqx,
+ variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"),
+ status = "complete")
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/dictionary.annotate.html b/docs/reference/dictionary.annotate.html
index 08eeae17..fa687aeb 100644
--- a/docs/reference/dictionary.annotate.html
+++ b/docs/reference/dictionary.annotate.html
@@ -69,13 +69,13 @@ Set variable annotation with a taxonomy term
- dictionary.annotate(
- tibble,
- variables = NULL,
- taxonomy = "Mlstr_area",
- vocabulary,
- term
-)
+ dictionary.annotate(
+ tibble,
+ variables = NULL,
+ taxonomy = "Mlstr_area",
+ vocabulary,
+ term
+)
@@ -111,16 +111,16 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-cqx <- dictionary.annotate(cqx,
- variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"),
- taxonomy = "Mlstr_area",
- vocabulary = "Sociodemographic_economic_characteristics",
- term = "Education")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+cqx <- dictionary.annotate(cqx,
+ variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"),
+ taxonomy = "Mlstr_area",
+ vocabulary = "Sociodemographic_economic_characteristics",
+ term = "Education")
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dictionary.annotations.html b/docs/reference/dictionary.annotations.html
index 122843f1..5f5227da 100644
--- a/docs/reference/dictionary.annotations.html
+++ b/docs/reference/dictionary.annotations.html
@@ -69,12 +69,12 @@ List the annotations
- dictionary.annotations(
- tibble,
- variables = NULL,
- taxonomy = NULL,
- vocabulary = NULL
-)
+ dictionary.annotations(
+ tibble,
+ variables = NULL,
+ taxonomy = NULL,
+ vocabulary = NULL
+)
@@ -105,12 +105,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-annot <- dictionary.annotations(cqx, taxonomy = "Mlstr_harmo", vocabulary = "status")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+annot <- dictionary.annotations(cqx, taxonomy = "Mlstr_harmo", vocabulary = "status")
+opal.logout(o)
+}
@@ -125,7 +125,7 @@ Examples
diff --git a/docs/reference/dictionary.apply.html b/docs/reference/dictionary.apply.html
index 51b924fc..6440dfee 100644
--- a/docs/reference/dictionary.apply.html
+++ b/docs/reference/dictionary.apply.html
@@ -69,7 +69,7 @@ Apply the dictionary to a tibble
- dictionary.apply(tibble, variables, categories = NULL)
+ dictionary.apply(tibble, variables, categories = NULL, merge = FALSE)
@@ -85,26 +85,30 @@ Arguments
categories
A data frame with one row per category (columns variable and name) and then column per property/attribute.
merge
+Either append attributes to existing ones or replace them. Default is FALSE, for dictionary consistency.
Examples
- if (FALSE) {
-data <- tibble::as_tibble(mtcars)
-variables <- tibble::tribble(
- ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
- "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
- "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
- "disp", "decimal", "Disp label", NA, NA, 1, 3
-)
-categories <- tibble::tribble(
- ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
- "cyl", "4", 0, "Four", "Quatre",
- "cyl", "6", 0, "Six", "Six",
- "cyl", "8", 1, "Height", "Huit"
-)
-data <- dictionary.apply(data, variables, categories)
-}
+ if (FALSE) {
+data <- tibble::as_tibble(mtcars)
+variables <- tibble::tribble(
+ ~name, ~valueType, ~`label:en`, ~`label:fr`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
+ "mpg", "decimal", "Mpg label", "Mpg libellé", "Value1", "years", 0, 1,
+ "cyl", "decimal", "Cyl label", "Cyl libellé", "Value2", "kg/m2", 0, 2,
+ "disp", "decimal", "Disp label", "Disp libellé", NA, NA, 1, 3
+)
+categories <- tibble::tribble(
+ ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
+ "cyl", "4", 0, "Four", "Quatre",
+ "cyl", "6", 0, "Six", "Six",
+ "cyl", "8", 1, "Height", "Huit"
+)
+data <- dictionary.apply(data, variables, categories)
+}
@@ -119,7 +123,7 @@ Examples
diff --git a/docs/reference/dictionary.inspect.html b/docs/reference/dictionary.inspect.html
index d0b9459d..7849106e 100644
--- a/docs/reference/dictionary.inspect.html
+++ b/docs/reference/dictionary.inspect.html
@@ -71,7 +71,7 @@ Inspect the dictionary of a tibble
- dictionary.inspect(tibble, id.name = "id", warn = TRUE)
+ dictionary.inspect(tibble, id.name = "id", warn = TRUE)
@@ -97,34 +97,34 @@ Value
Examples
- if (FALSE) {
-# prepare datasets of visits, several visits for one patient
-visits <- tibble::tribble(
-~id, ~patient_id, ~sex, ~visit_date,
-1, 1, "M", as.Date("2020-01-01"),
-2, 2, "F", as.Date("2020-01-02"),
-3, 3, "M", as.Date("2020-01-03"),
-4, 3, "M", as.Date("2020-01-04"))
-
-o <- opal.login("administrator", "password", url = "https://opal-demo.obiba.org")
-
-# save visits dataset
-opal.table_save(o, visits, "RSRC", "visits", type = "Visit", force = TRUE)
-
-# get visit and make it a dataset of patients
-patients <- opal.table_get(o, "RSRC", "visits", id.name = "id")
-# set dataset IDs
-patients$visit_id <- patients$id
-patients$id <- patients$patient_id
-patients$patient_id <- NULL
-patients
-
-# save patients dataset, there should be a warning that some variables are not repeatable
-# while there are patients with multiple data lines
-opal.table_save(o, patients, "RSRC", "patients", type = "Participant", force = TRUE)
-
-opal.logout(o)
-}
+ if (FALSE) {
+# prepare datasets of visits, several visits for one patient
+visits <- tibble::tribble(
+~id, ~patient_id, ~sex, ~visit_date,
+1, 1, "M", as.Date("2020-01-01"),
+2, 2, "F", as.Date("2020-01-02"),
+3, 3, "M", as.Date("2020-01-03"),
+4, 3, "M", as.Date("2020-01-04"))
+
+o <- opal.login("administrator", "password", url = "https://opal-demo.obiba.org")
+
+# save visits dataset
+opal.table_save(o, visits, "RSRC", "visits", type = "Visit", force = TRUE)
+
+# get visit and make it a dataset of patients
+patients <- opal.table_get(o, "RSRC", "visits", id.name = "id")
+# set dataset IDs
+patients$visit_id <- patients$id
+patients$id <- patients$patient_id
+patients$patient_id <- NULL
+patients
+
+# save patients dataset, there should be a warning that some variables are not repeatable
+# while there are patients with multiple data lines
+opal.table_save(o, patients, "RSRC", "patients", type = "Participant", force = TRUE)
+
+opal.logout(o)
+}
@@ -139,7 +139,7 @@ Examples
diff --git a/docs/reference/dot-aclsToDataFrame.html b/docs/reference/dot-aclsToDataFrame.html
index 0381ab4d..2ae1faef 100644
--- a/docs/reference/dot-aclsToDataFrame.html
+++ b/docs/reference/dot-aclsToDataFrame.html
@@ -69,7 +69,7 @@ Permsissions (ACLs) into a data frame.
- .aclsToDataFrame(perms, acls)
+ .aclsToDataFrame(perms, acls)
@@ -85,7 +85,7 @@ Permsissions (ACLs) into a data frame.
diff --git a/docs/reference/dot-as.zeroOne.html b/docs/reference/dot-as.zeroOne.html
index 9f8f9a3c..dabc54ad 100644
--- a/docs/reference/dot-as.zeroOne.html
+++ b/docs/reference/dot-as.zeroOne.html
@@ -69,7 +69,7 @@ Turns a value into 0/1 numeric.
- .as.zeroOne(value)
+ .as.zeroOne(value)
@@ -85,7 +85,7 @@ Turns a value into 0/1 numeric.
diff --git a/docs/reference/dot-authorizationHeader.html b/docs/reference/dot-authorizationHeader.html
index ede36fdb..e03112ce 100644
--- a/docs/reference/dot-authorizationHeader.html
+++ b/docs/reference/dot-authorizationHeader.html
@@ -69,7 +69,7 @@ Constructs the value for the Authorization header
- .authorizationHeader(username, password)
+ .authorizationHeader(username, password)
@@ -85,7 +85,7 @@ Constructs the value for the Authorization header
diff --git a/docs/reference/dot-deparse.html b/docs/reference/dot-deparse.html
index 55783b2a..e8d706e8 100644
--- a/docs/reference/dot-deparse.html
+++ b/docs/reference/dot-deparse.html
@@ -69,7 +69,7 @@ Turn expression into character strings.
- .deparse(expr)
+ .deparse(expr)
@@ -85,7 +85,7 @@ Turn expression into character strings.
diff --git a/docs/reference/dot-extractJsonField.html b/docs/reference/dot-extractJsonField.html
index d9a02ee7..413cef7a 100644
--- a/docs/reference/dot-extractJsonField.html
+++ b/docs/reference/dot-extractJsonField.html
@@ -69,7 +69,7 @@ Extract JSON
- .extractJsonField(json, fields = NULL, isArray = TRUE)
+ .extractJsonField(json, fields = NULL, isArray = TRUE)
@@ -85,7 +85,7 @@ Extract JSON
diff --git a/docs/reference/dot-extractLabel.html b/docs/reference/dot-extractLabel.html
index ccc51648..d43d866a 100644
--- a/docs/reference/dot-extractLabel.html
+++ b/docs/reference/dot-extractLabel.html
@@ -69,12 +69,12 @@ Extract label for locale. If not found, fallback to undefined language label
- .extractLabel(
- locale = "en",
- labels = list(),
- localeKey = "locale",
- valueKey = "value"
-)
+ .extractLabel(
+ locale = "en",
+ labels = list(),
+ localeKey = "locale",
+ valueKey = "value"
+)
@@ -90,7 +90,7 @@ Extract label for locale. If not found, fallback to undefined language label
diff --git a/docs/reference/dot-extractOpalSessionId.html b/docs/reference/dot-extractOpalSessionId.html
index be99f00f..65cacd0d 100644
--- a/docs/reference/dot-extractOpalSessionId.html
+++ b/docs/reference/dot-extractOpalSessionId.html
@@ -69,7 +69,7 @@ Extract opalsid from cookie data frame.
- .extractOpalSessionId(cookies)
+ .extractOpalSessionId(cookies)
@@ -85,7 +85,7 @@ Extract opalsid from cookie data frame.
diff --git a/docs/reference/dot-getContent.html b/docs/reference/dot-getContent.html
index 26d95ecf..d81a8ab3 100644
--- a/docs/reference/dot-getContent.html
+++ b/docs/reference/dot-getContent.html
@@ -69,7 +69,7 @@ Wrapper of httr::content()
- .getContent(opal, response)
+ .getContent(opal, response)
@@ -85,7 +85,7 @@ Wrapper of httr::content()
diff --git a/docs/reference/dot-getPEMFilePath.html b/docs/reference/dot-getPEMFilePath.html
index 0601b98d..bac96b2d 100644
--- a/docs/reference/dot-getPEMFilePath.html
+++ b/docs/reference/dot-getPEMFilePath.html
@@ -69,7 +69,7 @@ Extract absolute path to the pem file
- .getPEMFilePath(pem, directory = "~/.ssh")
+ .getPEMFilePath(pem, directory = "~/.ssh")
@@ -85,7 +85,7 @@ Extract absolute path to the pem file
diff --git a/docs/reference/dot-getRSessionId.html b/docs/reference/dot-getRSessionId.html
index 2c8ffd1f..10b997f2 100644
--- a/docs/reference/dot-getRSessionId.html
+++ b/docs/reference/dot-getRSessionId.html
@@ -69,7 +69,7 @@ Extract R session Id from opal object, create a new R session if not found.<
- .getRSessionId(opal)
+ .getRSessionId(opal)
@@ -85,7 +85,7 @@ Extract R session Id from opal object, create a new R session if not found.<
diff --git a/docs/reference/dot-getSessions.html b/docs/reference/dot-getSessions.html
index 6a91fb4e..32bbbbbb 100644
--- a/docs/reference/dot-getSessions.html
+++ b/docs/reference/dot-getSessions.html
@@ -69,7 +69,7 @@ Get all R session in Opal.
- .getSessions(opal)
+ .getSessions(opal)
@@ -85,7 +85,7 @@ Get all R session in Opal.
diff --git a/docs/reference/dot-handleError.html b/docs/reference/dot-handleError.html
index 3f25f7b3..10a4a4d6 100644
--- a/docs/reference/dot-handleError.html
+++ b/docs/reference/dot-handleError.html
@@ -69,7 +69,7 @@ Handle error response
- .handleError(opal, response)
+ .handleError(opal, response)
@@ -85,7 +85,7 @@ Handle error response
diff --git a/docs/reference/dot-handleResponse.html b/docs/reference/dot-handleResponse.html
index 135a5f63..812aabe6 100644
--- a/docs/reference/dot-handleResponse.html
+++ b/docs/reference/dot-handleResponse.html
@@ -69,7 +69,7 @@ Default request response handler.
- .handleResponse(opal, response)
+ .handleResponse(opal, response)
@@ -85,7 +85,7 @@ Default request response handler.
diff --git a/docs/reference/dot-handleResponseLocation.html b/docs/reference/dot-handleResponseLocation.html
index 2aa7fa4a..1a9c550a 100644
--- a/docs/reference/dot-handleResponseLocation.html
+++ b/docs/reference/dot-handleResponseLocation.html
@@ -69,7 +69,7 @@ Default request response Location handler.
- .handleResponseLocation(opal, response)
+ .handleResponseLocation(opal, response)
@@ -85,7 +85,7 @@ Default request response Location handler.
diff --git a/docs/reference/dot-handleResponseOrCallback.html b/docs/reference/dot-handleResponseOrCallback.html
index 1c19cded..fd75863d 100644
--- a/docs/reference/dot-handleResponseOrCallback.html
+++ b/docs/reference/dot-handleResponseOrCallback.html
@@ -69,7 +69,7 @@ Process response with default handler or the provided one
- .handleResponseOrCallback(opal, response, callback = NULL)
+ .handleResponseOrCallback(opal, response, callback = NULL)
@@ -85,7 +85,7 @@ Process response with default handler or the provided one
diff --git a/docs/reference/dot-is.verbose.html b/docs/reference/dot-is.verbose.html
index f3462be7..ddaab2ed 100644
--- a/docs/reference/dot-is.verbose.html
+++ b/docs/reference/dot-is.verbose.html
@@ -69,7 +69,7 @@ Verbose option
- .is.verbose()
+ .is.verbose()
@@ -85,7 +85,7 @@ Verbose option
diff --git a/docs/reference/dot-isContentEmpty.html b/docs/reference/dot-isContentEmpty.html
index 2ca189f6..88320efd 100644
--- a/docs/reference/dot-isContentEmpty.html
+++ b/docs/reference/dot-isContentEmpty.html
@@ -69,7 +69,7 @@ Check if response content is empty.
- .isContentEmpty(content)
+ .isContentEmpty(content)
@@ -85,7 +85,7 @@ Check if response content is empty.
diff --git a/docs/reference/dot-listToJson.html b/docs/reference/dot-listToJson.html
index 9c4d2140..c0bd2195 100644
--- a/docs/reference/dot-listToJson.html
+++ b/docs/reference/dot-listToJson.html
@@ -69,7 +69,7 @@ Simple transformation function of a list into a JSON object/array.
- .listToJson(l)
+ .listToJson(l)
@@ -85,7 +85,7 @@ Simple transformation function of a list into a JSON object/array.
diff --git a/docs/reference/dot-newProgress.html b/docs/reference/dot-newProgress.html
index cdfa936f..c801ff16 100644
--- a/docs/reference/dot-newProgress.html
+++ b/docs/reference/dot-newProgress.html
@@ -69,12 +69,12 @@ Create a new progress instance with default settings.
- .newProgress(
- format = " :what [:bar] :percent /:elapsed",
- clear = getOption("opal.progress.clear", FALSE),
- total,
- width = 100
-)
+ .newProgress(
+ format = " :what [:bar] :percent /:elapsed",
+ clear = getOption("opal.progress.clear", FALSE),
+ total,
+ width = 100
+)
@@ -90,7 +90,7 @@ Create a new progress instance with default settings.
diff --git a/docs/reference/dot-newSession.html b/docs/reference/dot-newSession.html
index a3d04f33..b15cdaa4 100644
--- a/docs/reference/dot-newSession.html
+++ b/docs/reference/dot-newSession.html
@@ -69,7 +69,7 @@ Create a new R session in Opal.
- .newSession(opal, restore = NULL, profile = NULL)
+ .newSession(opal, restore = NULL, profile = NULL)
@@ -85,7 +85,7 @@ Create a new R session in Opal.
diff --git a/docs/reference/dot-opal.login.html b/docs/reference/dot-opal.login.html
index cf5be580..a2d29cf6 100644
--- a/docs/reference/dot-opal.login.html
+++ b/docs/reference/dot-opal.login.html
@@ -69,15 +69,15 @@ Create the opal object
- .opal.login(
- username,
- password,
- token,
- url,
- opts = list(),
- profile = profile,
- restore = NULL
-)
+ .opal.login(
+ username,
+ password,
+ token,
+ url,
+ opts = list(),
+ profile = profile,
+ restore = NULL
+)
@@ -93,7 +93,7 @@ Create the opal object
diff --git a/docs/reference/dot-rmOpalSession.html b/docs/reference/dot-rmOpalSession.html
index bfd20a01..a29f9e94 100644
--- a/docs/reference/dot-rmOpalSession.html
+++ b/docs/reference/dot-rmOpalSession.html
@@ -69,7 +69,7 @@ Remove a Opal session (logout)
- .rmOpalSession(opal)
+ .rmOpalSession(opal)
@@ -85,7 +85,7 @@ Remove a Opal session (logout)
diff --git a/docs/reference/dot-rmRSession.html b/docs/reference/dot-rmRSession.html
index b521882a..827d5ccb 100644
--- a/docs/reference/dot-rmRSession.html
+++ b/docs/reference/dot-rmRSession.html
@@ -69,7 +69,7 @@ Remove a R session from Opal.
- .rmRSession(opal, save = FALSE)
+ .rmRSession(opal, save = FALSE)
@@ -85,7 +85,7 @@ Remove a R session from Opal.
diff --git a/docs/reference/dot-select.html b/docs/reference/dot-select.html
index 43f6c002..13df65cb 100644
--- a/docs/reference/dot-select.html
+++ b/docs/reference/dot-select.html
@@ -69,7 +69,7 @@ Returns a list r such that r[[i]] == l[[i]][field] for all i:length(l)
- .select(l, field)
+ .select(l, field)
@@ -85,7 +85,7 @@ Returns a list r such that r[[i]] == l[[i]][field] for all i:length(l)
diff --git a/docs/reference/dot-tickProgress.html b/docs/reference/dot-tickProgress.html
index 46e06caa..0777056f 100644
--- a/docs/reference/dot-tickProgress.html
+++ b/docs/reference/dot-tickProgress.html
@@ -69,7 +69,7 @@ Output the progress status if option "datashield.progress" is allows to.
@@ -85,7 +85,7 @@ Output the progress status if option "datashield.progress" is allows to.
diff --git a/docs/reference/dot-tokenHeader.html b/docs/reference/dot-tokenHeader.html
index e6d91a46..a6265701 100644
--- a/docs/reference/dot-tokenHeader.html
+++ b/docs/reference/dot-tokenHeader.html
@@ -69,7 +69,7 @@ Constructs the value for the X-Opal-Auth header
- .tokenHeader(token)
+ .tokenHeader(token)
@@ -85,7 +85,7 @@ Constructs the value for the X-Opal-Auth header
diff --git a/docs/reference/dot-url.html b/docs/reference/dot-url.html
index 6f7da3b7..41bd1de4 100644
--- a/docs/reference/dot-url.html
+++ b/docs/reference/dot-url.html
@@ -69,7 +69,7 @@ Utility method to build urls. Concatenates all arguments and adds a '/' sepa
- .url(opal, ...)
+ .url(opal, ...)
@@ -85,7 +85,7 @@ Utility method to build urls. Concatenates all arguments and adds a '/' sepa
diff --git a/docs/reference/dot-verbose.html b/docs/reference/dot-verbose.html
index f47a65e5..3cf22c86 100644
--- a/docs/reference/dot-verbose.html
+++ b/docs/reference/dot-verbose.html
@@ -69,7 +69,7 @@ Verbose flag
- .verbose()
+ .verbose()
@@ -85,7 +85,7 @@ Verbose flag
diff --git a/docs/reference/dsadmin.activity.html b/docs/reference/dsadmin.activity.html
new file mode 100644
index 00000000..a0d1cc75
--- /dev/null
+++ b/docs/reference/dsadmin.activity.html
@@ -0,0 +1,146 @@
+
+Get DataSHIELD activity — dsadmin.activity • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded DataSHIELD session metrics.
+
+
+
+ dsadmin.activity(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+dsadmin.activity(o)
+# user and profile specific session metrics
+dsadmin.activity(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+dsadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.activity_summary.html b/docs/reference/dsadmin.activity_summary.html
new file mode 100644
index 00000000..c291b9fe
--- /dev/null
+++ b/docs/reference/dsadmin.activity_summary.html
@@ -0,0 +1,146 @@
+
+Get DataSHIELD activity summary — dsadmin.activity_summary • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded DataSHIELD session metrics, grouped by profile and user.
+
+
+
+ dsadmin.activity_summary(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+dsadmin.activity_summary(o)
+# user and profile specific session metrics
+dsadmin.activity_summary(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+dsadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.get_method.html b/docs/reference/dsadmin.get_method.html
index 35d8bada..7e0286ab 100644
--- a/docs/reference/dsadmin.get_method.html
+++ b/docs/reference/dsadmin.get_method.html
@@ -69,7 +69,7 @@ Get a DataSHIELD method
- dsadmin.get_method(opal, name, type = "aggregate", profile = NULL)
+ dsadmin.get_method(opal, name, type = "aggregate", profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_method(o, 'class')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_method(o, 'class')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.get_methods.html b/docs/reference/dsadmin.get_methods.html
index eb9d116f..332bd2e6 100644
--- a/docs/reference/dsadmin.get_methods.html
+++ b/docs/reference/dsadmin.get_methods.html
@@ -69,7 +69,7 @@ Get DataSHIELD methods
- dsadmin.get_methods(opal, type = "aggregate", profile = NULL)
+ dsadmin.get_methods(opal, type = "aggregate", profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_methods(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_methods(o)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.get_options.html b/docs/reference/dsadmin.get_options.html
index 41b6d38f..936afd9a 100644
--- a/docs/reference/dsadmin.get_options.html
+++ b/docs/reference/dsadmin.get_options.html
@@ -69,7 +69,7 @@ Get the DataSHIELD options
- dsadmin.get_options(opal, profile = NULL)
+ dsadmin.get_options(opal, profile = NULL)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_options(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_options(o)
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_github_package.html b/docs/reference/dsadmin.install_github_package.html
index 3cd61327..9cac06c4 100644
--- a/docs/reference/dsadmin.install_github_package.html
+++ b/docs/reference/dsadmin.install_github_package.html
@@ -69,13 +69,13 @@ Install a DataSHIELD package from GitHub
- dsadmin.install_github_package(
- opal,
- pkg,
- username = "datashield",
- ref = "master",
- profile = NULL
-)
+ dsadmin.install_github_package(
+ opal,
+ pkg,
+ username = "datashield",
+ ref = "master",
+ profile = NULL
+)
@@ -132,11 +132,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge')
+opal.logout(o)
+}
@@ -151,7 +151,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_local_package.html b/docs/reference/dsadmin.install_local_package.html
index a1a1c76d..d1a6d9a2 100644
--- a/docs/reference/dsadmin.install_local_package.html
+++ b/docs/reference/dsadmin.install_local_package.html
@@ -71,7 +71,7 @@ Install a DataSHIELD package from a local archive file
- dsadmin.install_local_package(opal, path, profile = NULL)
+ dsadmin.install_local_package(opal, path, profile = NULL)
@@ -114,14 +114,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# install a pre-built local archive file
-dsadmin.install_local_package(o, '~/dsExposome_1.0.0.tar.gz')
-# or build archive file from local package source (in current working folder)
-dsadmin.install_local_package(o, devtools::build())
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# install a pre-built local archive file
+dsadmin.install_local_package(o, '~/dsExposome_1.0.0.tar.gz')
+# or build archive file from local package source (in current working folder)
+dsadmin.install_local_package(o, devtools::build())
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_package.html b/docs/reference/dsadmin.install_package.html
index 5a0c9ad1..904d1231 100644
--- a/docs/reference/dsadmin.install_package.html
+++ b/docs/reference/dsadmin.install_package.html
@@ -69,13 +69,13 @@ Install a DataSHIELD package
- dsadmin.install_package(
- opal,
- pkg,
- githubusername = NULL,
- ref = NULL,
- profile = NULL
-)
+ dsadmin.install_package(
+ opal,
+ pkg,
+ githubusername = NULL,
+ ref = NULL,
+ profile = NULL
+)
@@ -132,11 +132,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.install_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.install_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -151,7 +151,7 @@ Examples
diff --git a/docs/reference/dsadmin.installed_package.html b/docs/reference/dsadmin.installed_package.html
index 65240b16..d4e1e5f8 100644
--- a/docs/reference/dsadmin.installed_package.html
+++ b/docs/reference/dsadmin.installed_package.html
@@ -69,7 +69,7 @@ Check DataSHIELD package
- dsadmin.installed_package(opal, pkg, profile = NULL)
+ dsadmin.installed_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.installed_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.installed_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/dsadmin.log.html b/docs/reference/dsadmin.log.html
new file mode 100644
index 00000000..76fcc36d
--- /dev/null
+++ b/docs/reference/dsadmin.log.html
@@ -0,0 +1,155 @@
+
+Get DataSHIELD logs — dsadmin.log • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ The DataSHIELD log is structured as follows:
+
+
+
+ dsadmin.log(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+ Details
+ Common fields
timestamp: when action is logged
version: not used
message: human readable message
logger_name: name of the log channel
thread_name: java thread name
level: log level (TRACE, DEBUG, INFO, WARN, ERROR)
level_value: log level numeric value
ip: ip origin of the request, when available
ds_id: unique DS session ID
ds_profile: DS profile name (available after the R server session is created, can be after authentication)
username: DS user name
r_duration: time spent by the remote R server action (all except PARSE)
r_size: R result serialized object size in bytes
ds_action: DS operation (OPEN, CLOSE, PARSE, ASSIGN, AGGREGATE, LS, RM, WS_SAVE, WS_RESTORE)
DS operations fields
OPEN: DS session opened (note: happens after successful authentication as R server session creation is deferred)
CLOSE: DS session closed
PARSE: R expression parsed
ds_map: DS function mappings used in the R parser, separated by semicolons when several functions are called
ds_script_in: R script as sent by DS user
ds_script_out: R script rewritten by opal, to be evaluated
ASSIGN:
ds_symbol: assigned symbol name
ds_table: table name that is assigned
ds_resource: resource name that is assigned
ds_eval: assign R expression that is evaluated
AGGREGATE:
ds_eval: aggregate R expression that is evaluated
LS: R symbols listed
RM: R symbol removed
ds_symbol: symbol name to remove
WS_SAVE:
ds_ws: workspace name
WS_RESTORE:
ds_ws: workspace name
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.log(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.package_description.html b/docs/reference/dsadmin.package_description.html
index 3351e46a..29694b5b 100644
--- a/docs/reference/dsadmin.package_description.html
+++ b/docs/reference/dsadmin.package_description.html
@@ -69,7 +69,7 @@ Get DataSHIELD package description
- dsadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
+ dsadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
@@ -117,11 +117,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_description(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_description(o, 'dsBase')
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/dsadmin.package_descriptions.html b/docs/reference/dsadmin.package_descriptions.html
index 5fb8ebc9..7707a023 100644
--- a/docs/reference/dsadmin.package_descriptions.html
+++ b/docs/reference/dsadmin.package_descriptions.html
@@ -69,7 +69,7 @@ Get DataSHIELD package descriptions
- dsadmin.package_descriptions(opal, fields = NULL, df = TRUE, profile = NULL)
+ dsadmin.package_descriptions(opal, fields = NULL, df = TRUE, profile = NULL)
@@ -123,11 +123,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_descriptions(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_descriptions(o)
+opal.logout(o)
+}
@@ -142,7 +142,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm.html b/docs/reference/dsadmin.perm.html
index c397d495..50f5957c 100644
--- a/docs/reference/dsadmin.perm.html
+++ b/docs/reference/dsadmin.perm.html
@@ -69,7 +69,7 @@ Get the DataSHIELD permissions
- dsadmin.perm(opal)
+ dsadmin.perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm_add.html b/docs/reference/dsadmin.perm_add.html
index 832ce0ce..e17b5796 100644
--- a/docs/reference/dsadmin.perm_add.html
+++ b/docs/reference/dsadmin.perm_add.html
@@ -69,7 +69,7 @@ Add or update a DataSHIELD permission
- dsadmin.perm_add(opal, subject, type = "user", permission)
+ dsadmin.perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm_delete.html b/docs/reference/dsadmin.perm_delete.html
index 91a12ac8..a5ce771c 100644
--- a/docs/reference/dsadmin.perm_delete.html
+++ b/docs/reference/dsadmin.perm_delete.html
@@ -69,7 +69,7 @@ Delete a DataSHIELD permission
- dsadmin.perm_delete(opal, subject, type = "user")
+ dsadmin.perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile.html b/docs/reference/dsadmin.profile.html
index d16b82ac..d8859752 100644
--- a/docs/reference/dsadmin.profile.html
+++ b/docs/reference/dsadmin.profile.html
@@ -73,7 +73,7 @@ Get a DataSHIELD profile
- dsadmin.profile(opal, name)
+ dsadmin.profile(opal, name)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile(o, name = 'default')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile(o, name = 'default')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_access.html b/docs/reference/dsadmin.profile_access.html
index b23f41c7..64ad8674 100644
--- a/docs/reference/dsadmin.profile_access.html
+++ b/docs/reference/dsadmin.profile_access.html
@@ -73,7 +73,7 @@ Restrict or open access to a DataSHIELD profile
- dsadmin.profile_access(opal, name, restricted = TRUE)
+ dsadmin.profile_access(opal, name, restricted = TRUE)
@@ -108,12 +108,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_access(o, name = 'survival', restricted = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_access(o, name = 'survival', restricted = TRUE)
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_create.html b/docs/reference/dsadmin.profile_create.html
index 5f5fb762..e377a2b7 100644
--- a/docs/reference/dsadmin.profile_create.html
+++ b/docs/reference/dsadmin.profile_create.html
@@ -69,7 +69,7 @@ Create a DataSHIELD profile
- dsadmin.profile_create(opal, name, cluster = "default", rParser = NULL)
+ dsadmin.profile_create(opal, name, cluster = "default", rParser = NULL)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_delete.html b/docs/reference/dsadmin.profile_delete.html
index 8bb60e74..de86336c 100644
--- a/docs/reference/dsadmin.profile_delete.html
+++ b/docs/reference/dsadmin.profile_delete.html
@@ -69,7 +69,7 @@ Delete a DataSHIELD profile
- dsadmin.profile_delete(opal, name)
+ dsadmin.profile_delete(opal, name)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_delete(o, name = 'survival')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_delete(o, name = 'survival')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_enable.html b/docs/reference/dsadmin.profile_enable.html
index 8901ed93..36ba9503 100644
--- a/docs/reference/dsadmin.profile_enable.html
+++ b/docs/reference/dsadmin.profile_enable.html
@@ -69,7 +69,7 @@ Enable or disable a DataSHIELD profile
- dsadmin.profile_enable(opal, name, enabled = TRUE)
+ dsadmin.profile_enable(opal, name, enabled = TRUE)
@@ -104,12 +104,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_enable(o, name = 'survival', enabled = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_enable(o, name = 'survival', enabled = TRUE)
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_exists.html b/docs/reference/dsadmin.profile_exists.html
index e5c19c97..5ea51e86 100644
--- a/docs/reference/dsadmin.profile_exists.html
+++ b/docs/reference/dsadmin.profile_exists.html
@@ -69,7 +69,7 @@ Check a DataSHIELD profile exists
- dsadmin.profile_exists(opal, name)
+ dsadmin.profile_exists(opal, name)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-if (!dsadmin.profile_exists(o, name = 'survival'))
- dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+if (!dsadmin.profile_exists(o, name = 'survival'))
+ dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_init.html b/docs/reference/dsadmin.profile_init.html
index 1d117fad..ad4fc311 100644
--- a/docs/reference/dsadmin.profile_init.html
+++ b/docs/reference/dsadmin.profile_init.html
@@ -73,7 +73,7 @@ Initialize a DataSHIELD profile
- dsadmin.profile_init(opal, name, packages = NULL)
+ dsadmin.profile_init(opal, name, packages = NULL)
@@ -108,12 +108,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_init(o, name = 'survival', packages = c('dsSurvival'))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_init(o, name = 'survival', packages = c('dsSurvival'))
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm.html b/docs/reference/dsadmin.profile_perm.html
index ea1913ac..3f90f5de 100644
--- a/docs/reference/dsadmin.profile_perm.html
+++ b/docs/reference/dsadmin.profile_perm.html
@@ -69,7 +69,7 @@ Get the permissions of a DataSHIELD profile
- dsadmin.profile_perm(opal, name)
+ dsadmin.profile_perm(opal, name)
@@ -106,13 +106,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm_add.html b/docs/reference/dsadmin.profile_perm_add.html
index 5aa4f324..e9b60807 100644
--- a/docs/reference/dsadmin.profile_perm_add.html
+++ b/docs/reference/dsadmin.profile_perm_add.html
@@ -71,13 +71,13 @@ Add or update a permission on a DataSHIELD profile
- dsadmin.profile_perm_add(
- opal,
- name,
- subject,
- type = "user",
- permission = "use"
-)
+ dsadmin.profile_perm_add(
+ opal,
+ name,
+ subject,
+ type = "user",
+ permission = "use"
+)
@@ -120,13 +120,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -141,7 +141,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm_delete.html b/docs/reference/dsadmin.profile_perm_delete.html
index 5b218b2b..8d2fa69a 100644
--- a/docs/reference/dsadmin.profile_perm_delete.html
+++ b/docs/reference/dsadmin.profile_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a DataSHIELD profile
- dsadmin.profile_perm_delete(opal, name, subject, type = "user")
+ dsadmin.profile_perm_delete(opal, name, subject, type = "user")
@@ -108,13 +108,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_rparser.html b/docs/reference/dsadmin.profile_rparser.html
index f24c5242..bf9617df 100644
--- a/docs/reference/dsadmin.profile_rparser.html
+++ b/docs/reference/dsadmin.profile_rparser.html
@@ -69,7 +69,7 @@ Set or remove the R parser version of a DataSHIELD profile
- dsadmin.profile_rparser(opal, name, rParser = NULL)
+ dsadmin.profile_rparser(opal, name, rParser = NULL)
@@ -105,15 +105,15 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-# apply R parser version v2
-dsadmin.profile_rparser(o, name = 'survival', rParser = 'v2')
-# apply system's default R parser version
-dsadmin.profile_rparser(o, name = 'survival')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+# apply R parser version v2
+dsadmin.profile_rparser(o, name = 'survival', rParser = 'v2')
+# apply system's default R parser version
+dsadmin.profile_rparser(o, name = 'survival')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profiles.html b/docs/reference/dsadmin.profiles.html
index 7f97e3ad..2ab7201f 100644
--- a/docs/reference/dsadmin.profiles.html
+++ b/docs/reference/dsadmin.profiles.html
@@ -69,7 +69,7 @@ Get DataSHIELD profiles
- dsadmin.profiles(opal, df = TRUE)
+ dsadmin.profiles(opal, df = TRUE)
@@ -106,11 +106,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_descriptions(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_descriptions(o)
+opal.logout(o)
+}
@@ -125,7 +125,7 @@ Examples
diff --git a/docs/reference/dsadmin.publish_package.html b/docs/reference/dsadmin.publish_package.html
index 1aed7d0b..db0a16e3 100644
--- a/docs/reference/dsadmin.publish_package.html
+++ b/docs/reference/dsadmin.publish_package.html
@@ -69,7 +69,7 @@ Publish DataSHIELD package settings
- dsadmin.publish_package(opal, pkg, profile = NULL)
+ dsadmin.publish_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.publish_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.publish_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/dsadmin.remove_package.html b/docs/reference/dsadmin.remove_package.html
index a696d968..11d7e1d3 100644
--- a/docs/reference/dsadmin.remove_package.html
+++ b/docs/reference/dsadmin.remove_package.html
@@ -69,7 +69,7 @@ Remove DataSHIELD package
- dsadmin.remove_package(opal, pkg, profile = NULL)
+ dsadmin.remove_package(opal, pkg, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.remove_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.remove_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_method.html b/docs/reference/dsadmin.rm_method.html
index cca7bb9e..b2d596b8 100644
--- a/docs/reference/dsadmin.rm_method.html
+++ b/docs/reference/dsadmin.rm_method.html
@@ -69,7 +69,7 @@ Remove DataSHIELD method
- dsadmin.rm_method(opal, name, type = "aggregate", profile = NULL)
+ dsadmin.rm_method(opal, name, type = "aggregate", profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_method(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_method(o, 'foo')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_methods.html b/docs/reference/dsadmin.rm_methods.html
index 2532751f..470d8498 100644
--- a/docs/reference/dsadmin.rm_methods.html
+++ b/docs/reference/dsadmin.rm_methods.html
@@ -69,7 +69,7 @@ Remove DataSHIELD methods.
- dsadmin.rm_methods(opal, type = NULL, profile = NULL)
+ dsadmin.rm_methods(opal, type = NULL, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_methods(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_methods(o)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_option.html b/docs/reference/dsadmin.rm_option.html
index 64995c5f..1b4ed85b 100644
--- a/docs/reference/dsadmin.rm_option.html
+++ b/docs/reference/dsadmin.rm_option.html
@@ -69,7 +69,7 @@ Remove a DataSHIELD option
- dsadmin.rm_option(opal, name, profile = NULL)
+ dsadmin.rm_option(opal, name, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_option(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_option(o, 'foo')
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_options.html b/docs/reference/dsadmin.rm_options.html
index 80414f34..2e4e1b38 100644
--- a/docs/reference/dsadmin.rm_options.html
+++ b/docs/reference/dsadmin.rm_options.html
@@ -69,7 +69,7 @@ Remove all DataSHIELD options
- dsadmin.rm_options(opal, profile = NULL)
+ dsadmin.rm_options(opal, profile = NULL)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_options(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_options(o, 'foo')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_package_methods.html b/docs/reference/dsadmin.rm_package_methods.html
index 26a699ef..f86188d4 100644
--- a/docs/reference/dsadmin.rm_package_methods.html
+++ b/docs/reference/dsadmin.rm_package_methods.html
@@ -69,7 +69,7 @@ Remove DataSHIELD package methods
- dsadmin.rm_package_methods(opal, pkg, type = NULL, profile = NULL)
+ dsadmin.rm_package_methods(opal, pkg, type = NULL, profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_package_methods(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_package_methods(o, 'dsBase')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_method.html b/docs/reference/dsadmin.set_method.html
index ab7bc9ff..a1287cc2 100644
--- a/docs/reference/dsadmin.set_method.html
+++ b/docs/reference/dsadmin.set_method.html
@@ -69,14 +69,14 @@ Set DataSHIELD method
- dsadmin.set_method(
- opal,
- name,
- func = NULL,
- path = NULL,
- type = "aggregate",
- profile = NULL
-)
+ dsadmin.set_method(
+ opal,
+ name,
+ func = NULL,
+ path = NULL,
+ type = "aggregate",
+ profile = NULL
+)
@@ -131,14 +131,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# as a package's function
-dsadmin.set_method(o, 'foo', func = 'base::mean')
-# as a custom function
-dsadmin.set_method(o, 'foo', func = function(x) { base::mean(x) })
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# as a package's function
+dsadmin.set_method(o, 'foo', func = 'base::mean')
+# as a custom function
+dsadmin.set_method(o, 'foo', func = function(x) { base::mean(x) })
+opal.logout(o)
+}
@@ -153,7 +153,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_option.html b/docs/reference/dsadmin.set_option.html
index fa661b5b..af2b415b 100644
--- a/docs/reference/dsadmin.set_option.html
+++ b/docs/reference/dsadmin.set_option.html
@@ -69,7 +69,7 @@ Set DataSHIELD option
- dsadmin.set_option(opal, name, value, profile = NULL)
+ dsadmin.set_option(opal, name, value, profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.set_option(o, 'foo', 'bar')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.set_option(o, 'foo', 'bar')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_package_methods.html b/docs/reference/dsadmin.set_package_methods.html
index 663ff9fd..91a0f0e5 100644
--- a/docs/reference/dsadmin.set_package_methods.html
+++ b/docs/reference/dsadmin.set_package_methods.html
@@ -69,7 +69,7 @@ Set DataSHIELD package methods
- dsadmin.set_package_methods(opal, pkg, type = NULL, profile = NULL)
+ dsadmin.set_package_methods(opal, pkg, type = NULL, profile = NULL)
@@ -122,11 +122,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.set_package_methods(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.set_package_methods(o, 'dsBase')
+opal.logout(o)
+}
@@ -141,7 +141,7 @@ Examples
diff --git a/docs/reference/dsadmin.unpublish_package.html b/docs/reference/dsadmin.unpublish_package.html
index 59177cb6..2f4cb561 100644
--- a/docs/reference/dsadmin.unpublish_package.html
+++ b/docs/reference/dsadmin.unpublish_package.html
@@ -69,7 +69,7 @@ Unpublish DataSHIELD package settings
- dsadmin.unpublish_package(opal, pkg, profile = NULL)
+ dsadmin.unpublish_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.unpublish_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.unpublish_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 7b8fa952..1410bfd7 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -86,6 +86,14 @@ All functions dictionary.inspect()
Inspect the dictionary of a tibble
+
+
+ Get DataSHIELD activity
+
+
+ Get DataSHIELD activity summary
@@ -114,6 +122,10 @@ All functions dsadmin.installed_package()
Check DataSHIELD package
+
+
+ Get DataSHIELD logs
@@ -226,6 +238,14 @@ All functions dsadmin.unpublish_package()
Unpublish DataSHIELD package settings
+
+
+ Get R activity
+
+
+ Get R activity summary
@@ -262,6 +282,18 @@ All functions oadmin.installed_packages()
List installed packages
+
+
+ Get Opal main logs
+
+
+ Get Opal REST API logs
+
+
+ Get Opal SQL API logs
@@ -486,6 +518,10 @@ All functions opal.logout()
Logout from Opal(s)
+
+
+ Get the permissions of a subject
@@ -847,7 +883,7 @@ All functions
diff --git a/docs/reference/oadmin.activity.html b/docs/reference/oadmin.activity.html
new file mode 100644
index 00000000..a11491b6
--- /dev/null
+++ b/docs/reference/oadmin.activity.html
@@ -0,0 +1,146 @@
+
+Get R activity — oadmin.activity • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics.
+
+
+
+ oadmin.activity(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity(o)
+# user and profile specific session metrics
+oadmin.activity(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.activity_summary.html b/docs/reference/oadmin.activity_summary.html
new file mode 100644
index 00000000..a8159421
--- /dev/null
+++ b/docs/reference/oadmin.activity_summary.html
@@ -0,0 +1,146 @@
+
+Get R activity summary — oadmin.activity_summary • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics, grouped by profile and user.
+
+
+
+ oadmin.activity_summary(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity_summary(o)
+# user and profile specific session metrics
+oadmin.activity_summary(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.install_bioconductor_package.html b/docs/reference/oadmin.install_bioconductor_package.html
index adde90ec..2c0551ed 100644
--- a/docs/reference/oadmin.install_bioconductor_package.html
+++ b/docs/reference/oadmin.install_bioconductor_package.html
@@ -69,7 +69,7 @@ Install a package from Bioconductor
- oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
+ oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_bioconductor_package(o, 'GWASTools')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_bioconductor_package(o, 'GWASTools')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.install_cran_package.html b/docs/reference/oadmin.install_cran_package.html
index 3e7e3a18..d229933e 100644
--- a/docs/reference/oadmin.install_cran_package.html
+++ b/docs/reference/oadmin.install_cran_package.html
@@ -69,7 +69,7 @@ Install a package from CRAN
- oadmin.install_cran_package(opal, pkg, profile = NULL)
+ oadmin.install_cran_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_cran_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_cran_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.install_devtools.html b/docs/reference/oadmin.install_devtools.html
index 3f2bc53c..79b175d3 100644
--- a/docs/reference/oadmin.install_devtools.html
+++ b/docs/reference/oadmin.install_devtools.html
@@ -69,7 +69,7 @@ Install devtools package
- oadmin.install_devtools(opal, profile = NULL)
+ oadmin.install_devtools(opal, profile = NULL)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_devtools(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.install_github_package.html b/docs/reference/oadmin.install_github_package.html
index 496f0075..ae130887 100644
--- a/docs/reference/oadmin.install_github_package.html
+++ b/docs/reference/oadmin.install_github_package.html
@@ -69,13 +69,13 @@ Install a package from GitHub
- oadmin.install_github_package(
- opal,
- pkg,
- username = getOption("github.user"),
- ref = "master",
- profile = NULL
-)
+ oadmin.install_github_package(
+ opal,
+ pkg,
+ username = getOption("github.user"),
+ ref = "master",
+ profile = NULL
+)
@@ -117,11 +117,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_github_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_github_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/oadmin.install_local_package.html b/docs/reference/oadmin.install_local_package.html
index 17ddc429..9ddb56c3 100644
--- a/docs/reference/oadmin.install_local_package.html
+++ b/docs/reference/oadmin.install_local_package.html
@@ -71,7 +71,7 @@ Install a package from a local archive file
- oadmin.install_local_package(opal, path, profile = NULL)
+ oadmin.install_local_package(opal, path, profile = NULL)
@@ -105,14 +105,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# install a pre-built local archive file
-oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
-# or build archive file from local package source (in current working folder)
-oadmin.install_local_package(o, devtools::build())
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# install a pre-built local archive file
+oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
+# or build archive file from local package source (in current working folder)
+oadmin.install_local_package(o, devtools::build())
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/oadmin.install_package.html b/docs/reference/oadmin.install_package.html
index 0b2c26c5..7539e7fc 100644
--- a/docs/reference/oadmin.install_package.html
+++ b/docs/reference/oadmin.install_package.html
@@ -69,7 +69,7 @@ Install CRAN package
- oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
+ oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
@@ -113,11 +113,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_package(o, 'xxx')
+opal.logout(o)
+}
@@ -132,7 +132,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_devtools.html b/docs/reference/oadmin.installed_devtools.html
index eaf1b900..a90063c1 100644
--- a/docs/reference/oadmin.installed_devtools.html
+++ b/docs/reference/oadmin.installed_devtools.html
@@ -69,7 +69,7 @@ Check devtools package
- oadmin.installed_devtools(opal, profile = NULL)
+ oadmin.installed_devtools(opal, profile = NULL)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_devtools(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_package.html b/docs/reference/oadmin.installed_package.html
index 604bd8ef..aa802b54 100644
--- a/docs/reference/oadmin.installed_package.html
+++ b/docs/reference/oadmin.installed_package.html
@@ -69,7 +69,7 @@ Check package is installed
- oadmin.installed_package(opal, pkg, profile = NULL)
+ oadmin.installed_package(opal, pkg, profile = NULL)
@@ -109,12 +109,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_package(o, 'xxx')
-oadmin.installed_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_package(o, 'xxx')
+oadmin.installed_package(o, 'stats')
+opal.logout(o)
+}
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_packages.html b/docs/reference/oadmin.installed_packages.html
index 2bc6bfc8..2034f299 100644
--- a/docs/reference/oadmin.installed_packages.html
+++ b/docs/reference/oadmin.installed_packages.html
@@ -69,7 +69,7 @@ List installed packages
- oadmin.installed_packages(opal, profile = NULL)
+ oadmin.installed_packages(opal, profile = NULL)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_packages(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_packages(o)
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/oadmin.log.html b/docs/reference/oadmin.log.html
new file mode 100644
index 00000000..2204fa48
--- /dev/null
+++ b/docs/reference/oadmin.log.html
@@ -0,0 +1,118 @@
+
+Get Opal main logs — oadmin.log • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal main logs
+
+
+
+ oadmin.log(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.log_rest.html b/docs/reference/oadmin.log_rest.html
new file mode 100644
index 00000000..fd2f9ef2
--- /dev/null
+++ b/docs/reference/oadmin.log_rest.html
@@ -0,0 +1,118 @@
+
+Get Opal REST API logs — oadmin.log_rest • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal REST API logs
+
+
+
+ oadmin.log_rest(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_rest(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.log_sql.html b/docs/reference/oadmin.log_sql.html
new file mode 100644
index 00000000..0dc4fae5
--- /dev/null
+++ b/docs/reference/oadmin.log_sql.html
@@ -0,0 +1,118 @@
+
+Get Opal SQL API logs — oadmin.log_sql • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal SQL API logs
+
+
+
+ oadmin.log_sql(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_sql(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.package_description.html b/docs/reference/oadmin.package_description.html
index d07d871e..d402b336 100644
--- a/docs/reference/oadmin.package_description.html
+++ b/docs/reference/oadmin.package_description.html
@@ -69,7 +69,7 @@ Get package description
- oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
+ oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.package_description(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.package_description(o, 'stats')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/oadmin.perm.html b/docs/reference/oadmin.perm.html
index b61d3e13..20a30ecc 100644
--- a/docs/reference/oadmin.perm.html
+++ b/docs/reference/oadmin.perm.html
@@ -69,7 +69,7 @@ Get the R permissions (deprecated)
- oadmin.perm(opal)
+ oadmin.perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.perm_add.html b/docs/reference/oadmin.perm_add.html
index b3a39610..df43a7c7 100644
--- a/docs/reference/oadmin.perm_add.html
+++ b/docs/reference/oadmin.perm_add.html
@@ -69,7 +69,7 @@ Add or update a R permission (deprecated)
- oadmin.perm_add(opal, subject, type = "user", permission)
+ oadmin.perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.perm_delete.html b/docs/reference/oadmin.perm_delete.html
index f629e6fc..fa8fa4de 100644
--- a/docs/reference/oadmin.perm_delete.html
+++ b/docs/reference/oadmin.perm_delete.html
@@ -69,7 +69,7 @@ Delete a R permission (deprecated)
- oadmin.perm_delete(opal, subject, type = "user")
+ oadmin.perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm.html b/docs/reference/oadmin.r_perm.html
index 4bae064d..12b32d20 100644
--- a/docs/reference/oadmin.r_perm.html
+++ b/docs/reference/oadmin.r_perm.html
@@ -69,7 +69,7 @@ Get the R permissions
- oadmin.r_perm(opal)
+ oadmin.r_perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm_add.html b/docs/reference/oadmin.r_perm_add.html
index 06ec844e..fc74abf1 100644
--- a/docs/reference/oadmin.r_perm_add.html
+++ b/docs/reference/oadmin.r_perm_add.html
@@ -69,7 +69,7 @@ Add or update a R permission
- oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
+ oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm_delete.html b/docs/reference/oadmin.r_perm_delete.html
index c68d1ff5..01177602 100644
--- a/docs/reference/oadmin.r_perm_delete.html
+++ b/docs/reference/oadmin.r_perm_delete.html
@@ -69,7 +69,7 @@ Delete a R permission
- oadmin.r_perm_delete(opal, subject, type = "user")
+ oadmin.r_perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.remove_package.html b/docs/reference/oadmin.remove_package.html
index 7d9fd447..0953b827 100644
--- a/docs/reference/oadmin.remove_package.html
+++ b/docs/reference/oadmin.remove_package.html
@@ -69,7 +69,7 @@ Remove package
- oadmin.remove_package(opal, pkg, profile = NULL)
+ oadmin.remove_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.remove_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.remove_package(o, 'xxx')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.system_metrics.html b/docs/reference/oadmin.system_metrics.html
index 4e5ba20e..9eb7d54a 100644
--- a/docs/reference/oadmin.system_metrics.html
+++ b/docs/reference/oadmin.system_metrics.html
@@ -81,7 +81,7 @@ Get system metrics
- oadmin.system_metrics(opal)
+ oadmin.system_metrics(opal)
@@ -93,11 +93,11 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_metrics(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_metrics(o)
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm.html b/docs/reference/oadmin.system_perm.html
index a858025b..5cc5a542 100644
--- a/docs/reference/oadmin.system_perm.html
+++ b/docs/reference/oadmin.system_perm.html
@@ -69,7 +69,7 @@ Get the System permissions
- oadmin.system_perm(opal)
+ oadmin.system_perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm_add.html b/docs/reference/oadmin.system_perm_add.html
index 8b06fd5e..ecc56a90 100644
--- a/docs/reference/oadmin.system_perm_add.html
+++ b/docs/reference/oadmin.system_perm_add.html
@@ -69,7 +69,7 @@ Add or update a System permission
- oadmin.system_perm_add(opal, subject, type = "user", permission)
+ oadmin.system_perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm_delete.html b/docs/reference/oadmin.system_perm_delete.html
index c78fc7d4..5268feec 100644
--- a/docs/reference/oadmin.system_perm_delete.html
+++ b/docs/reference/oadmin.system_perm_delete.html
@@ -69,7 +69,7 @@ Delete a System permission
- oadmin.system_perm_delete(opal, subject, type = "user")
+ oadmin.system_perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.user_add.html b/docs/reference/oadmin.user_add.html
index e5a58e5b..1b82c9b6 100644
--- a/docs/reference/oadmin.user_add.html
+++ b/docs/reference/oadmin.user_add.html
@@ -69,7 +69,7 @@ Add a user
- oadmin.user_add(opal, name, groups = NULL, password = NULL)
+ oadmin.user_add(opal, name, groups = NULL, password = NULL)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/oadmin.user_delete.html b/docs/reference/oadmin.user_delete.html
index 123be6e5..1ae1cb20 100644
--- a/docs/reference/oadmin.user_delete.html
+++ b/docs/reference/oadmin.user_delete.html
@@ -69,7 +69,7 @@ Delete a user
- oadmin.user_delete(opal, name)
+ oadmin.user_delete(opal, name)
@@ -96,12 +96,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_delete(o, "foo")
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/oadmin.user_enable.html b/docs/reference/oadmin.user_enable.html
index 1b531f3a..5b480d04 100644
--- a/docs/reference/oadmin.user_enable.html
+++ b/docs/reference/oadmin.user_enable.html
@@ -69,7 +69,7 @@ Enable a user
- oadmin.user_enable(opal, name, enabled = TRUE)
+ oadmin.user_enable(opal, name, enabled = TRUE)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_enable(o, "foo", enabled = FALSE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_enable(o, "foo", enabled = FALSE)
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/oadmin.user_exists.html b/docs/reference/oadmin.user_exists.html
index e05a1f79..fad76e33 100644
--- a/docs/reference/oadmin.user_exists.html
+++ b/docs/reference/oadmin.user_exists.html
@@ -71,7 +71,7 @@ Check user exists
- oadmin.user_exists(opal, name)
+ oadmin.user_exists(opal, name)
@@ -98,12 +98,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-if (!oadmin.user_exists(o, "foo"))
- oadmin.user_add(o, "foo", password = "bar123")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+if (!oadmin.user_exists(o, "foo"))
+ oadmin.user_add(o, "foo", password = "bar123")
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.user_profile_delete.html b/docs/reference/oadmin.user_profile_delete.html
index e1aab115..2e585266 100644
--- a/docs/reference/oadmin.user_profile_delete.html
+++ b/docs/reference/oadmin.user_profile_delete.html
@@ -75,7 +75,7 @@ Delete a user profile
- oadmin.user_profile_delete(opal, name)
+ oadmin.user_profile_delete(opal, name)
@@ -102,12 +102,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_profile_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_profile_delete(o, "foo")
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.user_profiles.html b/docs/reference/oadmin.user_profiles.html
index 2c1e5a94..f23f1669 100644
--- a/docs/reference/oadmin.user_profiles.html
+++ b/docs/reference/oadmin.user_profiles.html
@@ -71,7 +71,7 @@ Get user profiles
- oadmin.user_profiles(opal, df = TRUE)
+ oadmin.user_profiles(opal, df = TRUE)
@@ -98,11 +98,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.user_profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.user_profiles(o)
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/oadmin.user_reset_password.html b/docs/reference/oadmin.user_reset_password.html
index 7bc446ae..75e27675 100644
--- a/docs/reference/oadmin.user_reset_password.html
+++ b/docs/reference/oadmin.user_reset_password.html
@@ -69,7 +69,7 @@ Reset user password
- oadmin.user_reset_password(opal, name, password = NULL)
+ oadmin.user_reset_password(opal, name, password = NULL)
@@ -100,13 +100,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_reset_password(o, "foo", password = "password1234")
-oadmin.user_rm(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_reset_password(o, "foo", password = "password1234")
+oadmin.user_rm(o, "foo")
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/oadmin.users.html b/docs/reference/oadmin.users.html
index e16383d7..f7a3388e 100644
--- a/docs/reference/oadmin.users.html
+++ b/docs/reference/oadmin.users.html
@@ -69,7 +69,7 @@ Get the users
- oadmin.users(opal, df = TRUE)
+ oadmin.users(opal, df = TRUE)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.users(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.users(o)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.annotate.html b/docs/reference/opal.annotate.html
index f8b0529c..d0970046 100644
--- a/docs/reference/opal.annotate.html
+++ b/docs/reference/opal.annotate.html
@@ -71,7 +71,7 @@ Apply the annotations to a Opal table
- opal.annotate(opal, datasource, table, annotations)
+ opal.annotate(opal, datasource, table, annotations)
@@ -111,12 +111,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/opal.annotations.html b/docs/reference/opal.annotations.html
index 54727239..9f6b17eb 100644
--- a/docs/reference/opal.annotations.html
+++ b/docs/reference/opal.annotations.html
@@ -69,7 +69,7 @@ Get the annotations of a Opal table
- opal.annotations(opal, datasource, table)
+ opal.annotations(opal, datasource, table)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.as_md_table.html b/docs/reference/opal.as_md_table.html
index e37dd66e..b6b4c121 100644
--- a/docs/reference/opal.as_md_table.html
+++ b/docs/reference/opal.as_md_table.html
@@ -69,14 +69,14 @@ Array to Markdown
-
+
@@ -108,11 +108,11 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/opal.assign.data.html b/docs/reference/opal.assign.data.html
index e7b39e90..2be27522 100644
--- a/docs/reference/opal.assign.data.html
+++ b/docs/reference/opal.assign.data.html
@@ -69,7 +69,7 @@ Data assignment
- opal.assign.data(opal, symbol, value, async = FALSE)
+ opal.assign.data(opal, symbol, value, async = FALSE)
@@ -102,16 +102,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# push an arbitrary data frame to the R server
-opal.assign.data(o, "D", mtcars)
-# push an arbitrary vector to the R server
-opal.assign.data(o, "C", mtcars$cyl)
-# push a string
-opal.assign.data(o, "S", "Hello!")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# push an arbitrary data frame to the R server
+opal.assign.data(o, "D", mtcars)
+# push an arbitrary vector to the R server
+opal.assign.data(o, "C", mtcars$cyl)
+# push a string
+opal.assign.data(o, "S", "Hello!")
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.assign.html b/docs/reference/opal.assign.html
index c0c14727..83bab276 100644
--- a/docs/reference/opal.assign.html
+++ b/docs/reference/opal.assign.html
@@ -69,17 +69,17 @@ Data or expression assignment
- opal.assign(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- async = FALSE
-)
+ opal.assign(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ async = FALSE
+)
@@ -132,21 +132,21 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-# push an arbitrary data frame to the R server
-#opal.assign(o, "D", mtcars)
-# push an arbitrary vector to the R server
-#opal.assign(o, "C", mtcars$cyl)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+# push an arbitrary data frame to the R server
+#opal.assign(o, "D", mtcars)
+# push an arbitrary vector to the R server
+#opal.assign(o, "C", mtcars$cyl)
+opal.logout(o)
+}
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/opal.assign.resource.html b/docs/reference/opal.assign.resource.html
index 649d475e..b06c3fee 100644
--- a/docs/reference/opal.assign.resource.html
+++ b/docs/reference/opal.assign.resource.html
@@ -69,7 +69,7 @@ Resource assignment
- opal.assign.resource(opal, symbol, value, async = FALSE)
+ opal.assign.resource(opal, symbol, value, async = FALSE)
@@ -102,13 +102,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a resource and make some operation on it
-opal.assign.resource(o, "D", "datashield.cram1")
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a resource and make some operation on it
+opal.assign.resource(o, "D", "datashield.cram1")
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.assign.script.html b/docs/reference/opal.assign.script.html
index ce2ee8a8..4826146e 100644
--- a/docs/reference/opal.assign.script.html
+++ b/docs/reference/opal.assign.script.html
@@ -69,7 +69,7 @@ R script assignment
- opal.assign.script(opal, symbol, value, async = FALSE)
+ opal.assign.script(opal, symbol, value, async = FALSE)
@@ -102,13 +102,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.assign.table.html b/docs/reference/opal.assign.table.html
index f23b63b9..b853219b 100644
--- a/docs/reference/opal.assign.table.html
+++ b/docs/reference/opal.assign.table.html
@@ -69,18 +69,18 @@ Data assignment to a data.frame
- opal.assign.table(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- class = "data.frame",
- async = FALSE
-)
+ opal.assign.table(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ class = "data.frame",
+ async = FALSE
+)
@@ -137,19 +137,19 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-opal.execute(o, "colnames(D)")
-# assign a table CNSIM1 with a identifiers column
-opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
-opal.execute(o, "colnames(H)")
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-opal.execute(o, "colnames(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+opal.execute(o, "colnames(D)")
+# assign a table CNSIM1 with a identifiers column
+opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
+opal.execute(o, "colnames(H)")
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+opal.execute(o, "colnames(D)")
+opal.logout(o)
+}
@@ -164,7 +164,7 @@ Examples
diff --git a/docs/reference/opal.assign.table.tibble.html b/docs/reference/opal.assign.table.tibble.html
index 95dc04a3..e508e729 100644
--- a/docs/reference/opal.assign.table.tibble.html
+++ b/docs/reference/opal.assign.table.tibble.html
@@ -69,18 +69,18 @@ Data assignment to a tibble
- opal.assign.table.tibble(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = "id",
- with.factors = FALSE,
- updated.name = NULL,
- async = FALSE
-)
+ opal.assign.table.tibble(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = "id",
+ with.factors = FALSE,
+ updated.name = NULL,
+ async = FALSE
+)
@@ -137,13 +137,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a table and make some operation on it
-opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a table and make some operation on it
+opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
@@ -158,7 +158,7 @@ Examples
diff --git a/docs/reference/opal.attribute_values.html b/docs/reference/opal.attribute_values.html
index dd1b1537..98a94106 100644
--- a/docs/reference/opal.attribute_values.html
+++ b/docs/reference/opal.attribute_values.html
@@ -69,7 +69,7 @@ Get a vector of attribute values
- opal.attribute_values(attributes, namespace = NULL, name = "label")
+ opal.attribute_values(attributes, namespace = NULL, name = "label")
@@ -103,12 +103,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.attribute_values(var$attributes)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.attribute_values(var$attributes)
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.command.html b/docs/reference/opal.command.html
index 0f88509d..4f419a6e 100644
--- a/docs/reference/opal.command.html
+++ b/docs/reference/opal.command.html
@@ -69,7 +69,7 @@ Get an asynchronous command
- opal.command(opal, id, wait = FALSE)
+ opal.command(opal, id, wait = FALSE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command(o, '1234')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.command_result.html b/docs/reference/opal.command_result.html
index 5289b55a..35bc7964 100644
--- a/docs/reference/opal.command_result.html
+++ b/docs/reference/opal.command_result.html
@@ -71,7 +71,7 @@ Get result of an asynchronous command
- opal.command_result(opal, id, wait = FALSE)
+ opal.command_result(opal, id, wait = FALSE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_result(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_result(o, '1234')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.command_rm.html b/docs/reference/opal.command_rm.html
index c43351fa..e7fea6bb 100644
--- a/docs/reference/opal.command_rm.html
+++ b/docs/reference/opal.command_rm.html
@@ -69,7 +69,7 @@ Remove an asynchronous command
- opal.command_rm(opal, id)
+ opal.command_rm(opal, id)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_rm(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_rm(o, '1234')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.commands.html b/docs/reference/opal.commands.html
index f184c2a2..e5067c0f 100644
--- a/docs/reference/opal.commands.html
+++ b/docs/reference/opal.commands.html
@@ -69,7 +69,7 @@ List the asynchronous commands
- opal.commands(opal, df = TRUE)
+ opal.commands(opal, df = TRUE)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands(o)
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.commands_rm.html b/docs/reference/opal.commands_rm.html
index a79be20b..dad19270 100644
--- a/docs/reference/opal.commands_rm.html
+++ b/docs/reference/opal.commands_rm.html
@@ -69,7 +69,7 @@ Remove all asynchronous commands
- opal.commands_rm(opal)
+ opal.commands_rm(opal)
@@ -89,11 +89,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands_rm(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands_rm(o)
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/opal.datasource.html b/docs/reference/opal.datasource.html
index db4e3140..18ec94fc 100644
--- a/docs/reference/opal.datasource.html
+++ b/docs/reference/opal.datasource.html
@@ -69,7 +69,7 @@ Get a datasource
- opal.datasource(opal, datasource)
+ opal.datasource(opal, datasource)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasource(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasource(o, 'CNSIM')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.datasources.html b/docs/reference/opal.datasources.html
index 2c0c3136..b541b556 100644
--- a/docs/reference/opal.datasources.html
+++ b/docs/reference/opal.datasources.html
@@ -69,7 +69,7 @@ Get datasources
- opal.datasources(opal, df = TRUE)
+ opal.datasources(opal, df = TRUE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasources(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasources(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.delete.html b/docs/reference/opal.delete.html
index 9acf1da1..97b75ae3 100644
--- a/docs/reference/opal.delete.html
+++ b/docs/reference/opal.delete.html
@@ -69,7 +69,7 @@ Generic REST resource deletion.
- opal.delete(opal, ..., query = list(), callback = NULL)
+ opal.delete(opal, ..., query = list(), callback = NULL)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.delete(o, 'some', 'resource')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.delete(o, 'some', 'resource')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.execute.html b/docs/reference/opal.execute.html
index 244ade02..f91dcca6 100644
--- a/docs/reference/opal.execute.html
+++ b/docs/reference/opal.execute.html
@@ -69,7 +69,7 @@ Execute a R script
- opal.execute(opal, script, async = FALSE)
+ opal.execute(opal, script, async = FALSE)
@@ -97,12 +97,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute(o, "x <- 'foo'")
-opal.execute(o, "ls()")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute(o, "x <- 'foo'")
+opal.execute(o, "ls()")
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/opal.execute.source.html b/docs/reference/opal.execute.source.html
index 9ad4eef0..f512ffb2 100644
--- a/docs/reference/opal.execute.source.html
+++ b/docs/reference/opal.execute.source.html
@@ -69,7 +69,7 @@ Execute a R file script
- opal.execute.source(opal, path, async = FALSE)
+ opal.execute.source(opal, path, async = FALSE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute.source(o, "myscript.R")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute.source(o, "myscript.R")
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.file.html b/docs/reference/opal.file.html
index 074023d1..72a13d97 100644
--- a/docs/reference/opal.file.html
+++ b/docs/reference/opal.file.html
@@ -69,7 +69,7 @@ Get file content
- opal.file(opal, path, key = NULL)
+ opal.file(opal, path, key = NULL)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.file(o, '/home/administrator/joins/join-src-3.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.file(o, '/home/administrator/joins/join-src-3.csv')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.file_cp.html b/docs/reference/opal.file_cp.html
index c895e41c..33bb18fd 100644
--- a/docs/reference/opal.file_cp.html
+++ b/docs/reference/opal.file_cp.html
@@ -69,7 +69,7 @@ Copy a file
- opal.file_cp(opal, source, destination)
+ opal.file_cp(opal, source, destination)
@@ -104,14 +104,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# copy a file to another folder
-opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# copy recursively a folder to another folder
-opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# copy a file to another folder
+opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# copy recursively a folder to another folder
+opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.file_download.html b/docs/reference/opal.file_download.html
index dde0cba7..e6770678 100644
--- a/docs/reference/opal.file_download.html
+++ b/docs/reference/opal.file_download.html
@@ -69,7 +69,7 @@ Download a file
- opal.file_download(opal, source, destination = NULL, key = NULL)
+ opal.file_download(opal, source, destination = NULL, key = NULL)
@@ -108,19 +108,19 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# download a file
-opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
-# download a file encrypted by a key: resulting file is a zip with an encrypted content
-opal.file_download(o, '/home/administrator/export/some-data.csv',
- destination='some-data.zip', key='AZF57893FBDE')
-# download, create destination folder and rename file
-opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
-# download a folder
-opal.file_download(o, '/home/administrator/export', 'export.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# download a file
+opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
+# download a file encrypted by a key: resulting file is a zip with an encrypted content
+opal.file_download(o, '/home/administrator/export/some-data.csv',
+ destination='some-data.zip', key='AZF57893FBDE')
+# download, create destination folder and rename file
+opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
+# download a folder
+opal.file_download(o, '/home/administrator/export', 'export.zip')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.file_ls.html b/docs/reference/opal.file_ls.html
index c57e02da..8664df11 100644
--- a/docs/reference/opal.file_ls.html
+++ b/docs/reference/opal.file_ls.html
@@ -69,7 +69,7 @@ List content of a folder
- opal.file_ls(opal, path)
+ opal.file_ls(opal, path)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# list content of a folder
-opal.file_ls(o, '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# list content of a folder
+opal.file_ls(o, '/home/administrator')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.file_mkdir.html b/docs/reference/opal.file_mkdir.html
index 0ed72ad7..d15743df 100644
--- a/docs/reference/opal.file_mkdir.html
+++ b/docs/reference/opal.file_mkdir.html
@@ -71,7 +71,7 @@ Make a folder
- opal.file_mkdir(opal, path, parents = FALSE)
+ opal.file_mkdir(opal, path, parents = FALSE)
@@ -106,12 +106,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.file_mkdir_tmp.html b/docs/reference/opal.file_mkdir_tmp.html
index 396c04ff..8e187fcb 100644
--- a/docs/reference/opal.file_mkdir_tmp.html
+++ b/docs/reference/opal.file_mkdir_tmp.html
@@ -69,7 +69,7 @@ Make a temporary folder
- opal.file_mkdir_tmp(opal)
+ opal.file_mkdir_tmp(opal)
@@ -102,12 +102,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-path <- opal.file_mkdir_tmp(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+path <- opal.file_mkdir_tmp(o)
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/opal.file_mv.html b/docs/reference/opal.file_mv.html
index fc322297..1d6874df 100644
--- a/docs/reference/opal.file_mv.html
+++ b/docs/reference/opal.file_mv.html
@@ -69,7 +69,7 @@ Move and/or rename a file
- opal.file_mv(opal, source, destination)
+ opal.file_mv(opal, source, destination)
@@ -104,18 +104,18 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# move a file to another folder
-opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/administrator/export/some-data.csv')
-# move and rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/userx/deliverables/some-data.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# move a file to another folder
+opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/administrator/export/some-data.csv')
+# move and rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/userx/deliverables/some-data.csv')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.file_read.html b/docs/reference/opal.file_read.html
index 64f4982d..1807b28c 100644
--- a/docs/reference/opal.file_read.html
+++ b/docs/reference/opal.file_read.html
@@ -69,7 +69,7 @@ Read a file
- opal.file_read(opal, source, destination)
+ opal.file_read(opal, source, destination)
@@ -104,16 +104,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# read into folder
-opal.file_read(o,"DatabaseTest.sav", "/tmp")
-# read and rename
-opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
-# user home expansion
-opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# read into folder
+opal.file_read(o,"DatabaseTest.sav", "/tmp")
+# read and rename
+opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
+# user home expansion
+opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.file_rm.html b/docs/reference/opal.file_rm.html
index a23dee2e..5d79795c 100644
--- a/docs/reference/opal.file_rm.html
+++ b/docs/reference/opal.file_rm.html
@@ -69,7 +69,7 @@ Remove a file
- opal.file_rm(opal, path)
+ opal.file_rm(opal, path)
@@ -100,14 +100,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# remove a file
-opal.file_rm(o, '/home/administrator/export/some-data.csv')
-# remove recursively a folder
-opal.file_rm(o, '/home/administrator/export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# remove a file
+opal.file_rm(o, '/home/administrator/export/some-data.csv')
+# remove recursively a folder
+opal.file_rm(o, '/home/administrator/export')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/opal.file_unzip.html b/docs/reference/opal.file_unzip.html
index 66eaea32..a695dfec 100644
--- a/docs/reference/opal.file_unzip.html
+++ b/docs/reference/opal.file_unzip.html
@@ -69,7 +69,7 @@ Unzip a zip archive file
- opal.file_unzip(opal, source, destination, key = NULL)
+ opal.file_unzip(opal, source, destination, key = NULL)
@@ -114,12 +114,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# unzip
-path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# unzip
+path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.file_upload.html b/docs/reference/opal.file_upload.html
index 83a6426c..70c2faea 100644
--- a/docs/reference/opal.file_upload.html
+++ b/docs/reference/opal.file_upload.html
@@ -71,7 +71,7 @@ Upload a file or a folder
- opal.file_upload(opal, source, destination, all.files = TRUE)
+ opal.file_upload(opal, source, destination, all.files = TRUE)
@@ -111,14 +111,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# upload a file
-opal.file_upload(o, 'some_data.csv', '/home/administrator')
-# upload a folder
-opal.file_upload(o, 'some_data', '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# upload a file
+opal.file_upload(o, 'some_data.csv', '/home/administrator')
+# upload a folder
+opal.file_upload(o, 'some_data', '/home/administrator')
+opal.logout(o)
+}
@@ -133,7 +133,7 @@ Examples
diff --git a/docs/reference/opal.file_write.html b/docs/reference/opal.file_write.html
index a1bfb19d..f0835d11 100644
--- a/docs/reference/opal.file_write.html
+++ b/docs/reference/opal.file_write.html
@@ -69,7 +69,7 @@ Write a file
- opal.file_write(opal, source, destination = NULL)
+ opal.file_write(opal, source, destination = NULL)
@@ -104,16 +104,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# user home expansion
-opal.file_write(o, "~/spss/DatabaseTest.sav")
-# rename file
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
-# create sub-folder
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# user home expansion
+opal.file_write(o, "~/spss/DatabaseTest.sav")
+# rename file
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
+# create sub-folder
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.get.html b/docs/reference/opal.get.html
index 19e0f260..f83d5cb9 100644
--- a/docs/reference/opal.get.html
+++ b/docs/reference/opal.get.html
@@ -69,14 +69,14 @@ Generic REST resource getter.
- opal.get(
- opal,
- ...,
- query = list(),
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)
+ opal.get(
+ opal,
+ ...,
+ query = list(),
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)
@@ -115,11 +115,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.get(o, 'project', 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.get(o, 'project', 'CNSIM')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.load_package.html b/docs/reference/opal.load_package.html
index 15e9967f..cba05243 100644
--- a/docs/reference/opal.load_package.html
+++ b/docs/reference/opal.load_package.html
@@ -69,7 +69,7 @@ Load package
- opal.load_package(opal, pkg)
+ opal.load_package(opal, pkg)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.load_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.load_package(o, 'stats')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.login.html b/docs/reference/opal.login.html
index f9523698..549cdc71 100644
--- a/docs/reference/opal.login.html
+++ b/docs/reference/opal.login.html
@@ -73,15 +73,15 @@ Opal login
-
+
@@ -132,44 +132,44 @@ See also
Examples
- if (FALSE) {
-#### The below examples illustrate the different ways to login in opal ####
-
-# explicite username/password login
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
- # explicite personal access token login
-o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login using options and user credentials
-options(opal.username = 'administrator',
- opal.password = 'password',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using options and personal access token
-options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using ssl key pair
-options(opal.opts = list(
- sslcert = 'my-publickey.pem',
- sslkey = 'my-privatekey.pem'))
-o <- opal.login(url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login with a R server profile
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org', profile = 'default')
-opal.logout(o)
-}
+ if (FALSE) {
+#### The below examples illustrate the different ways to login in opal ####
+
+# explicite username/password login
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+ # explicite personal access token login
+o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login using options and user credentials
+options(opal.username = 'administrator',
+ opal.password = 'password',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using options and personal access token
+options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using ssl key pair
+options(opal.opts = list(
+ sslcert = 'my-publickey.pem',
+ sslkey = 'my-privatekey.pem'))
+o <- opal.login(url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login with a R server profile
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org', profile = 'default')
+opal.logout(o)
+}
@@ -184,7 +184,7 @@ Examples
diff --git a/docs/reference/opal.logout.html b/docs/reference/opal.logout.html
index e64f3e86..b91868aa 100644
--- a/docs/reference/opal.logout.html
+++ b/docs/reference/opal.logout.html
@@ -69,7 +69,7 @@ Logout from Opal(s)
- opal.logout(opal, save = FALSE)
+ opal.logout(opal, save = FALSE)
@@ -91,10 +91,10 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+}
@@ -109,7 +109,7 @@ Examples
diff --git a/docs/reference/opal.perms.html b/docs/reference/opal.perms.html
new file mode 100644
index 00000000..aab233ff
--- /dev/null
+++ b/docs/reference/opal.perms.html
@@ -0,0 +1,154 @@
+
+Get the permissions of a subject — opal.perms • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the permissions of a subject. If the subject is a user, the permissions of
+the groups to which the user belongs are also added to the result.
+
+
+
+ opal.perms(opal, subject, type = "user")
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- subject
+A subject identifier: user or group name.
- type
+The type of subject: user (default) or group.
+
+ Value
+
+
+A data.frame with columns: subject, type, target (path to the opal object to which
+the permission applies), target_type and perm (the permission name)
+
+
+ See also
+ Other table functions:
+opal.resource_view_create(),
+opal.resource_view_reconnect(),
+opal.table_create(),
+opal.table_delete(),
+opal.table_dictionary_get(),
+opal.table_dictionary_update(),
+opal.table_exists(),
+opal.table_export(),
+opal.table_get(),
+opal.table_import(),
+opal.table_perm_add(),
+opal.table_perm_delete(),
+opal.table_perm(),
+opal.table_save(),
+opal.table_truncate(),
+opal.table_view_create(),
+opal.table_view_update()
+
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.perms(o, 'andrei')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/opal.post.html b/docs/reference/opal.post.html
index d93bb6bf..f7d80068 100644
--- a/docs/reference/opal.post.html
+++ b/docs/reference/opal.post.html
@@ -69,16 +69,16 @@ Generic REST resource creation.
- opal.post(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)
+ opal.post(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)
@@ -125,11 +125,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.post(o, 'some', 'resources', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.post(o, 'some', 'resources', body = '{"some":"value"}')
+opal.logout(o)
+}
@@ -144,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.profiles.html b/docs/reference/opal.profiles.html
index 067273c2..1e96f85c 100644
--- a/docs/reference/opal.profiles.html
+++ b/docs/reference/opal.profiles.html
@@ -71,7 +71,7 @@ List R profiles
- opal.profiles(opal, df = TRUE)
+ opal.profiles(opal, df = TRUE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.profiles(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.project.html b/docs/reference/opal.project.html
index cd3a4f68..3e6b4a16 100644
--- a/docs/reference/opal.project.html
+++ b/docs/reference/opal.project.html
@@ -69,7 +69,7 @@ Get a project
- opal.project(opal, project)
+ opal.project(opal, project)
@@ -94,11 +94,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project(o, 'datashield')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project(o, 'datashield')
+opal.logout(o)
+}
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/opal.project_backup.html b/docs/reference/opal.project_backup.html
index 9fe7543f..58bf4b6e 100644
--- a/docs/reference/opal.project_backup.html
+++ b/docs/reference/opal.project_backup.html
@@ -75,14 +75,14 @@ Backup a project
- opal.project_backup(
- opal,
- project,
- archive,
- viewsAsTables = FALSE,
- override = TRUE,
- wait = TRUE
-)
+ opal.project_backup(
+ opal,
+ project,
+ archive,
+ viewsAsTables = FALSE,
+ override = TRUE,
+ wait = TRUE
+)
@@ -120,12 +120,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
-opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
+opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
+opal.logout(o)
+}
@@ -140,7 +140,7 @@ Examples
diff --git a/docs/reference/opal.project_command.html b/docs/reference/opal.project_command.html
index 13740837..9e6c5e62 100644
--- a/docs/reference/opal.project_command.html
+++ b/docs/reference/opal.project_command.html
@@ -69,7 +69,7 @@ Get project task
- opal.project_command(opal, project, id)
+ opal.project_command(opal, project, id)
@@ -95,12 +95,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
-opal.project_command(opal, 'GREENSPACE', id)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
+opal.project_command(opal, 'GREENSPACE', id)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.project_create.html b/docs/reference/opal.project_create.html
index 2524037d..d1eb8488 100644
--- a/docs/reference/opal.project_create.html
+++ b/docs/reference/opal.project_create.html
@@ -69,15 +69,15 @@ Create a project
- opal.project_create(
- opal,
- project,
- database = NULL,
- title = NULL,
- description = NULL,
- tags = NULL,
- exportFolder = NULL
-)
+ opal.project_create(
+ opal,
+ project,
+ database = NULL,
+ title = NULL,
+ description = NULL,
+ tags = NULL,
+ exportFolder = NULL
+)
@@ -124,16 +124,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with named database
-opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
-# with default database
-opal.project_create(o, 'test_default_db', database = TRUE)
-# no database, for views and resources only
-opal.project_create(o, 'test_no_db')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with named database
+opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
+# with default database
+opal.project_create(o, 'test_default_db', database = TRUE)
+# no database, for views and resources only
+opal.project_create(o, 'test_no_db')
+opal.logout(o)
+}
@@ -148,7 +148,7 @@ Examples
diff --git a/docs/reference/opal.project_delete.html b/docs/reference/opal.project_delete.html
index 0975b5d4..249dfdd3 100644
--- a/docs/reference/opal.project_delete.html
+++ b/docs/reference/opal.project_delete.html
@@ -69,7 +69,7 @@ Delete a project
- opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
+ opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
@@ -102,11 +102,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_delete(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_delete(o, 'test')
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/opal.project_exists.html b/docs/reference/opal.project_exists.html
index 2d217cab..10266208 100644
--- a/docs/reference/opal.project_exists.html
+++ b/docs/reference/opal.project_exists.html
@@ -69,7 +69,7 @@ Check a project exists
- opal.project_exists(opal, project)
+ opal.project_exists(opal, project)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_exists(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_exists(o, 'test')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.project_perm.html b/docs/reference/opal.project_perm.html
index 07a974c3..abba6946 100644
--- a/docs/reference/opal.project_perm.html
+++ b/docs/reference/opal.project_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a project
- opal.project_perm(opal, project)
+ opal.project_perm(opal, project)
@@ -91,13 +91,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.project_perm_add.html b/docs/reference/opal.project_perm_add.html
index 1fd19072..e134d7b0 100644
--- a/docs/reference/opal.project_perm_add.html
+++ b/docs/reference/opal.project_perm_add.html
@@ -69,13 +69,13 @@ Add or update a permission on a project
- opal.project_perm_add(
- opal,
- project,
- subject,
- type = "user",
- permission = "administrate"
-)
+ opal.project_perm_add(
+ opal,
+ project,
+ subject,
+ type = "user",
+ permission = "administrate"
+)
@@ -103,13 +103,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.project_perm_delete.html b/docs/reference/opal.project_perm_delete.html
index 8a290c35..885e9c53 100644
--- a/docs/reference/opal.project_perm_delete.html
+++ b/docs/reference/opal.project_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a project
- opal.project_perm_delete(opal, project, subject, type = "user")
+ opal.project_perm_delete(opal, project, subject, type = "user")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/opal.project_restore.html b/docs/reference/opal.project_restore.html
index 76c5f138..8f4c0d05 100644
--- a/docs/reference/opal.project_restore.html
+++ b/docs/reference/opal.project_restore.html
@@ -75,14 +75,14 @@ Restore a project
- opal.project_restore(
- opal,
- project,
- archive,
- key = NULL,
- override = TRUE,
- wait = TRUE
-)
+ opal.project_restore(
+ opal,
+ project,
+ archive,
+ key = NULL,
+ override = TRUE,
+ wait = TRUE
+)
@@ -120,15 +120,15 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# create the project to restore, with the default database (to store tables)
-opal.project_create(o, 'GREENSPACE2', database = TRUE)
-# upload backup zip and launch restore task
-opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
-opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# create the project to restore, with the default database (to store tables)
+opal.project_create(o, 'GREENSPACE2', database = TRUE)
+# upload backup zip and launch restore task
+opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
+opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
+opal.logout(o)
+}
@@ -143,7 +143,7 @@ Examples
diff --git a/docs/reference/opal.projects.html b/docs/reference/opal.projects.html
index e8d51a41..73e9e973 100644
--- a/docs/reference/opal.projects.html
+++ b/docs/reference/opal.projects.html
@@ -69,7 +69,7 @@ Get projects
- opal.projects(opal, df = TRUE)
+ opal.projects(opal, df = TRUE)
@@ -94,11 +94,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects(o)
+opal.logout(o)
+}
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/opal.projects_databases.html b/docs/reference/opal.projects_databases.html
index 45f818b3..2a9dc9f0 100644
--- a/docs/reference/opal.projects_databases.html
+++ b/docs/reference/opal.projects_databases.html
@@ -69,7 +69,7 @@ Get projects databases
- opal.projects_databases(opal)
+ opal.projects_databases(opal)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects_databases(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects_databases(o)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.put.html b/docs/reference/opal.put.html
index de59ef78..1622010c 100644
--- a/docs/reference/opal.put.html
+++ b/docs/reference/opal.put.html
@@ -69,14 +69,14 @@ Generic REST resource update.
- opal.put(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- callback = NULL
-)
+ opal.put(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ callback = NULL
+)
@@ -115,11 +115,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.report.html b/docs/reference/opal.report.html
index eaf6c399..efc8d7c1 100644
--- a/docs/reference/opal.report.html
+++ b/docs/reference/opal.report.html
@@ -69,13 +69,13 @@ Opal report
- opal.report(
- input,
- output = NULL,
- progress = FALSE,
- verbose = FALSE,
- boot_style = NULL
-)
+ opal.report(
+ input,
+ output = NULL,
+ progress = FALSE,
+ verbose = FALSE,
+ boot_style = NULL
+)
@@ -103,9 +103,9 @@ Arguments
Examples
- if (FALSE) {
-opal.report('input.Rmd', 'report', progress=TRUE)
-}
+ if (FALSE) {
+opal.report('input.Rmd', 'report', progress=TRUE)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.report_md.html b/docs/reference/opal.report_md.html
index ad0cadd5..50a44df1 100644
--- a/docs/reference/opal.report_md.html
+++ b/docs/reference/opal.report_md.html
@@ -69,7 +69,7 @@ Turn a R markdown file to html.
- opal.report_md(inputFile, progress, verbose)
+ opal.report_md(inputFile, progress, verbose)
@@ -85,7 +85,7 @@ Turn a R markdown file to html.
diff --git a/docs/reference/opal.resource.html b/docs/reference/opal.resource.html
index 8040add0..128ece62 100644
--- a/docs/reference/opal.resource.html
+++ b/docs/reference/opal.resource.html
@@ -69,7 +69,7 @@ Get a resource reference of a project
- opal.resource(opal, project, resource)
+ opal.resource(opal, project, resource)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.resource_create.html b/docs/reference/opal.resource_create.html
index a7f47634..9ed343f2 100644
--- a/docs/reference/opal.resource_create.html
+++ b/docs/reference/opal.resource_create.html
@@ -69,17 +69,17 @@ Create a resource reference in a project
- opal.resource_create(
- opal,
- project,
- name,
- url,
- description = NULL,
- format = NULL,
- package = NULL,
- identity = NULL,
- secret = NULL
-)
+ opal.resource_create(
+ opal,
+ project,
+ name,
+ url,
+ description = NULL,
+ format = NULL,
+ package = NULL,
+ identity = NULL,
+ secret = NULL
+)
@@ -139,13 +139,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_create(o, 'RSRC', 'CNSIM4',
- url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
- format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_create(o, 'RSRC', 'CNSIM4',
+ url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
+ format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
+opal.logout(o)
+}
@@ -160,7 +160,7 @@ Examples
diff --git a/docs/reference/opal.resource_delete.html b/docs/reference/opal.resource_delete.html
index 41eee541..a3e48fb8 100644
--- a/docs/reference/opal.resource_delete.html
+++ b/docs/reference/opal.resource_delete.html
@@ -69,7 +69,7 @@ Delete a resource reference
- opal.resource_delete(opal, project, resource, silent = TRUE)
+ opal.resource_delete(opal, project, resource, silent = TRUE)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_delete(o, "RSRC", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_delete(o, "RSRC", "CNSIM4")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.resource_exists.html b/docs/reference/opal.resource_exists.html
index 7a5852e1..700fd693 100644
--- a/docs/reference/opal.resource_exists.html
+++ b/docs/reference/opal.resource_exists.html
@@ -69,7 +69,7 @@ Check a resource reference exists
- opal.resource_exists(opal, project, resource)
+ opal.resource_exists(opal, project, resource)
@@ -111,11 +111,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_exists(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_exists(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.resource_extension_create.html b/docs/reference/opal.resource_extension_create.html
index c0a045fe..1c8013c4 100644
--- a/docs/reference/opal.resource_extension_create.html
+++ b/docs/reference/opal.resource_extension_create.html
@@ -69,16 +69,16 @@ Create an extended resource reference in a project
- opal.resource_extension_create(
- opal,
- project,
- name,
- provider,
- factory,
- parameters,
- description = NULL,
- credentials = NULL
-)
+ opal.resource_extension_create(
+ opal,
+ project,
+ name,
+ provider,
+ factory,
+ parameters,
+ description = NULL,
+ credentials = NULL
+)
@@ -134,21 +134,21 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
- provider = 'dsOmics', factory = 'ga4gh-htsget',
- parameters = list(
- host = 'https://htsget.ga4gh.org',
- sample = '1000genomes.phase1.chr1',
- reference = '1',
- start = '1',
- end = '100000',
- format = 'GA4GHVCF'
- )
-)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
+ provider = 'dsOmics', factory = 'ga4gh-htsget',
+ parameters = list(
+ host = 'https://htsget.ga4gh.org',
+ sample = '1000genomes.phase1.chr1',
+ reference = '1',
+ start = '1',
+ end = '100000',
+ format = 'GA4GHVCF'
+ )
+)
+opal.logout(o)
+}
@@ -163,7 +163,7 @@ Examples
diff --git a/docs/reference/opal.resource_get.html b/docs/reference/opal.resource_get.html
index ae00707a..80a02871 100644
--- a/docs/reference/opal.resource_get.html
+++ b/docs/reference/opal.resource_get.html
@@ -69,7 +69,7 @@ Get the resource object of a project
- opal.resource_get(opal, project, resource)
+ opal.resource_get(opal, project, resource)
@@ -105,17 +105,17 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
-# then interpret locally the resource object (load the appropriate R packages)
-library(resourcer)
-# coerce to a data.frame
-as.data.frame(res)
-# or get the resource client object for low-level interactions
-rescli <- resourcer::newResourceClient(res)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
+# then interpret locally the resource object (load the appropriate R packages)
+library(resourcer)
+# coerce to a data.frame
+as.data.frame(res)
+# or get the resource client object for low-level interactions
+rescli <- resourcer::newResourceClient(res)
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm.html b/docs/reference/opal.resource_perm.html
index e6856cab..d97e7fef 100644
--- a/docs/reference/opal.resource_perm.html
+++ b/docs/reference/opal.resource_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a resource
- opal.resource_perm(opal, project, resource)
+ opal.resource_perm(opal, project, resource)
@@ -111,13 +111,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -132,7 +132,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm_add.html b/docs/reference/opal.resource_perm_add.html
index 9c3d1438..6ad84919 100644
--- a/docs/reference/opal.resource_perm_add.html
+++ b/docs/reference/opal.resource_perm_add.html
@@ -69,14 +69,14 @@ Add or update a permission on a resource
- opal.resource_perm_add(
- opal,
- project,
- resource,
- subject,
- type = "user",
- permission
-)
+ opal.resource_perm_add(
+ opal,
+ project,
+ resource,
+ subject,
+ type = "user",
+ permission
+)
@@ -125,13 +125,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -146,7 +146,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm_delete.html b/docs/reference/opal.resource_perm_delete.html
index df299ed2..541396ce 100644
--- a/docs/reference/opal.resource_perm_delete.html
+++ b/docs/reference/opal.resource_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a resource
- opal.resource_perm_delete(opal, project, resource, subject, type = "user")
+ opal.resource_perm_delete(opal, project, resource, subject, type = "user")
@@ -113,13 +113,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.resource_view_create.html b/docs/reference/opal.resource_view_create.html
index d653a1cf..f3a7a1f2 100644
--- a/docs/reference/opal.resource_view_create.html
+++ b/docs/reference/opal.resource_view_create.html
@@ -73,15 +73,15 @@ Create an Opal view over a resource reference
- opal.resource_view_create(
- opal,
- project,
- table,
- resource,
- type = "Participant",
- idColumn = NULL,
- profile = NULL
-)
+ opal.resource_view_create(
+ opal,
+ project,
+ table,
+ resource,
+ type = "Participant",
+ idColumn = NULL,
+ profile = NULL
+)
@@ -119,6 +119,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
@@ -139,14 +140,14 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
- resource = "RSRC.FEMALE_2439", idColumn = "Name")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
+ resource = "RSRC.FEMALE_2439", idColumn = "Name")
+opal.logout(o)
+}
@@ -161,7 +162,7 @@ Examples
diff --git a/docs/reference/opal.resource_view_reconnect.html b/docs/reference/opal.resource_view_reconnect.html
index e8650b92..06f03a44 100644
--- a/docs/reference/opal.resource_view_reconnect.html
+++ b/docs/reference/opal.resource_view_reconnect.html
@@ -73,7 +73,7 @@ Reconnect an Opal view to its underlying resource
- opal.resource_view_reconnect(opal, project, table)
+ opal.resource_view_reconnect(opal, project, table)
@@ -93,6 +93,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.table_create(),
opal.table_delete(),
@@ -113,14 +114,14 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-# re-initialize the view's connection to the resource
-opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+# re-initialize the view's connection to the resource
+opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
+opal.logout(o)
+}
@@ -135,7 +136,7 @@ Examples
diff --git a/docs/reference/opal.resources.html b/docs/reference/opal.resources.html
index 305236d9..1219e1b9 100644
--- a/docs/reference/opal.resources.html
+++ b/docs/reference/opal.resources.html
@@ -69,7 +69,7 @@ Get the resource references of a project
- opal.resources(opal, project, df = TRUE)
+ opal.resources(opal, project, df = TRUE)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources(o, 'RSRC')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources(o, 'RSRC')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm.html b/docs/reference/opal.resources_perm.html
index ba3302b2..c53289ba 100644
--- a/docs/reference/opal.resources_perm.html
+++ b/docs/reference/opal.resources_perm.html
@@ -69,7 +69,7 @@ Get the permissions on any resource
- opal.resources_perm(opal, project)
+ opal.resources_perm(opal, project)
@@ -107,13 +107,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm_add.html b/docs/reference/opal.resources_perm_add.html
index 1a4a38e2..f1c870b4 100644
--- a/docs/reference/opal.resources_perm_add.html
+++ b/docs/reference/opal.resources_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on any resource
- opal.resources_perm_add(opal, project, subject, type = "user", permission)
+ opal.resources_perm_add(opal, project, subject, type = "user", permission)
@@ -114,13 +114,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm_delete.html b/docs/reference/opal.resources_perm_delete.html
index e7c09535..5c093566 100644
--- a/docs/reference/opal.resources_perm_delete.html
+++ b/docs/reference/opal.resources_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from any resource
- opal.resources_perm_delete(opal, project, subject, type = "user")
+ opal.resources_perm_delete(opal, project, subject, type = "user")
@@ -109,13 +109,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM', 'CNSIM1')
-opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM', 'CNSIM1')
+opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.rm.html b/docs/reference/opal.rm.html
index f444e41c..728ec6d4 100644
--- a/docs/reference/opal.rm.html
+++ b/docs/reference/opal.rm.html
@@ -69,7 +69,7 @@ Remove a R symbol (deprecated)
- opal.rm(opal, symbol)
+ opal.rm(opal, symbol)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.rm(o, 'D')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.sql.html b/docs/reference/opal.sql.html
index 41f13417..5fa1f9b8 100644
--- a/docs/reference/opal.sql.html
+++ b/docs/reference/opal.sql.html
@@ -75,7 +75,7 @@ Execute a SQL query on tables
- opal.sql(opal, query, project = NULL, id.name = "_id")
+ opal.sql(opal, query, project = NULL, id.name = "_id")
@@ -106,23 +106,23 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from CNSIM1
- where LAB_HDL is not null
- group by GENDER',
- 'CNSIM')
-# without project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from `CNSIM.CNSIM1`
- where LAB_HDL is not null
- group by GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from CNSIM1
+ where LAB_HDL is not null
+ group by GENDER',
+ 'CNSIM')
+# without project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from `CNSIM.CNSIM1`
+ where LAB_HDL is not null
+ group by GENDER')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/opal.sql_history.html b/docs/reference/opal.sql_history.html
index ff53d0db..1bd338f2 100644
--- a/docs/reference/opal.sql_history.html
+++ b/docs/reference/opal.sql_history.html
@@ -71,14 +71,14 @@ SQL query execution history
- opal.sql_history(
- opal,
- project = NULL,
- offset = 0,
- limit = 100,
- user = NULL,
- df = TRUE
-)
+ opal.sql_history(
+ opal,
+ project = NULL,
+ offset = 0,
+ limit = 100,
+ user = NULL,
+ df = TRUE
+)
@@ -118,16 +118,16 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql_history(o, 'CNSIM')
-# without project context
-opal.sql_history(o, NA)
-# with or without project context
-opal.sql_history(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql_history(o, 'CNSIM')
+# without project context
+opal.sql_history(o, NA)
+# with or without project context
+opal.sql_history(o)
+opal.logout(o)
+}
@@ -142,7 +142,7 @@ Examples
diff --git a/docs/reference/opal.symbol_import.html b/docs/reference/opal.symbol_import.html
index ae50bd82..5ee219a5 100644
--- a/docs/reference/opal.symbol_import.html
+++ b/docs/reference/opal.symbol_import.html
@@ -71,16 +71,16 @@ Import a tibble
- opal.symbol_import(
- opal,
- symbol,
- project,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)
+ opal.symbol_import(
+ opal,
+ symbol,
+ project,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)
@@ -128,11 +128,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_import(o, 'D', 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_import(o, 'D', 'test')
+opal.logout(o)
+}
@@ -147,7 +147,7 @@ Examples
diff --git a/docs/reference/opal.symbol_rm.html b/docs/reference/opal.symbol_rm.html
index d0cfd696..6d16a689 100644
--- a/docs/reference/opal.symbol_rm.html
+++ b/docs/reference/opal.symbol_rm.html
@@ -69,7 +69,7 @@ Remove a R symbol
- opal.symbol_rm(opal, symbol)
+ opal.symbol_rm(opal, symbol)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_rm(o, 'D')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.symbol_save.html b/docs/reference/opal.symbol_save.html
index f2a900f1..79035aa9 100644
--- a/docs/reference/opal.symbol_save.html
+++ b/docs/reference/opal.symbol_save.html
@@ -69,7 +69,7 @@ Save a tibble
- opal.symbol_save(opal, symbol, destination)
+ opal.symbol_save(opal, symbol, destination)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_save(o, 'D', 'test.sav')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_save(o, 'D', 'test.sav')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.symbols.html b/docs/reference/opal.symbols.html
index bb88de70..1b7894c4 100644
--- a/docs/reference/opal.symbols.html
+++ b/docs/reference/opal.symbols.html
@@ -69,7 +69,7 @@ List R symbols
- opal.symbols(opal)
+ opal.symbols(opal)
@@ -89,11 +89,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbols(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbols(o)
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/opal.table.html b/docs/reference/opal.table.html
index b4d05790..be03e321 100644
--- a/docs/reference/opal.table.html
+++ b/docs/reference/opal.table.html
@@ -69,7 +69,7 @@ Get a table of a datasource
- opal.table(opal, datasource, table, counts = FALSE)
+ opal.table(opal, datasource, table, counts = FALSE)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.table_create.html b/docs/reference/opal.table_create.html
index 44e433ba..46cf045b 100644
--- a/docs/reference/opal.table_create.html
+++ b/docs/reference/opal.table_create.html
@@ -73,7 +73,7 @@ Create an Opal table or view
- opal.table_create(opal, project, table, type = "Participant", tables = NULL)
+ opal.table_create(opal, project, table, type = "Participant", tables = NULL)
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_delete(),
@@ -122,15 +123,15 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a raw table
-opal.table_create(o, "CNSIM", "CNSIM4")
-# make a view
-opal.table_create(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a raw table
+opal.table_create(o, "CNSIM", "CNSIM4")
+# make a view
+opal.table_create(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
@@ -145,7 +146,7 @@ Examples
diff --git a/docs/reference/opal.table_delete.html b/docs/reference/opal.table_delete.html
index 778f2343..cba12a39 100644
--- a/docs/reference/opal.table_delete.html
+++ b/docs/reference/opal.table_delete.html
@@ -71,7 +71,7 @@ Delete a Opal table
- opal.table_delete(opal, project, table, silent = TRUE)
+ opal.table_delete(opal, project, table, silent = TRUE)
@@ -95,6 +95,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,11 +116,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_delete(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_delete(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -134,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.table_dictionary_get.html b/docs/reference/opal.table_dictionary_get.html
index 95a5c21a..59126cc2 100644
--- a/docs/reference/opal.table_dictionary_get.html
+++ b/docs/reference/opal.table_dictionary_get.html
@@ -69,7 +69,7 @@ Get the dictionary of a Opal table
- opal.table_dictionary_get(opal, project, table)
+ opal.table_dictionary_get(opal, project, table)
@@ -89,6 +89,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -109,11 +110,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -128,7 +129,7 @@ Examples
diff --git a/docs/reference/opal.table_dictionary_update.html b/docs/reference/opal.table_dictionary_update.html
index c2e5bfc5..090a7d91 100644
--- a/docs/reference/opal.table_dictionary_update.html
+++ b/docs/reference/opal.table_dictionary_update.html
@@ -69,13 +69,13 @@ Update the dictionary of a Opal table
- opal.table_dictionary_update(
- opal,
- project,
- table,
- variables,
- categories = NULL
-)
+ opal.table_dictionary_update(
+ opal,
+ project,
+ table,
+ variables,
+ categories = NULL
+)
@@ -104,6 +104,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -124,23 +125,23 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-variables <- tibble::tribble(
- ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
- "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
- "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
- "disp", "decimal", "Disp label", NA, NA, 1, 3
-)
-categories <- tibble::tribble(
- ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
- "cyl", "4", 0, "Four", "Quatre",
- "cyl", "6", 0, "Six", "Six",
- "cyl", "8", 1, "Height", "Huit"
-)
-opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+variables <- tibble::tribble(
+ ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
+ "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
+ "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
+ "disp", "decimal", "Disp label", NA, NA, 1, 3
+)
+categories <- tibble::tribble(
+ ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
+ "cyl", "4", 0, "Four", "Quatre",
+ "cyl", "6", 0, "Six", "Six",
+ "cyl", "8", 1, "Height", "Huit"
+)
+opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
+opal.logout(o)
+}
@@ -155,7 +156,7 @@ Examples
diff --git a/docs/reference/opal.table_exists.html b/docs/reference/opal.table_exists.html
index 10649da8..e4ac20bb 100644
--- a/docs/reference/opal.table_exists.html
+++ b/docs/reference/opal.table_exists.html
@@ -71,7 +71,7 @@ Check a Opal table exists
- opal.table_exists(opal, project, table, view = NA)
+ opal.table_exists(opal, project, table, view = NA)
@@ -96,6 +96,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -116,16 +117,16 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# check table exists
-opal.table_exists(o, "CNSIM", "CNSIM1")
-# check table exists AND is a NOT a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
-# check table exists AND is a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# check table exists
+opal.table_exists(o, "CNSIM", "CNSIM1")
+# check table exists AND is a NOT a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
+# check table exists AND is a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
+opal.logout(o)
+}
@@ -140,7 +141,7 @@ Examples
diff --git a/docs/reference/opal.table_export.html b/docs/reference/opal.table_export.html
index f5eb8c76..5110bb07 100644
--- a/docs/reference/opal.table_export.html
+++ b/docs/reference/opal.table_export.html
@@ -73,15 +73,15 @@ Export a table as a file
- opal.table_export(
- opal,
- project,
- table,
- file,
- identifiers = NULL,
- id.name = "id",
- wait = TRUE
-)
+ opal.table_export(
+ opal,
+ project,
+ table,
+ file,
+ identifiers = NULL,
+ id.name = "id",
+ wait = TRUE
+)
@@ -120,6 +120,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -140,12 +141,12 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
- file = "/home/administrator/cnsim1.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
+ file = "/home/administrator/cnsim1.sav")
+opal.logout(o)
+}
@@ -160,7 +161,7 @@ Examples
diff --git a/docs/reference/opal.table_get.html b/docs/reference/opal.table_get.html
index 8a695e18..50b31621 100644
--- a/docs/reference/opal.table_get.html
+++ b/docs/reference/opal.table_get.html
@@ -73,14 +73,14 @@ Get a Opal table as a tibble
- opal.table_get(
- opal,
- project,
- table,
- id.name = "id",
- variables = NULL,
- missings = TRUE
-)
+ opal.table_get(
+ opal,
+ project,
+ table,
+ id.name = "id",
+ variables = NULL,
+ missings = TRUE
+)
@@ -112,6 +112,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -132,11 +133,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+opal.logout(o)
+}
@@ -151,7 +152,7 @@ Examples
diff --git a/docs/reference/opal.table_import.html b/docs/reference/opal.table_import.html
index e7a050a5..587ba457 100644
--- a/docs/reference/opal.table_import.html
+++ b/docs/reference/opal.table_import.html
@@ -77,17 +77,17 @@ Import a file as table
- opal.table_import(
- opal,
- file,
- project,
- table,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)
+ opal.table_import(
+ opal,
+ file,
+ project,
+ table,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)
@@ -131,6 +131,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -151,11 +152,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
+opal.logout(o)
+}
@@ -170,7 +171,7 @@ Examples
diff --git a/docs/reference/opal.table_perm.html b/docs/reference/opal.table_perm.html
index d6ebf2a3..b007ebba 100644
--- a/docs/reference/opal.table_perm.html
+++ b/docs/reference/opal.table_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a table
- opal.table_perm(opal, project, table)
+ opal.table_perm(opal, project, table)
@@ -95,6 +95,7 @@ Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,13 +116,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -136,7 +137,7 @@ Examples
diff --git a/docs/reference/opal.table_perm_add.html b/docs/reference/opal.table_perm_add.html
index dcd7c7bc..0a6d3975 100644
--- a/docs/reference/opal.table_perm_add.html
+++ b/docs/reference/opal.table_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on a table
- opal.table_perm_add(opal, project, table, subject, type = "user", permission)
+ opal.table_perm_add(opal, project, table, subject, type = "user", permission)
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -143,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.table_perm_delete.html b/docs/reference/opal.table_perm_delete.html
index 8b9b72de..940dd6c6 100644
--- a/docs/reference/opal.table_perm_delete.html
+++ b/docs/reference/opal.table_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a table
- opal.table_perm_delete(opal, project, table, subject, type = "user")
+ opal.table_perm_delete(opal, project, table, subject, type = "user")
@@ -97,6 +97,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -117,13 +118,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -138,7 +139,7 @@ Examples
diff --git a/docs/reference/opal.table_save.html b/docs/reference/opal.table_save.html
index 99d85274..b60ae4ab 100644
--- a/docs/reference/opal.table_save.html
+++ b/docs/reference/opal.table_save.html
@@ -71,18 +71,18 @@ Save a local tibble as a Opal table
- opal.table_save(
- opal,
- tibble,
- project,
- table,
- overwrite = TRUE,
- force = FALSE,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant"
-)
+ opal.table_save(
+ opal,
+ tibble,
+ project,
+ table,
+ overwrite = TRUE,
+ force = FALSE,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant"
+)
@@ -142,6 +142,7 @@ Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -162,15 +163,15 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-# do some (meta)data transformations, then save in opal's database
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
-# or overwrite data only (keep original data dictionary)
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+# do some (meta)data transformations, then save in opal's database
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
+# or overwrite data only (keep original data dictionary)
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
+opal.logout(o)
+}
@@ -185,7 +186,7 @@ Examples
diff --git a/docs/reference/opal.table_truncate.html b/docs/reference/opal.table_truncate.html
index 13487c0d..41394336 100644
--- a/docs/reference/opal.table_truncate.html
+++ b/docs/reference/opal.table_truncate.html
@@ -71,7 +71,7 @@ Truncate a Opal table
- opal.table_truncate(opal, project, table)
+ opal.table_truncate(opal, project, table)
@@ -91,6 +91,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -111,11 +112,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_truncate(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_truncate(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -130,7 +131,7 @@ Examples
diff --git a/docs/reference/opal.table_view_create.html b/docs/reference/opal.table_view_create.html
index 9b40db41..704d8e1c 100644
--- a/docs/reference/opal.table_view_create.html
+++ b/docs/reference/opal.table_view_create.html
@@ -73,7 +73,7 @@ Create an Opal view over tables
- opal.table_view_create(opal, project, table, tables, type = "Participant")
+ opal.table_view_create(opal, project, table, tables, type = "Participant")
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
@@ -143,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.table_view_update.html b/docs/reference/opal.table_view_update.html
index c4892e57..edf8750f 100644
--- a/docs/reference/opal.table_view_update.html
+++ b/docs/reference/opal.table_view_update.html
@@ -73,7 +73,7 @@ Update the table references and the entity filter of an Opal view
- opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
+ opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
@@ -101,6 +101,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -121,28 +122,28 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1"))
-
-# update the table references
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-
-# update the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
-
-# remove the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
-
-# update both the table references and the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
- where = "$('LAB_TSC').ge(5)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1"))
+
+# update the table references
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+
+# update the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
+
+# remove the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
+
+# update both the table references and the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
+ where = "$('LAB_TSC').ge(5)")
+opal.logout(o)
+}
@@ -157,7 +158,7 @@ Examples
diff --git a/docs/reference/opal.tables.html b/docs/reference/opal.tables.html
index da771ccc..3523f1ce 100644
--- a/docs/reference/opal.tables.html
+++ b/docs/reference/opal.tables.html
@@ -69,7 +69,7 @@ Get tables of a datasource
- opal.tables(opal, datasource, counts = FALSE, df = TRUE)
+ opal.tables(opal, datasource, counts = FALSE, df = TRUE)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables(o, 'CNSIM')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm.html b/docs/reference/opal.tables_perm.html
index e401969e..eaf76e27 100644
--- a/docs/reference/opal.tables_perm.html
+++ b/docs/reference/opal.tables_perm.html
@@ -69,7 +69,7 @@ Get the permissions on any table of a project
- opal.tables_perm(opal, project)
+ opal.tables_perm(opal, project)
@@ -91,13 +91,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm_add.html b/docs/reference/opal.tables_perm_add.html
index f9f318fe..34f1092b 100644
--- a/docs/reference/opal.tables_perm_add.html
+++ b/docs/reference/opal.tables_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on any table of a project
- opal.tables_perm_add(opal, project, subject, type = "user", permission)
+ opal.tables_perm_add(opal, project, subject, type = "user", permission)
@@ -97,13 +97,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm_delete.html b/docs/reference/opal.tables_perm_delete.html
index 58317fa1..c6c2bbb4 100644
--- a/docs/reference/opal.tables_perm_delete.html
+++ b/docs/reference/opal.tables_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from any table of a project
- opal.tables_perm_delete(opal, project, subject, type = "user")
+ opal.tables_perm_delete(opal, project, subject, type = "user")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/opal.task.html b/docs/reference/opal.task.html
index 5f63c0bb..9f2abe58 100644
--- a/docs/reference/opal.task.html
+++ b/docs/reference/opal.task.html
@@ -69,7 +69,7 @@ Get a task
- opal.task(opal, id)
+ opal.task(opal, id)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task(o, '1')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.task_cancel.html b/docs/reference/opal.task_cancel.html
index 4d2f68ff..a6d3af66 100644
--- a/docs/reference/opal.task_cancel.html
+++ b/docs/reference/opal.task_cancel.html
@@ -69,7 +69,7 @@ Cancel a task
- opal.task_cancel(opal, id)
+ opal.task_cancel(opal, id)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_cancel(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_cancel(o, '1')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.task_wait.html b/docs/reference/opal.task_wait.html
index e46c9ad1..c75baf8d 100644
--- a/docs/reference/opal.task_wait.html
+++ b/docs/reference/opal.task_wait.html
@@ -69,7 +69,7 @@ Wait for a task to complete.
- opal.task_wait(opal, id, max = NULL)
+ opal.task_wait(opal, id, max = NULL)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_wait(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_wait(o, '1')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.tasks.html b/docs/reference/opal.tasks.html
index b03cca25..bbc1909c 100644
--- a/docs/reference/opal.tasks.html
+++ b/docs/reference/opal.tasks.html
@@ -69,7 +69,7 @@ Get the tasks
- opal.tasks(opal, df = TRUE)
+ opal.tasks(opal, df = TRUE)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tasks(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tasks(o)
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.taxonomies.html b/docs/reference/opal.taxonomies.html
index 6eb7c9fc..7fdeb65c 100644
--- a/docs/reference/opal.taxonomies.html
+++ b/docs/reference/opal.taxonomies.html
@@ -71,7 +71,7 @@ Get taxonomies
- opal.taxonomies(opal, locale = "en", df = TRUE)
+ opal.taxonomies(opal, locale = "en", df = TRUE)
@@ -102,11 +102,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomies(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomies(o)
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy.html b/docs/reference/opal.taxonomy.html
index 588356cb..830f2f20 100644
--- a/docs/reference/opal.taxonomy.html
+++ b/docs/reference/opal.taxonomy.html
@@ -69,7 +69,7 @@ Get a taxonomy
- opal.taxonomy(opal, taxonomy)
+ opal.taxonomy(opal, taxonomy)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_delete.html b/docs/reference/opal.taxonomy_delete.html
index 56a28d51..16c5fe75 100644
--- a/docs/reference/opal.taxonomy_delete.html
+++ b/docs/reference/opal.taxonomy_delete.html
@@ -69,7 +69,7 @@ Delete a taxonomy
- opal.taxonomy_delete(opal, taxonomy)
+ opal.taxonomy_delete(opal, taxonomy)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_delete(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_delete(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_download.html b/docs/reference/opal.taxonomy_download.html
index bde9b7cc..72ddba73 100644
--- a/docs/reference/opal.taxonomy_download.html
+++ b/docs/reference/opal.taxonomy_download.html
@@ -69,7 +69,7 @@ Download a taxonomy file
- opal.taxonomy_download(opal, taxonomy, destination = NULL)
+ opal.taxonomy_download(opal, taxonomy, destination = NULL)
@@ -101,11 +101,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_upload.html b/docs/reference/opal.taxonomy_upload.html
index f64a1c9c..33aa2918 100644
--- a/docs/reference/opal.taxonomy_upload.html
+++ b/docs/reference/opal.taxonomy_upload.html
@@ -71,7 +71,7 @@ Upload a taxonomy file
- opal.taxonomy_upload(opal, path)
+ opal.taxonomy_upload(opal, path)
@@ -98,11 +98,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/opal.terms.html b/docs/reference/opal.terms.html
index 42d3ba1c..4514444d 100644
--- a/docs/reference/opal.terms.html
+++ b/docs/reference/opal.terms.html
@@ -69,7 +69,7 @@ Get the terms of a vocabulary
- opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
+ opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/opal.token.html b/docs/reference/opal.token.html
index 139cfb7f..2b23254c 100644
--- a/docs/reference/opal.token.html
+++ b/docs/reference/opal.token.html
@@ -71,7 +71,7 @@ Get a personal access token
- opal.token(opal, name)
+ opal.token(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_datashield_create.html b/docs/reference/opal.token_datashield_create.html
index 3eb7cd13..2f127a6b 100644
--- a/docs/reference/opal.token_datashield_create.html
+++ b/docs/reference/opal.token_datashield_create.html
@@ -71,7 +71,7 @@ Create a personal access token for Datashield usage
- opal.token_datashield_create(opal, name, projects = NULL)
+ opal.token_datashield_create(opal, name, projects = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_datashield_create(o, 'ds-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_datashield_create(o, 'ds-1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.token_delete.html b/docs/reference/opal.token_delete.html
index 780eb5ed..402a3d26 100644
--- a/docs/reference/opal.token_delete.html
+++ b/docs/reference/opal.token_delete.html
@@ -71,7 +71,7 @@ Delete a personal access token
- opal.token_delete(opal, name)
+ opal.token_delete(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_delete(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_delete(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_r_create.html b/docs/reference/opal.token_r_create.html
index b0b36787..c8222189 100644
--- a/docs/reference/opal.token_r_create.html
+++ b/docs/reference/opal.token_r_create.html
@@ -71,13 +71,13 @@ Create a personal access token for R usage
- opal.token_r_create(
- opal,
- name,
- projects = NULL,
- access = NULL,
- commands = c("export")
-)
+ opal.token_r_create(
+ opal,
+ name,
+ projects = NULL,
+ access = NULL,
+ commands = c("export")
+)
@@ -121,11 +121,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
+opal.logout(o)
+}
@@ -140,7 +140,7 @@ Examples
diff --git a/docs/reference/opal.token_renew.html b/docs/reference/opal.token_renew.html
index 72208339..e11a4f33 100644
--- a/docs/reference/opal.token_renew.html
+++ b/docs/reference/opal.token_renew.html
@@ -71,7 +71,7 @@ Renew an inactive personal access token
- opal.token_renew(opal, name)
+ opal.token_renew(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_renew(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_renew(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_sql_create.html b/docs/reference/opal.token_sql_create.html
index b618980e..d65e177c 100644
--- a/docs/reference/opal.token_sql_create.html
+++ b/docs/reference/opal.token_sql_create.html
@@ -71,7 +71,7 @@ Create a personal access token for SQL usage
- opal.token_sql_create(opal, name, projects = NULL)
+ opal.token_sql_create(opal, name, projects = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_sql_create(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_sql_create(o, 'sql-1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.tokens.html b/docs/reference/opal.tokens.html
index 59d4edfa..703771e5 100644
--- a/docs/reference/opal.tokens.html
+++ b/docs/reference/opal.tokens.html
@@ -71,7 +71,7 @@ Get the personal access tokens
- opal.tokens(opal, df = TRUE)
+ opal.tokens(opal, df = TRUE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tokens(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tokens(o)
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.unload_package.html b/docs/reference/opal.unload_package.html
index cb7ded42..6b5ebac0 100644
--- a/docs/reference/opal.unload_package.html
+++ b/docs/reference/opal.unload_package.html
@@ -69,7 +69,7 @@ Unload package
- opal.unload_package(opal, pkg)
+ opal.unload_package(opal, pkg)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.unload_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.unload_package(o, 'stats')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.valueset.html b/docs/reference/opal.valueset.html
index 7bbd50a4..d0c5c00a 100644
--- a/docs/reference/opal.valueset.html
+++ b/docs/reference/opal.valueset.html
@@ -69,7 +69,7 @@ Get the values of an entity
- opal.valueset(opal, datasource, table, identifier)
+ opal.valueset(opal, datasource, table, identifier)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.variable.html b/docs/reference/opal.variable.html
index 3e2e9155..2269ea5d 100644
--- a/docs/reference/opal.variable.html
+++ b/docs/reference/opal.variable.html
@@ -69,7 +69,7 @@ Get a variable of a table
- opal.variable(opal, datasource, table, variable)
+ opal.variable(opal, datasource, table, variable)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.variable_summary.html b/docs/reference/opal.variable_summary.html
index 75fda252..5686692d 100644
--- a/docs/reference/opal.variable_summary.html
+++ b/docs/reference/opal.variable_summary.html
@@ -69,14 +69,14 @@ Get summary statistics of a variable of a table
- opal.variable_summary(
- opal,
- datasource,
- table,
- variable,
- cached = TRUE,
- nature = NULL
-)
+ opal.variable_summary(
+ opal,
+ datasource,
+ table,
+ variable,
+ cached = TRUE,
+ nature = NULL
+)
@@ -124,11 +124,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
@@ -143,7 +143,7 @@ Examples
diff --git a/docs/reference/opal.variables.html b/docs/reference/opal.variables.html
index e1072df8..3ea90c87 100644
--- a/docs/reference/opal.variables.html
+++ b/docs/reference/opal.variables.html
@@ -69,7 +69,7 @@ Get variables of a table
- opal.variables(opal, datasource, table, locale = "en", df = TRUE)
+ opal.variables(opal, datasource, table, locale = "en", df = TRUE)
@@ -111,11 +111,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variables(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variables(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.version_compare.html b/docs/reference/opal.version_compare.html
index f9a8bc44..b8a11b96 100644
--- a/docs/reference/opal.version_compare.html
+++ b/docs/reference/opal.version_compare.html
@@ -71,7 +71,7 @@ Compare
- opal.version_compare(opal, version)
+ opal.version_compare(opal, version)
@@ -93,11 +93,11 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.version_compare(o, "2.6.0")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.version_compare(o, "2.6.0")
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.vocabularies.html b/docs/reference/opal.vocabularies.html
index 2a4ae4ac..edaf165e 100644
--- a/docs/reference/opal.vocabularies.html
+++ b/docs/reference/opal.vocabularies.html
@@ -69,7 +69,7 @@ Get the vocabularies of a taxonomy
- opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
+ opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabularies(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabularies(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.vocabulary.html b/docs/reference/opal.vocabulary.html
index 8dd847d4..18c471f7 100644
--- a/docs/reference/opal.vocabulary.html
+++ b/docs/reference/opal.vocabulary.html
@@ -69,7 +69,7 @@ Get a taxonomy vocabulary
- opal.vocabulary(opal, taxonomy, vocabulary)
+ opal.vocabulary(opal, taxonomy, vocabulary)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.workspace_restore.html b/docs/reference/opal.workspace_restore.html
index 192c945b..705b823a 100644
--- a/docs/reference/opal.workspace_restore.html
+++ b/docs/reference/opal.workspace_restore.html
@@ -69,7 +69,7 @@ Restore a R workspace from a opal.
- opal.workspace_restore(opal, ws)
+ opal.workspace_restore(opal, ws)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_restore(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_restore(o, 'test')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.workspace_rm.html b/docs/reference/opal.workspace_rm.html
index e33cf1d2..4bce81f9 100644
--- a/docs/reference/opal.workspace_rm.html
+++ b/docs/reference/opal.workspace_rm.html
@@ -69,7 +69,7 @@ Remove a R workspace from a opal.
- opal.workspace_rm(opal, ws, user = NULL)
+ opal.workspace_rm(opal, ws, user = NULL)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_rm(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_rm(o, 'test')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.workspace_save.html b/docs/reference/opal.workspace_save.html
index 074274e0..aa974933 100644
--- a/docs/reference/opal.workspace_save.html
+++ b/docs/reference/opal.workspace_save.html
@@ -69,7 +69,7 @@ Save the current session in a opal R workspace.
- opal.workspace_save(opal, save = TRUE)
+ opal.workspace_save(opal, save = TRUE)
@@ -98,14 +98,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# provide a workspace ID
-opal.workspace_save(o, 'test')
-# or use default one
-id <- opal.workspace_save(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# provide a workspace ID
+opal.workspace_save(o, 'test')
+# or use default one
+id <- opal.workspace_save(o)
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.workspaces.html b/docs/reference/opal.workspaces.html
index 83f92fdc..f4b0c155 100644
--- a/docs/reference/opal.workspaces.html
+++ b/docs/reference/opal.workspaces.html
@@ -69,7 +69,7 @@ Get the R workspaces from a opal.
- opal.workspaces(opal)
+ opal.workspaces(opal)
@@ -88,11 +88,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspaces(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspaces(o)
+opal.logout(o)
+}
@@ -107,7 +107,7 @@ Examples
diff --git a/docs/reference/opalr-package.html b/docs/reference/opalr-package.html
index acf0539c..7a3957ef 100644
--- a/docs/reference/opalr-package.html
+++ b/docs/reference/opalr-package.html
@@ -99,7 +99,7 @@ Author
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index db0185af..5d5b6ce2 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -123,6 +123,12 @@
/reference/dot-verbose.html
+
+ /reference/dsadmin.activity.html
+
+
+ /reference/dsadmin.activity_summary.html
+
/reference/dsadmin.get_method.html
@@ -144,6 +150,9 @@
/reference/dsadmin.installed_package.html
+
+ /reference/dsadmin.log.html
+
/reference/dsadmin.package_description.html
@@ -231,6 +240,12 @@
/reference/index.html
+
+ /reference/oadmin.activity.html
+
+
+ /reference/oadmin.activity_summary.html
+
/reference/oadmin.install_bioconductor_package.html
@@ -258,6 +273,15 @@
/reference/oadmin.installed_packages.html
+
+ /reference/oadmin.log.html
+
+
+ /reference/oadmin.log_rest.html
+
+
+ /reference/oadmin.log_sql.html
+
/reference/oadmin.package_description.html
@@ -426,6 +450,9 @@
/reference/opal.logout.html
+
+ /reference/opal.perms.html
+
/reference/opal.post.html
-opal.logout(o)Site built with pkgdown 2.0.6.
+Site built with pkgdown 2.0.7.
diff --git a/docs/articles/index.html b/docs/articles/index.html index ab9919fd..501db9f7 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@All vignettes
diff --git a/docs/articles/opal-files.html b/docs/articles/opal-files.html index 31d37924..f34618c3 100644 --- a/docs/articles/opal-files.html +++ b/docs/articles/opal-files.html @@ -88,7 +88,7 @@Opal Files
Yannick Marcon
-2023-02-03
+2023-12-20
Source:vignettes/opal-files.Rmd
opal-files.Rmd2023-02-03
Setup the connection with Opal:
-library(opalr)
-o <- opal.login("administrator", "password", "https://opal-demo.obiba.org")library(opalr)
+o <- opal.login("administrator", "password", "https://opal-demo.obiba.org")
Download a file:
-opal.file_download(o, "/home/administrator/CNSIM.zip")opal.file_download(o, "/home/administrator/CNSIM.zip")
Download a file, protected by a password:
-opal.file_download(o, "/home/administrator/CNSIM.zip", "CNSIM-encrypted.zip", key="ABCDEFGHIJKL")opal.file_download(o, "/home/administrator/CNSIM.zip", "CNSIM-encrypted.zip", key="ABCDEFGHIJKL")
Upload the file at another location:
-opal.file_upload(o, "CNSIM.zip", "/projects/CNSIM")opal.file_upload(o, "CNSIM.zip", "/projects/CNSIM")
Create a folder and list folder content:
-fooDir <- paste0("/projects/CNSIM/foo-", sample(10000:99999, 1))
-opal.file_mkdir(o, fooDir)
-opal.file_ls(o, "/projects/CNSIM")fooDir <- paste0("/projects/CNSIM/foo-", sample(10000:99999, 1))
+opal.file_mkdir(o, fooDir)
+opal.file_ls(o, "/projects/CNSIM")
Move file to the new folder and list folder content:
-opal.file_mv(o, "/projects/CNSIM/CNSIM.zip", fooDir)
-opal.file_ls(o, fooDir)opal.file_mv(o, "/projects/CNSIM/CNSIM.zip", fooDir)
+opal.file_ls(o, fooDir)
Rename the new folder and list folder content:
-barDir <- paste0("/projects/CNSIM/bar-", sample(10000:99999, 1))
-opal.file_mv(o, fooDir, barDir)
-opal.file_ls(o, "/projects/CNSIM")barDir <- paste0("/projects/CNSIM/bar-", sample(10000:99999, 1))
+opal.file_mv(o, fooDir, barDir)
+opal.file_ls(o, "/projects/CNSIM")
Extract the content of the archive file into a folder:
-out <- opal.file_unzip(o, paste0(barDir, "/CNSIM.zip"), barDir)
-opal.file_ls(o, out)out <- opal.file_unzip(o, paste0(barDir, "/CNSIM.zip"), barDir)
+opal.file_ls(o, out)
Write a file from the Opal file system into the R server session workspace:
-opal.file_write(o, paste0(barDir, "/CNSIM.zip"))
-opal.execute(o, "list.files()")opal.file_write(o, paste0(barDir, "/CNSIM.zip"))
+opal.execute(o, "list.files()")
Read back the file into the Opal file system:
-opal.file_read(o, "CNSIM.zip", paste0(barDir, "/ds.zip"))
-opal.file_ls(o, barDir)opal.file_read(o, "CNSIM.zip", paste0(barDir, "/ds.zip"))
+opal.file_ls(o, barDir)
Remove created folder and list folder content:
-opal.file_rm(o, barDir)
-opal.file_ls(o, "/projects/CNSIM")opal.file_rm(o, barDir)
+opal.file_ls(o, "/projects/CNSIM")
Good practice is to free server resources by sending a logout request:
-# clean server side
-opal.logout(o)
-# clean client side
-unlink("CNSIM-encrypted.zip")
-unlink("CNSIM.zip")# clean server side
+opal.logout(o)
+# clean client side
+unlink("CNSIM-encrypted.zip")
+unlink("CNSIM.zip")
Create a project, linked to a database (default or first one):
-if (opal.project_exists(o, "dummy"))
- opal.project_delete(o, "dummy")
-opal.project_create(o, "dummy", database = TRUE)
-opal.project(o, "dummy")if (opal.project_exists(o, "dummy"))
+ opal.project_delete(o, "dummy")
+opal.project_create(o, "dummy", database = TRUE)
+opal.project(o, "dummy")
Backup and Restore
Backup a project and download the backup archive (encrypted):
-opal.project_backup(o, 'CNSIM', '/home/administrator/backup/CNSIM')
-opal.file_download(o, '/home/administrator/backup/CNSIM', '/tmp/CNSIM.zip', key = "12345abcdef")opal.project_backup(o, 'CNSIM', '/home/administrator/backup/CNSIM')
+opal.file_download(o, '/home/administrator/backup/CNSIM', '/tmp/CNSIM.zip', key = "12345abcdef")Restore a project from an uploaded (and encrypted) archive:
-opal.file_upload(o, '/tmp/CNSIM.zip', '/home/administrator')
-opal.project_restore(o, 'dummy', '/home/administrator/CNSIM.zip', key = "12345abcdef")
-# verify tables
-opal.tables(o, "CNSIM")opal.file_upload(o, '/tmp/CNSIM.zip', '/home/administrator')
+opal.project_restore(o, 'dummy', '/home/administrator/CNSIM.zip', key = "12345abcdef")
+# verify tables
+opal.tables(o, "CNSIM")
@@ -162,23 +162,23 @@
+
Tables
List the tables in a project, with their count of variables and entities:
-opal.tables(o, "CNSIM", counts = TRUE)opal.tables(o, "CNSIM", counts = TRUE)The table object can be retrieved as follow:
-opal.table(o, "CNSIM", "CNSIM1", counts = TRUE)opal.table(o, "CNSIM", "CNSIM1", counts = TRUE)
The existence of a table can be checked:
-opal.table_exists(o, "CNSIM", "CNSIM1")opal.table_exists(o, "CNSIM", "CNSIM1")
And more specifically, verify whether a table is a view or not:
-opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
A table can be created, either as a raw table or a view. To create a view, specify which tables are referred:
-# drop table if it exists
-opal.table_delete(o, "CNSIM", "CNSIM123")
-# then create a view, no variables
-opal.table_create(o, "CNSIM", "CNSIM123", tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))# drop table if it exists
+opal.table_delete(o, "CNSIM", "CNSIM123")
+# then create a view, no variables
+opal.table_create(o, "CNSIM", "CNSIM123", tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
Dictionaries
@@ -187,68 +187,68 @@Dictionaries
-opal.variables(o, "CNSIM", "CNSIM1")
opal.variables(o, "CNSIM", "CNSIM1")opal.variables(o, "CNSIM", "CNSIM1")
It is also possible to get the full data dictionary of a table, as separate data frames of variables and categories. This is the recommended format for working with a data dictionary:
-dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
-dico$variables
-dico$categoriesdico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
+dico$variables
+dico$categories
Here we modify the data dictionary by appending a derivation script to each of the variables:
-dico$variables$script <- paste0("$('", dico$variables$name, "')")
-dico$variablesdico$variables$script <- paste0("$('", dico$variables$name, "')")
+dico$variables
Then we apply this derived variables dictionary to the view we have previously created and verify the counts of columns (variables) and rows (entities) in this table:
-opal.table_dictionary_update(o, "CNSIM", "CNSIM123", variables = dico$variables, categories = dico$categories)
-opal.table(o, "CNSIM", "CNSIM123", counts = TRUE)opal.table_dictionary_update(o, "CNSIM", "CNSIM123", variables = dico$variables, categories = dico$categories)
+opal.table(o, "CNSIM", "CNSIM123", counts = TRUE)
Assign this view to a symbol in the R server, and get the summary statics:
-opal.assign(o, "D", "CNSIM.CNSIM123")
-opal.execute(o, "summary(D)")opal.assign(o, "D", "CNSIM.CNSIM123")
+opal.execute(o, "summary(D)")
Values
Get the values in a table for a specific Participant entity:
-opal.valueset(o, "CNSIM", "CNSIM123", identifier = "1454")opal.valueset(o, "CNSIM", "CNSIM123", identifier = "1454")Get all the values of a table in our local R session as a data.frame (tibble) object:
-cnsim1 <- opal.table_get(o, "CNSIM", "CNSIM1")
-cnsim2 <- opal.table_get(o, "CNSIM", "CNSIM2")
-cnsim3 <- opal.table_get(o, "CNSIM", "CNSIM3")cnsim1 <- opal.table_get(o, "CNSIM", "CNSIM1")
+cnsim2 <- opal.table_get(o, "CNSIM", "CNSIM2")
+cnsim3 <- opal.table_get(o, "CNSIM", "CNSIM3")
Then do some alterations on this data.frame and save it back as a raw table:
-# make sure IDs are unique
-cnsim1$id <- paste0(cnsim1$id, "-1")
-cnsim2$id <- paste0(cnsim2$id, "-2")
-cnsim3$id <- paste0(cnsim3$id, "-3")
-# bind tables
-cnsim123 <- rbind(cnsim1, cnsim2, cnsim3)
-# remove some columns
-cnsim123$DIS_AMI <- NULL
-cnsim123$DIS_CVA <- NULL
-cnsim123$DIS_DIAB <- NULL
-# save as a raw table
-opal.table_save(o, cnsim123, "CNSIM", "CNSIM", overwrite = TRUE, force = TRUE)
-opal.table(o, "CNSIM", "CNSIM", counts = TRUE)# make sure IDs are unique
+cnsim1$id <- paste0(cnsim1$id, "-1")
+cnsim2$id <- paste0(cnsim2$id, "-2")
+cnsim3$id <- paste0(cnsim3$id, "-3")
+# bind tables
+cnsim123 <- rbind(cnsim1, cnsim2, cnsim3)
+# remove some columns
+cnsim123$DIS_AMI <- NULL
+cnsim123$DIS_CVA <- NULL
+cnsim123$DIS_DIAB <- NULL
+# save as a raw table
+opal.table_save(o, cnsim123, "CNSIM", "CNSIM", overwrite = TRUE, force = TRUE)
+opal.table(o, "CNSIM", "CNSIM", counts = TRUE)
Verify that this raw table resulting from the merge of the other tables as same values for a given Participant:
-opal.valueset(o, "CNSIM", "CNSIM", identifier = "1454-1")opal.valueset(o, "CNSIM", "CNSIM", identifier = "1454-1")
It is possible to truncate a table, i.e. delete ALL the values of a table (which must not be a view), without modifying the dictionary:
-opal.table_truncate(o, "CNSIM", "CNSIM")
-opal.table(o, "CNSIM", "CNSIM", counts = TRUE)opal.table_truncate(o, "CNSIM", "CNSIM")
+opal.table(o, "CNSIM", "CNSIM", counts = TRUE)
Annotations
@@ -257,27 +257,27 @@ Annotations
-opal.taxonomies(o)
-opal.taxonomies(o)opal.taxonomies(o)
List the vocabularies of a taxonomy:
-opal.vocabularies(o, taxonomy = "Mlstr_area")opal.vocabularies(o, taxonomy = "Mlstr_area")
List the terms of a vocabulary:
-opal.terms(o, taxonomy = "Mlstr_area", vocabulary = "Lifestyle_behaviours")opal.terms(o, taxonomy = "Mlstr_area", vocabulary = "Lifestyle_behaviours")
To apply a taxonomy term to a table dictionary, use the following for batch annotation:
-annotations <- tibble::tribble(
- ~variable, ~taxonomy, ~vocabulary, ~term,
- "LAB_TSC", "Mlstr_area", "Physical_measures", "Physical_characteristics",
- "LAB_TRIG", "Mlstr_area", "Physical_measures", "Physical_characteristics",
- "LAB_HDL", "Mlstr_area", "Physical_measures", "Physical_characteristics",
- "LAB_GLUC_ADJUSTED", "Mlstr_area", "Physical_measures", "Physical_characteristics"
-)
-opal.annotate(o, "CNSIM", "CNSIM123", annotations = annotations)annotations <- tibble::tribble(
+ ~variable, ~taxonomy, ~vocabulary, ~term,
+ "LAB_TSC", "Mlstr_area", "Physical_measures", "Physical_characteristics",
+ "LAB_TRIG", "Mlstr_area", "Physical_measures", "Physical_characteristics",
+ "LAB_HDL", "Mlstr_area", "Physical_measures", "Physical_characteristics",
+ "LAB_GLUC_ADJUSTED", "Mlstr_area", "Physical_measures", "Physical_characteristics"
+)
+opal.annotate(o, "CNSIM", "CNSIM123", annotations = annotations)
To list the variable annotations:
-opal.annotations(o, "CNSIM", "CNSIM123")opal.annotations(o, "CNSIM", "CNSIM123")
@@ -289,34 +289,34 @@ Resources
+Resources
-opal.resources(o, "RSRC")
opal.resources(o, "RSRC")opal.resources(o, "RSRC")
To create a reference to a resource (a compressed CSV file, stored in a Opal file system, authorized by a personal access token):
-if (opal.resource_exists(o, "RSRC", "CNSIM4"))
- opal.resource_delete(o, "RSRC", "CNSIM4")
-opal.resource_create(o, "RSRC", "CNSIM4",
- url = "opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip",
- format = "csv", secret = "EeTtQGIob6haio5bx6FUfVvIGkeZJfGq")
-# verify the resource reference object
-opal.resource(o, "RSRC", "CNSIM4")if (opal.resource_exists(o, "RSRC", "CNSIM4"))
+ opal.resource_delete(o, "RSRC", "CNSIM4")
+opal.resource_create(o, "RSRC", "CNSIM4",
+ url = "opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip",
+ format = "csv", secret = "EeTtQGIob6haio5bx6FUfVvIGkeZJfGq")
+# verify the resource reference object
+opal.resource(o, "RSRC", "CNSIM4")
From a resource reference, it is possible to build and get the resource object in the local R session:
-opal.resource_get(o, "RSRC", "CNSIM4")opal.resource_get(o, "RSRC", "CNSIM4")
Depending on the nature of the resource, it may be possible to coerce it to a data.frame in the client side:
-library(resourcer)
-as.data.frame(opal.resource_get(o, "RSRC", "CNSIM4"))library(resourcer)
+as.data.frame(opal.resource_get(o, "RSRC", "CNSIM4"))
The same operation can be done on the R server side:
-# assign the resource object
-opal.assign.resource(o, "rsrc", "RSRC.CNSIM4")
-# coerce it to a data.frame
-opal.assign.script(o, "D", quote(as.data.frame(rsrc)))
-# get some summary statistics
-opal.execute(o, "summary(as.factor(D$GENDER))")# assign the resource object
+opal.assign.resource(o, "rsrc", "RSRC.CNSIM4")
+# coerce it to a data.frame
+opal.assign.script(o, "D", quote(as.data.frame(rsrc)))
+# get some summary statistics
+opal.execute(o, "summary(as.factor(D$GENDER))")
Permissions
@@ -337,7 +337,7 @@ TeardownGood practice is to free server resources by sending a logout
request:
-opal.logout(o)
+opal.logout(o)
-opal.logout(o)opal.logout(o)Teardown
-Site built with pkgdown 2.0.6.
+Site built with pkgdown 2.0.7.
diff --git a/docs/articles/opal-rsession.html b/docs/articles/opal-rsession.html
index 7a892618..17bece90 100644
--- a/docs/articles/opal-rsession.html
+++ b/docs/articles/opal-rsession.html
@@ -88,7 +88,7 @@ Opal R Session
Yannick
Marcon
- 2023-02-03
+ 2023-12-20
Source: vignettes/opal-rsession.Rmd
opal-rsession.Rmd
@@ -118,8 +118,8 @@ Setup
must be created with the “default” profile, i.e. in the “default” R
servers cluster (note that the profile parameter is optional):
-library(opalr)
-o <- opal.login("administrator", "password", "https://opal-demo.obiba.org", profile = "default")
+library(opalr)
+o <- opal.login("administrator", "password", "https://opal-demo.obiba.org", profile = "default")
Assign
@@ -127,42 +127,42 @@ Assign
Assign a Opal table to a data.frame (if user has permission
to see values of the Opal table):
-opal.assign.table(o, symbol = "df", value = "CNSIM.CNSIM1")
+opal.assign.table(o, symbol = "df", value = "CNSIM.CNSIM1")
In place of a standard data.frame, Opal can assign data into
a tibble:
-opal.assign.table.tibble(o, symbol = "tbl", value = "CNSIM.CNSIM1")
+opal.assign.table.tibble(o, symbol = "tbl", value = "CNSIM.CNSIM1")
Resource objects can be assigned to the R server session:
-opal.assign.resource(o, symbol = "rsrc", value = "RSRC.CNSIM3")
+opal.assign.resource(o, symbol = "rsrc", value = "RSRC.CNSIM3")
An R expression can also be assigned to a symbol (use
quote() to not interpret the expression in the client side
R session). As an example assign a function body:
-opal.assign.script(o, symbol = "hello", value = quote(function(x) { paste0("Hello ", x, "!") }))
+opal.assign.script(o, symbol = "hello", value = quote(function(x) { paste0("Hello ", x, "!") }))
List the R symbols that lives in the remote R session:
-opal.symbols(o)
+opal.symbols(o)
Execute
R expressions can be executed on the server side:
-# column names
-opal.execute(o, script = "names(tbl)")
-# get variable description from column attributes
-opal.execute(o, script = "attributes(tbl$GENDER)")
-# coerce resource to a data.frame and plot histogram of one column
-plot(opal.execute(o, script = "hist(as.data.frame(rsrc)$LAB_HDL)"))
-# execute the custom function
-opal.execute(o, script = "hello('friends')")
+# column names
+opal.execute(o, script = "names(tbl)")
+# get variable description from column attributes
+opal.execute(o, script = "attributes(tbl$GENDER)")
+# coerce resource to a data.frame and plot histogram of one column
+plot(opal.execute(o, script = "hist(as.data.frame(rsrc)$LAB_HDL)"))
+# execute the custom function
+opal.execute(o, script = "hello('friends')")
The remote data can be downloaded into the client side R session:
-GENDER <- opal.execute(o, script = "tbl$GENDER")
+GENDER <- opal.execute(o, script = "tbl$GENDER")
To execute more complex R code, use a local source file:
-opal.execute.source(o, path = "/path/to/some_code.R")
+opal.execute.source(o, path = "/path/to/some_code.R")
Files
@@ -170,11 +170,11 @@ Files
Files can be written from the Opal file system to the R server
session folder:
-opal.file_write(o, source = "/projects/CNSIM/CNSIM3.zip", "test.zip")
+opal.file_write(o, source = "/projects/CNSIM/CNSIM3.zip", "test.zip")
Similarly, files can be read from the R server session folder into
the Opal file system:
-opal.file_read(o, source = "test.zip", destination = "/tmp")
+opal.file_read(o, source = "test.zip", destination = "/tmp")
+opal.workspace_save(o, save="demo")
+opal.workspaces(o)
Teardown
@@ -191,7 +191,7 @@ TeardownGood practice is to free server resources by sending a logout
request:
-opal.logout(o)
+opal.logout(o)
@@ -212,7 +212,7 @@ Teardown
-Site built with pkgdown 2.0.6.
+Site built with pkgdown 2.0.7.
diff --git a/docs/authors.html b/docs/authors.html
index e777bdac..a50c4cbc 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -117,7 +117,7 @@ Citation
diff --git a/docs/index.html b/docs/index.html
index c90832dc..05f8608f 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -95,27 +95,27 @@
-
+
Opal R Client for the Opal data warehouse. Most of the web services of Opal can be reached by an opalr function: import/export, data dictionaries, projects, tables, resources, permissions, users, DataSHIELD profiles etc.
See opalr documentation.
Installation:
-# install from CRAN
-install.packages("opalr")
-
-# or install latest development version
-remotes::install_github("obiba/opalr")
+# install from CRAN
+install.packages("opalr")
+
+# or install latest development version
+remotes::install_github("obiba/opalr")
Basic usage:
-library(opalr)
-o <- opal.login('administrator', 'password', url = 'https://opal-demo.obiba.org')
-
-# assign a table (as a data.frame) to a R symbol
-opal.assign(o, 'D', 'CNSIM.CNSIM1')
-
-# perform R operations on the server side
-opal.execute(o, 'summary(D$GENDER)')
-opal.execute(o, 'summary(D$LAB_GLUC)')
-
-opal.logout(o)
+library(opalr)
+o <- opal.login('administrator', 'password', url = 'https://opal-demo.obiba.org')
+
+# assign a table (as a data.frame) to a R symbol
+opal.assign(o, 'D', 'CNSIM.CNSIM1')
+
+# perform R operations on the server side
+opal.execute(o, 'summary(D$GENDER)')
+opal.execute(o, 'summary(D$LAB_GLUC)')
+
+opal.logout(o)
-
-Dev status
-
-
-
+
@@ -190,7 +184,7 @@ Dev status
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 384d3091..5adc2f4d 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,10 +1,10 @@
-pandoc: 2.19.2
-pkgdown: 2.0.6
+pandoc: 3.1.1
+pkgdown: 2.0.7
pkgdown_sha: ~
articles:
datashield-admin: datashield-admin.html
opal-files: opal-files.html
opal-projects: opal-projects.html
opal-rsession: opal-rsession.html
-last_built: 2023-02-03T12:50Z
+last_built: 2023-12-20T07:25Z
diff --git a/docs/reference/dictionary.annotate.harmo_status.html b/docs/reference/dictionary.annotate.harmo_status.html
index ff50a785..90a2c2bd 100644
--- a/docs/reference/dictionary.annotate.harmo_status.html
+++ b/docs/reference/dictionary.annotate.harmo_status.html
@@ -71,7 +71,7 @@ Set variable annotation with Harmonization Status term
- dictionary.annotate.harmo_status(tibble, variables = NULL, status)
+ dictionary.annotate.harmo_status(tibble, variables = NULL, status)
@@ -98,14 +98,14 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-cqx <- dictionary.annotate.harmo_status(cqx,
- variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"),
- status = "complete")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+cqx <- dictionary.annotate.harmo_status(cqx,
+ variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"),
+ status = "complete")
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/dictionary.annotate.html b/docs/reference/dictionary.annotate.html
index 08eeae17..fa687aeb 100644
--- a/docs/reference/dictionary.annotate.html
+++ b/docs/reference/dictionary.annotate.html
@@ -69,13 +69,13 @@ Set variable annotation with a taxonomy term
- dictionary.annotate(
- tibble,
- variables = NULL,
- taxonomy = "Mlstr_area",
- vocabulary,
- term
-)
+ dictionary.annotate(
+ tibble,
+ variables = NULL,
+ taxonomy = "Mlstr_area",
+ vocabulary,
+ term
+)
@@ -111,16 +111,16 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-cqx <- dictionary.annotate(cqx,
- variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"),
- taxonomy = "Mlstr_area",
- vocabulary = "Sociodemographic_economic_characteristics",
- term = "Education")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+cqx <- dictionary.annotate(cqx,
+ variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"),
+ taxonomy = "Mlstr_area",
+ vocabulary = "Sociodemographic_economic_characteristics",
+ term = "Education")
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dictionary.annotations.html b/docs/reference/dictionary.annotations.html
index 122843f1..5f5227da 100644
--- a/docs/reference/dictionary.annotations.html
+++ b/docs/reference/dictionary.annotations.html
@@ -69,12 +69,12 @@ List the annotations
- dictionary.annotations(
- tibble,
- variables = NULL,
- taxonomy = NULL,
- vocabulary = NULL
-)
+ dictionary.annotations(
+ tibble,
+ variables = NULL,
+ taxonomy = NULL,
+ vocabulary = NULL
+)
@@ -105,12 +105,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-annot <- dictionary.annotations(cqx, taxonomy = "Mlstr_harmo", vocabulary = "status")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+annot <- dictionary.annotations(cqx, taxonomy = "Mlstr_harmo", vocabulary = "status")
+opal.logout(o)
+}
@@ -125,7 +125,7 @@ Examples
diff --git a/docs/reference/dictionary.apply.html b/docs/reference/dictionary.apply.html
index 51b924fc..6440dfee 100644
--- a/docs/reference/dictionary.apply.html
+++ b/docs/reference/dictionary.apply.html
@@ -69,7 +69,7 @@ Apply the dictionary to a tibble
- dictionary.apply(tibble, variables, categories = NULL)
+ dictionary.apply(tibble, variables, categories = NULL, merge = FALSE)
@@ -85,26 +85,30 @@ Arguments
categories
A data frame with one row per category (columns variable and name) and then column per property/attribute.
merge
+Either append attributes to existing ones or replace them. Default is FALSE, for dictionary consistency.
Examples
- if (FALSE) {
-data <- tibble::as_tibble(mtcars)
-variables <- tibble::tribble(
- ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
- "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
- "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
- "disp", "decimal", "Disp label", NA, NA, 1, 3
-)
-categories <- tibble::tribble(
- ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
- "cyl", "4", 0, "Four", "Quatre",
- "cyl", "6", 0, "Six", "Six",
- "cyl", "8", 1, "Height", "Huit"
-)
-data <- dictionary.apply(data, variables, categories)
-}
+ if (FALSE) {
+data <- tibble::as_tibble(mtcars)
+variables <- tibble::tribble(
+ ~name, ~valueType, ~`label:en`, ~`label:fr`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
+ "mpg", "decimal", "Mpg label", "Mpg libellé", "Value1", "years", 0, 1,
+ "cyl", "decimal", "Cyl label", "Cyl libellé", "Value2", "kg/m2", 0, 2,
+ "disp", "decimal", "Disp label", "Disp libellé", NA, NA, 1, 3
+)
+categories <- tibble::tribble(
+ ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
+ "cyl", "4", 0, "Four", "Quatre",
+ "cyl", "6", 0, "Six", "Six",
+ "cyl", "8", 1, "Height", "Huit"
+)
+data <- dictionary.apply(data, variables, categories)
+}
@@ -119,7 +123,7 @@ Examples
diff --git a/docs/reference/dictionary.inspect.html b/docs/reference/dictionary.inspect.html
index d0b9459d..7849106e 100644
--- a/docs/reference/dictionary.inspect.html
+++ b/docs/reference/dictionary.inspect.html
@@ -71,7 +71,7 @@ Inspect the dictionary of a tibble
- dictionary.inspect(tibble, id.name = "id", warn = TRUE)
+ dictionary.inspect(tibble, id.name = "id", warn = TRUE)
@@ -97,34 +97,34 @@ Value
Examples
- if (FALSE) {
-# prepare datasets of visits, several visits for one patient
-visits <- tibble::tribble(
-~id, ~patient_id, ~sex, ~visit_date,
-1, 1, "M", as.Date("2020-01-01"),
-2, 2, "F", as.Date("2020-01-02"),
-3, 3, "M", as.Date("2020-01-03"),
-4, 3, "M", as.Date("2020-01-04"))
-
-o <- opal.login("administrator", "password", url = "https://opal-demo.obiba.org")
-
-# save visits dataset
-opal.table_save(o, visits, "RSRC", "visits", type = "Visit", force = TRUE)
-
-# get visit and make it a dataset of patients
-patients <- opal.table_get(o, "RSRC", "visits", id.name = "id")
-# set dataset IDs
-patients$visit_id <- patients$id
-patients$id <- patients$patient_id
-patients$patient_id <- NULL
-patients
-
-# save patients dataset, there should be a warning that some variables are not repeatable
-# while there are patients with multiple data lines
-opal.table_save(o, patients, "RSRC", "patients", type = "Participant", force = TRUE)
-
-opal.logout(o)
-}
+ if (FALSE) {
+# prepare datasets of visits, several visits for one patient
+visits <- tibble::tribble(
+~id, ~patient_id, ~sex, ~visit_date,
+1, 1, "M", as.Date("2020-01-01"),
+2, 2, "F", as.Date("2020-01-02"),
+3, 3, "M", as.Date("2020-01-03"),
+4, 3, "M", as.Date("2020-01-04"))
+
+o <- opal.login("administrator", "password", url = "https://opal-demo.obiba.org")
+
+# save visits dataset
+opal.table_save(o, visits, "RSRC", "visits", type = "Visit", force = TRUE)
+
+# get visit and make it a dataset of patients
+patients <- opal.table_get(o, "RSRC", "visits", id.name = "id")
+# set dataset IDs
+patients$visit_id <- patients$id
+patients$id <- patients$patient_id
+patients$patient_id <- NULL
+patients
+
+# save patients dataset, there should be a warning that some variables are not repeatable
+# while there are patients with multiple data lines
+opal.table_save(o, patients, "RSRC", "patients", type = "Participant", force = TRUE)
+
+opal.logout(o)
+}
@@ -139,7 +139,7 @@ Examples
diff --git a/docs/reference/dot-aclsToDataFrame.html b/docs/reference/dot-aclsToDataFrame.html
index 0381ab4d..2ae1faef 100644
--- a/docs/reference/dot-aclsToDataFrame.html
+++ b/docs/reference/dot-aclsToDataFrame.html
@@ -69,7 +69,7 @@ Permsissions (ACLs) into a data frame.
- .aclsToDataFrame(perms, acls)
+ .aclsToDataFrame(perms, acls)
@@ -85,7 +85,7 @@ Permsissions (ACLs) into a data frame.
diff --git a/docs/reference/dot-as.zeroOne.html b/docs/reference/dot-as.zeroOne.html
index 9f8f9a3c..dabc54ad 100644
--- a/docs/reference/dot-as.zeroOne.html
+++ b/docs/reference/dot-as.zeroOne.html
@@ -69,7 +69,7 @@ Turns a value into 0/1 numeric.
- .as.zeroOne(value)
+ .as.zeroOne(value)
@@ -85,7 +85,7 @@ Turns a value into 0/1 numeric.
diff --git a/docs/reference/dot-authorizationHeader.html b/docs/reference/dot-authorizationHeader.html
index ede36fdb..e03112ce 100644
--- a/docs/reference/dot-authorizationHeader.html
+++ b/docs/reference/dot-authorizationHeader.html
@@ -69,7 +69,7 @@ Constructs the value for the Authorization header
- .authorizationHeader(username, password)
+ .authorizationHeader(username, password)
@@ -85,7 +85,7 @@ Constructs the value for the Authorization header
diff --git a/docs/reference/dot-deparse.html b/docs/reference/dot-deparse.html
index 55783b2a..e8d706e8 100644
--- a/docs/reference/dot-deparse.html
+++ b/docs/reference/dot-deparse.html
@@ -69,7 +69,7 @@ Turn expression into character strings.
- .deparse(expr)
+ .deparse(expr)
@@ -85,7 +85,7 @@ Turn expression into character strings.
diff --git a/docs/reference/dot-extractJsonField.html b/docs/reference/dot-extractJsonField.html
index d9a02ee7..413cef7a 100644
--- a/docs/reference/dot-extractJsonField.html
+++ b/docs/reference/dot-extractJsonField.html
@@ -69,7 +69,7 @@ Extract JSON
- .extractJsonField(json, fields = NULL, isArray = TRUE)
+ .extractJsonField(json, fields = NULL, isArray = TRUE)
@@ -85,7 +85,7 @@ Extract JSON
diff --git a/docs/reference/dot-extractLabel.html b/docs/reference/dot-extractLabel.html
index ccc51648..d43d866a 100644
--- a/docs/reference/dot-extractLabel.html
+++ b/docs/reference/dot-extractLabel.html
@@ -69,12 +69,12 @@ Extract label for locale. If not found, fallback to undefined language label
- .extractLabel(
- locale = "en",
- labels = list(),
- localeKey = "locale",
- valueKey = "value"
-)
+ .extractLabel(
+ locale = "en",
+ labels = list(),
+ localeKey = "locale",
+ valueKey = "value"
+)
@@ -90,7 +90,7 @@ Extract label for locale. If not found, fallback to undefined language label
diff --git a/docs/reference/dot-extractOpalSessionId.html b/docs/reference/dot-extractOpalSessionId.html
index be99f00f..65cacd0d 100644
--- a/docs/reference/dot-extractOpalSessionId.html
+++ b/docs/reference/dot-extractOpalSessionId.html
@@ -69,7 +69,7 @@ Extract opalsid from cookie data frame.
- .extractOpalSessionId(cookies)
+ .extractOpalSessionId(cookies)
@@ -85,7 +85,7 @@ Extract opalsid from cookie data frame.
diff --git a/docs/reference/dot-getContent.html b/docs/reference/dot-getContent.html
index 26d95ecf..d81a8ab3 100644
--- a/docs/reference/dot-getContent.html
+++ b/docs/reference/dot-getContent.html
@@ -69,7 +69,7 @@ Wrapper of httr::content()
- .getContent(opal, response)
+ .getContent(opal, response)
@@ -85,7 +85,7 @@ Wrapper of httr::content()
diff --git a/docs/reference/dot-getPEMFilePath.html b/docs/reference/dot-getPEMFilePath.html
index 0601b98d..bac96b2d 100644
--- a/docs/reference/dot-getPEMFilePath.html
+++ b/docs/reference/dot-getPEMFilePath.html
@@ -69,7 +69,7 @@ Extract absolute path to the pem file
- .getPEMFilePath(pem, directory = "~/.ssh")
+ .getPEMFilePath(pem, directory = "~/.ssh")
@@ -85,7 +85,7 @@ Extract absolute path to the pem file
diff --git a/docs/reference/dot-getRSessionId.html b/docs/reference/dot-getRSessionId.html
index 2c8ffd1f..10b997f2 100644
--- a/docs/reference/dot-getRSessionId.html
+++ b/docs/reference/dot-getRSessionId.html
@@ -69,7 +69,7 @@ Extract R session Id from opal object, create a new R session if not found.<
- .getRSessionId(opal)
+ .getRSessionId(opal)
@@ -85,7 +85,7 @@ Extract R session Id from opal object, create a new R session if not found.<
diff --git a/docs/reference/dot-getSessions.html b/docs/reference/dot-getSessions.html
index 6a91fb4e..32bbbbbb 100644
--- a/docs/reference/dot-getSessions.html
+++ b/docs/reference/dot-getSessions.html
@@ -69,7 +69,7 @@ Get all R session in Opal.
- .getSessions(opal)
+ .getSessions(opal)
@@ -85,7 +85,7 @@ Get all R session in Opal.
diff --git a/docs/reference/dot-handleError.html b/docs/reference/dot-handleError.html
index 3f25f7b3..10a4a4d6 100644
--- a/docs/reference/dot-handleError.html
+++ b/docs/reference/dot-handleError.html
@@ -69,7 +69,7 @@ Handle error response
- .handleError(opal, response)
+ .handleError(opal, response)
@@ -85,7 +85,7 @@ Handle error response
diff --git a/docs/reference/dot-handleResponse.html b/docs/reference/dot-handleResponse.html
index 135a5f63..812aabe6 100644
--- a/docs/reference/dot-handleResponse.html
+++ b/docs/reference/dot-handleResponse.html
@@ -69,7 +69,7 @@ Default request response handler.
- .handleResponse(opal, response)
+ .handleResponse(opal, response)
@@ -85,7 +85,7 @@ Default request response handler.
diff --git a/docs/reference/dot-handleResponseLocation.html b/docs/reference/dot-handleResponseLocation.html
index 2aa7fa4a..1a9c550a 100644
--- a/docs/reference/dot-handleResponseLocation.html
+++ b/docs/reference/dot-handleResponseLocation.html
@@ -69,7 +69,7 @@ Default request response Location handler.
- .handleResponseLocation(opal, response)
+ .handleResponseLocation(opal, response)
@@ -85,7 +85,7 @@ Default request response Location handler.
diff --git a/docs/reference/dot-handleResponseOrCallback.html b/docs/reference/dot-handleResponseOrCallback.html
index 1c19cded..fd75863d 100644
--- a/docs/reference/dot-handleResponseOrCallback.html
+++ b/docs/reference/dot-handleResponseOrCallback.html
@@ -69,7 +69,7 @@ Process response with default handler or the provided one
- .handleResponseOrCallback(opal, response, callback = NULL)
+ .handleResponseOrCallback(opal, response, callback = NULL)
@@ -85,7 +85,7 @@ Process response with default handler or the provided one
diff --git a/docs/reference/dot-is.verbose.html b/docs/reference/dot-is.verbose.html
index f3462be7..ddaab2ed 100644
--- a/docs/reference/dot-is.verbose.html
+++ b/docs/reference/dot-is.verbose.html
@@ -69,7 +69,7 @@ Verbose option
- .is.verbose()
+ .is.verbose()
@@ -85,7 +85,7 @@ Verbose option
diff --git a/docs/reference/dot-isContentEmpty.html b/docs/reference/dot-isContentEmpty.html
index 2ca189f6..88320efd 100644
--- a/docs/reference/dot-isContentEmpty.html
+++ b/docs/reference/dot-isContentEmpty.html
@@ -69,7 +69,7 @@ Check if response content is empty.
- .isContentEmpty(content)
+ .isContentEmpty(content)
@@ -85,7 +85,7 @@ Check if response content is empty.
diff --git a/docs/reference/dot-listToJson.html b/docs/reference/dot-listToJson.html
index 9c4d2140..c0bd2195 100644
--- a/docs/reference/dot-listToJson.html
+++ b/docs/reference/dot-listToJson.html
@@ -69,7 +69,7 @@ Simple transformation function of a list into a JSON object/array.
- .listToJson(l)
+ .listToJson(l)
@@ -85,7 +85,7 @@ Simple transformation function of a list into a JSON object/array.
diff --git a/docs/reference/dot-newProgress.html b/docs/reference/dot-newProgress.html
index cdfa936f..c801ff16 100644
--- a/docs/reference/dot-newProgress.html
+++ b/docs/reference/dot-newProgress.html
@@ -69,12 +69,12 @@ Create a new progress instance with default settings.
- .newProgress(
- format = " :what [:bar] :percent /:elapsed",
- clear = getOption("opal.progress.clear", FALSE),
- total,
- width = 100
-)
+ .newProgress(
+ format = " :what [:bar] :percent /:elapsed",
+ clear = getOption("opal.progress.clear", FALSE),
+ total,
+ width = 100
+)
@@ -90,7 +90,7 @@ Create a new progress instance with default settings.
diff --git a/docs/reference/dot-newSession.html b/docs/reference/dot-newSession.html
index a3d04f33..b15cdaa4 100644
--- a/docs/reference/dot-newSession.html
+++ b/docs/reference/dot-newSession.html
@@ -69,7 +69,7 @@ Create a new R session in Opal.
- .newSession(opal, restore = NULL, profile = NULL)
+ .newSession(opal, restore = NULL, profile = NULL)
@@ -85,7 +85,7 @@ Create a new R session in Opal.
diff --git a/docs/reference/dot-opal.login.html b/docs/reference/dot-opal.login.html
index cf5be580..a2d29cf6 100644
--- a/docs/reference/dot-opal.login.html
+++ b/docs/reference/dot-opal.login.html
@@ -69,15 +69,15 @@ Create the opal object
- .opal.login(
- username,
- password,
- token,
- url,
- opts = list(),
- profile = profile,
- restore = NULL
-)
+ .opal.login(
+ username,
+ password,
+ token,
+ url,
+ opts = list(),
+ profile = profile,
+ restore = NULL
+)
@@ -93,7 +93,7 @@ Create the opal object
diff --git a/docs/reference/dot-rmOpalSession.html b/docs/reference/dot-rmOpalSession.html
index bfd20a01..a29f9e94 100644
--- a/docs/reference/dot-rmOpalSession.html
+++ b/docs/reference/dot-rmOpalSession.html
@@ -69,7 +69,7 @@ Remove a Opal session (logout)
- .rmOpalSession(opal)
+ .rmOpalSession(opal)
@@ -85,7 +85,7 @@ Remove a Opal session (logout)
diff --git a/docs/reference/dot-rmRSession.html b/docs/reference/dot-rmRSession.html
index b521882a..827d5ccb 100644
--- a/docs/reference/dot-rmRSession.html
+++ b/docs/reference/dot-rmRSession.html
@@ -69,7 +69,7 @@ Remove a R session from Opal.
- .rmRSession(opal, save = FALSE)
+ .rmRSession(opal, save = FALSE)
@@ -85,7 +85,7 @@ Remove a R session from Opal.
diff --git a/docs/reference/dot-select.html b/docs/reference/dot-select.html
index 43f6c002..13df65cb 100644
--- a/docs/reference/dot-select.html
+++ b/docs/reference/dot-select.html
@@ -69,7 +69,7 @@ Returns a list r such that r[[i]] == l[[i]][field] for all i:length(l)
- .select(l, field)
+ .select(l, field)
@@ -85,7 +85,7 @@ Returns a list r such that r[[i]] == l[[i]][field] for all i:length(l)
diff --git a/docs/reference/dot-tickProgress.html b/docs/reference/dot-tickProgress.html
index 46e06caa..0777056f 100644
--- a/docs/reference/dot-tickProgress.html
+++ b/docs/reference/dot-tickProgress.html
@@ -69,7 +69,7 @@ Output the progress status if option "datashield.progress" is allows to.
@@ -85,7 +85,7 @@ Output the progress status if option "datashield.progress" is allows to.
diff --git a/docs/reference/dot-tokenHeader.html b/docs/reference/dot-tokenHeader.html
index e6d91a46..a6265701 100644
--- a/docs/reference/dot-tokenHeader.html
+++ b/docs/reference/dot-tokenHeader.html
@@ -69,7 +69,7 @@ Constructs the value for the X-Opal-Auth header
- .tokenHeader(token)
+ .tokenHeader(token)
@@ -85,7 +85,7 @@ Constructs the value for the X-Opal-Auth header
diff --git a/docs/reference/dot-url.html b/docs/reference/dot-url.html
index 6f7da3b7..41bd1de4 100644
--- a/docs/reference/dot-url.html
+++ b/docs/reference/dot-url.html
@@ -69,7 +69,7 @@ Utility method to build urls. Concatenates all arguments and adds a '/' sepa
- .url(opal, ...)
+ .url(opal, ...)
@@ -85,7 +85,7 @@ Utility method to build urls. Concatenates all arguments and adds a '/' sepa
diff --git a/docs/reference/dot-verbose.html b/docs/reference/dot-verbose.html
index f47a65e5..3cf22c86 100644
--- a/docs/reference/dot-verbose.html
+++ b/docs/reference/dot-verbose.html
@@ -69,7 +69,7 @@ Verbose flag
- .verbose()
+ .verbose()
@@ -85,7 +85,7 @@ Verbose flag
diff --git a/docs/reference/dsadmin.activity.html b/docs/reference/dsadmin.activity.html
new file mode 100644
index 00000000..a0d1cc75
--- /dev/null
+++ b/docs/reference/dsadmin.activity.html
@@ -0,0 +1,146 @@
+
+Get DataSHIELD activity — dsadmin.activity • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded DataSHIELD session metrics.
+
+
+
+ dsadmin.activity(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+dsadmin.activity(o)
+# user and profile specific session metrics
+dsadmin.activity(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+dsadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.activity_summary.html b/docs/reference/dsadmin.activity_summary.html
new file mode 100644
index 00000000..c291b9fe
--- /dev/null
+++ b/docs/reference/dsadmin.activity_summary.html
@@ -0,0 +1,146 @@
+
+Get DataSHIELD activity summary — dsadmin.activity_summary • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded DataSHIELD session metrics, grouped by profile and user.
+
+
+
+ dsadmin.activity_summary(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+dsadmin.activity_summary(o)
+# user and profile specific session metrics
+dsadmin.activity_summary(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+dsadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.get_method.html b/docs/reference/dsadmin.get_method.html
index 35d8bada..7e0286ab 100644
--- a/docs/reference/dsadmin.get_method.html
+++ b/docs/reference/dsadmin.get_method.html
@@ -69,7 +69,7 @@ Get a DataSHIELD method
- dsadmin.get_method(opal, name, type = "aggregate", profile = NULL)
+ dsadmin.get_method(opal, name, type = "aggregate", profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_method(o, 'class')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_method(o, 'class')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.get_methods.html b/docs/reference/dsadmin.get_methods.html
index eb9d116f..332bd2e6 100644
--- a/docs/reference/dsadmin.get_methods.html
+++ b/docs/reference/dsadmin.get_methods.html
@@ -69,7 +69,7 @@ Get DataSHIELD methods
- dsadmin.get_methods(opal, type = "aggregate", profile = NULL)
+ dsadmin.get_methods(opal, type = "aggregate", profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_methods(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_methods(o)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.get_options.html b/docs/reference/dsadmin.get_options.html
index 41b6d38f..936afd9a 100644
--- a/docs/reference/dsadmin.get_options.html
+++ b/docs/reference/dsadmin.get_options.html
@@ -69,7 +69,7 @@ Get the DataSHIELD options
- dsadmin.get_options(opal, profile = NULL)
+ dsadmin.get_options(opal, profile = NULL)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_options(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_options(o)
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_github_package.html b/docs/reference/dsadmin.install_github_package.html
index 3cd61327..9cac06c4 100644
--- a/docs/reference/dsadmin.install_github_package.html
+++ b/docs/reference/dsadmin.install_github_package.html
@@ -69,13 +69,13 @@ Install a DataSHIELD package from GitHub
- dsadmin.install_github_package(
- opal,
- pkg,
- username = "datashield",
- ref = "master",
- profile = NULL
-)
+ dsadmin.install_github_package(
+ opal,
+ pkg,
+ username = "datashield",
+ ref = "master",
+ profile = NULL
+)
@@ -132,11 +132,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge')
+opal.logout(o)
+}
@@ -151,7 +151,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_local_package.html b/docs/reference/dsadmin.install_local_package.html
index a1a1c76d..d1a6d9a2 100644
--- a/docs/reference/dsadmin.install_local_package.html
+++ b/docs/reference/dsadmin.install_local_package.html
@@ -71,7 +71,7 @@ Install a DataSHIELD package from a local archive file
- dsadmin.install_local_package(opal, path, profile = NULL)
+ dsadmin.install_local_package(opal, path, profile = NULL)
@@ -114,14 +114,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# install a pre-built local archive file
-dsadmin.install_local_package(o, '~/dsExposome_1.0.0.tar.gz')
-# or build archive file from local package source (in current working folder)
-dsadmin.install_local_package(o, devtools::build())
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# install a pre-built local archive file
+dsadmin.install_local_package(o, '~/dsExposome_1.0.0.tar.gz')
+# or build archive file from local package source (in current working folder)
+dsadmin.install_local_package(o, devtools::build())
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_package.html b/docs/reference/dsadmin.install_package.html
index 5a0c9ad1..904d1231 100644
--- a/docs/reference/dsadmin.install_package.html
+++ b/docs/reference/dsadmin.install_package.html
@@ -69,13 +69,13 @@ Install a DataSHIELD package
- dsadmin.install_package(
- opal,
- pkg,
- githubusername = NULL,
- ref = NULL,
- profile = NULL
-)
+ dsadmin.install_package(
+ opal,
+ pkg,
+ githubusername = NULL,
+ ref = NULL,
+ profile = NULL
+)
@@ -132,11 +132,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.install_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.install_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -151,7 +151,7 @@ Examples
diff --git a/docs/reference/dsadmin.installed_package.html b/docs/reference/dsadmin.installed_package.html
index 65240b16..d4e1e5f8 100644
--- a/docs/reference/dsadmin.installed_package.html
+++ b/docs/reference/dsadmin.installed_package.html
@@ -69,7 +69,7 @@ Check DataSHIELD package
- dsadmin.installed_package(opal, pkg, profile = NULL)
+ dsadmin.installed_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.installed_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.installed_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/dsadmin.log.html b/docs/reference/dsadmin.log.html
new file mode 100644
index 00000000..76fcc36d
--- /dev/null
+++ b/docs/reference/dsadmin.log.html
@@ -0,0 +1,155 @@
+
+Get DataSHIELD logs — dsadmin.log • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ The DataSHIELD log is structured as follows:
+
+
+
+ dsadmin.log(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+ Details
+ Common fields
timestamp: when action is logged
version: not used
message: human readable message
logger_name: name of the log channel
thread_name: java thread name
level: log level (TRACE, DEBUG, INFO, WARN, ERROR)
level_value: log level numeric value
ip: ip origin of the request, when available
ds_id: unique DS session ID
ds_profile: DS profile name (available after the R server session is created, can be after authentication)
username: DS user name
r_duration: time spent by the remote R server action (all except PARSE)
r_size: R result serialized object size in bytes
ds_action: DS operation (OPEN, CLOSE, PARSE, ASSIGN, AGGREGATE, LS, RM, WS_SAVE, WS_RESTORE)
DS operations fields
OPEN: DS session opened (note: happens after successful authentication as R server session creation is deferred)
CLOSE: DS session closed
PARSE: R expression parsed
ds_map: DS function mappings used in the R parser, separated by semicolons when several functions are called
ds_script_in: R script as sent by DS user
ds_script_out: R script rewritten by opal, to be evaluated
ASSIGN:
ds_symbol: assigned symbol name
ds_table: table name that is assigned
ds_resource: resource name that is assigned
ds_eval: assign R expression that is evaluated
AGGREGATE:
ds_eval: aggregate R expression that is evaluated
LS: R symbols listed
RM: R symbol removed
ds_symbol: symbol name to remove
WS_SAVE:
ds_ws: workspace name
WS_RESTORE:
ds_ws: workspace name
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.log(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.package_description.html b/docs/reference/dsadmin.package_description.html
index 3351e46a..29694b5b 100644
--- a/docs/reference/dsadmin.package_description.html
+++ b/docs/reference/dsadmin.package_description.html
@@ -69,7 +69,7 @@ Get DataSHIELD package description
- dsadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
+ dsadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
@@ -117,11 +117,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_description(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_description(o, 'dsBase')
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/dsadmin.package_descriptions.html b/docs/reference/dsadmin.package_descriptions.html
index 5fb8ebc9..7707a023 100644
--- a/docs/reference/dsadmin.package_descriptions.html
+++ b/docs/reference/dsadmin.package_descriptions.html
@@ -69,7 +69,7 @@ Get DataSHIELD package descriptions
- dsadmin.package_descriptions(opal, fields = NULL, df = TRUE, profile = NULL)
+ dsadmin.package_descriptions(opal, fields = NULL, df = TRUE, profile = NULL)
@@ -123,11 +123,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_descriptions(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_descriptions(o)
+opal.logout(o)
+}
@@ -142,7 +142,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm.html b/docs/reference/dsadmin.perm.html
index c397d495..50f5957c 100644
--- a/docs/reference/dsadmin.perm.html
+++ b/docs/reference/dsadmin.perm.html
@@ -69,7 +69,7 @@ Get the DataSHIELD permissions
- dsadmin.perm(opal)
+ dsadmin.perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm_add.html b/docs/reference/dsadmin.perm_add.html
index 832ce0ce..e17b5796 100644
--- a/docs/reference/dsadmin.perm_add.html
+++ b/docs/reference/dsadmin.perm_add.html
@@ -69,7 +69,7 @@ Add or update a DataSHIELD permission
- dsadmin.perm_add(opal, subject, type = "user", permission)
+ dsadmin.perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm_delete.html b/docs/reference/dsadmin.perm_delete.html
index 91a12ac8..a5ce771c 100644
--- a/docs/reference/dsadmin.perm_delete.html
+++ b/docs/reference/dsadmin.perm_delete.html
@@ -69,7 +69,7 @@ Delete a DataSHIELD permission
- dsadmin.perm_delete(opal, subject, type = "user")
+ dsadmin.perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile.html b/docs/reference/dsadmin.profile.html
index d16b82ac..d8859752 100644
--- a/docs/reference/dsadmin.profile.html
+++ b/docs/reference/dsadmin.profile.html
@@ -73,7 +73,7 @@ Get a DataSHIELD profile
- dsadmin.profile(opal, name)
+ dsadmin.profile(opal, name)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile(o, name = 'default')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile(o, name = 'default')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_access.html b/docs/reference/dsadmin.profile_access.html
index b23f41c7..64ad8674 100644
--- a/docs/reference/dsadmin.profile_access.html
+++ b/docs/reference/dsadmin.profile_access.html
@@ -73,7 +73,7 @@ Restrict or open access to a DataSHIELD profile
- dsadmin.profile_access(opal, name, restricted = TRUE)
+ dsadmin.profile_access(opal, name, restricted = TRUE)
@@ -108,12 +108,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_access(o, name = 'survival', restricted = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_access(o, name = 'survival', restricted = TRUE)
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_create.html b/docs/reference/dsadmin.profile_create.html
index 5f5fb762..e377a2b7 100644
--- a/docs/reference/dsadmin.profile_create.html
+++ b/docs/reference/dsadmin.profile_create.html
@@ -69,7 +69,7 @@ Create a DataSHIELD profile
- dsadmin.profile_create(opal, name, cluster = "default", rParser = NULL)
+ dsadmin.profile_create(opal, name, cluster = "default", rParser = NULL)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_delete.html b/docs/reference/dsadmin.profile_delete.html
index 8bb60e74..de86336c 100644
--- a/docs/reference/dsadmin.profile_delete.html
+++ b/docs/reference/dsadmin.profile_delete.html
@@ -69,7 +69,7 @@ Delete a DataSHIELD profile
- dsadmin.profile_delete(opal, name)
+ dsadmin.profile_delete(opal, name)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_delete(o, name = 'survival')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_delete(o, name = 'survival')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_enable.html b/docs/reference/dsadmin.profile_enable.html
index 8901ed93..36ba9503 100644
--- a/docs/reference/dsadmin.profile_enable.html
+++ b/docs/reference/dsadmin.profile_enable.html
@@ -69,7 +69,7 @@ Enable or disable a DataSHIELD profile
- dsadmin.profile_enable(opal, name, enabled = TRUE)
+ dsadmin.profile_enable(opal, name, enabled = TRUE)
@@ -104,12 +104,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_enable(o, name = 'survival', enabled = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_enable(o, name = 'survival', enabled = TRUE)
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_exists.html b/docs/reference/dsadmin.profile_exists.html
index e5c19c97..5ea51e86 100644
--- a/docs/reference/dsadmin.profile_exists.html
+++ b/docs/reference/dsadmin.profile_exists.html
@@ -69,7 +69,7 @@ Check a DataSHIELD profile exists
- dsadmin.profile_exists(opal, name)
+ dsadmin.profile_exists(opal, name)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-if (!dsadmin.profile_exists(o, name = 'survival'))
- dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+if (!dsadmin.profile_exists(o, name = 'survival'))
+ dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_init.html b/docs/reference/dsadmin.profile_init.html
index 1d117fad..ad4fc311 100644
--- a/docs/reference/dsadmin.profile_init.html
+++ b/docs/reference/dsadmin.profile_init.html
@@ -73,7 +73,7 @@ Initialize a DataSHIELD profile
- dsadmin.profile_init(opal, name, packages = NULL)
+ dsadmin.profile_init(opal, name, packages = NULL)
@@ -108,12 +108,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_init(o, name = 'survival', packages = c('dsSurvival'))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_init(o, name = 'survival', packages = c('dsSurvival'))
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm.html b/docs/reference/dsadmin.profile_perm.html
index ea1913ac..3f90f5de 100644
--- a/docs/reference/dsadmin.profile_perm.html
+++ b/docs/reference/dsadmin.profile_perm.html
@@ -69,7 +69,7 @@ Get the permissions of a DataSHIELD profile
- dsadmin.profile_perm(opal, name)
+ dsadmin.profile_perm(opal, name)
@@ -106,13 +106,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm_add.html b/docs/reference/dsadmin.profile_perm_add.html
index 5aa4f324..e9b60807 100644
--- a/docs/reference/dsadmin.profile_perm_add.html
+++ b/docs/reference/dsadmin.profile_perm_add.html
@@ -71,13 +71,13 @@ Add or update a permission on a DataSHIELD profile
- dsadmin.profile_perm_add(
- opal,
- name,
- subject,
- type = "user",
- permission = "use"
-)
+ dsadmin.profile_perm_add(
+ opal,
+ name,
+ subject,
+ type = "user",
+ permission = "use"
+)
@@ -120,13 +120,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -141,7 +141,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm_delete.html b/docs/reference/dsadmin.profile_perm_delete.html
index 5b218b2b..8d2fa69a 100644
--- a/docs/reference/dsadmin.profile_perm_delete.html
+++ b/docs/reference/dsadmin.profile_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a DataSHIELD profile
- dsadmin.profile_perm_delete(opal, name, subject, type = "user")
+ dsadmin.profile_perm_delete(opal, name, subject, type = "user")
@@ -108,13 +108,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_rparser.html b/docs/reference/dsadmin.profile_rparser.html
index f24c5242..bf9617df 100644
--- a/docs/reference/dsadmin.profile_rparser.html
+++ b/docs/reference/dsadmin.profile_rparser.html
@@ -69,7 +69,7 @@ Set or remove the R parser version of a DataSHIELD profile
- dsadmin.profile_rparser(opal, name, rParser = NULL)
+ dsadmin.profile_rparser(opal, name, rParser = NULL)
@@ -105,15 +105,15 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-# apply R parser version v2
-dsadmin.profile_rparser(o, name = 'survival', rParser = 'v2')
-# apply system's default R parser version
-dsadmin.profile_rparser(o, name = 'survival')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+# apply R parser version v2
+dsadmin.profile_rparser(o, name = 'survival', rParser = 'v2')
+# apply system's default R parser version
+dsadmin.profile_rparser(o, name = 'survival')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profiles.html b/docs/reference/dsadmin.profiles.html
index 7f97e3ad..2ab7201f 100644
--- a/docs/reference/dsadmin.profiles.html
+++ b/docs/reference/dsadmin.profiles.html
@@ -69,7 +69,7 @@ Get DataSHIELD profiles
- dsadmin.profiles(opal, df = TRUE)
+ dsadmin.profiles(opal, df = TRUE)
@@ -106,11 +106,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_descriptions(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_descriptions(o)
+opal.logout(o)
+}
@@ -125,7 +125,7 @@ Examples
diff --git a/docs/reference/dsadmin.publish_package.html b/docs/reference/dsadmin.publish_package.html
index 1aed7d0b..db0a16e3 100644
--- a/docs/reference/dsadmin.publish_package.html
+++ b/docs/reference/dsadmin.publish_package.html
@@ -69,7 +69,7 @@ Publish DataSHIELD package settings
- dsadmin.publish_package(opal, pkg, profile = NULL)
+ dsadmin.publish_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.publish_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.publish_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/dsadmin.remove_package.html b/docs/reference/dsadmin.remove_package.html
index a696d968..11d7e1d3 100644
--- a/docs/reference/dsadmin.remove_package.html
+++ b/docs/reference/dsadmin.remove_package.html
@@ -69,7 +69,7 @@ Remove DataSHIELD package
- dsadmin.remove_package(opal, pkg, profile = NULL)
+ dsadmin.remove_package(opal, pkg, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.remove_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.remove_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_method.html b/docs/reference/dsadmin.rm_method.html
index cca7bb9e..b2d596b8 100644
--- a/docs/reference/dsadmin.rm_method.html
+++ b/docs/reference/dsadmin.rm_method.html
@@ -69,7 +69,7 @@ Remove DataSHIELD method
- dsadmin.rm_method(opal, name, type = "aggregate", profile = NULL)
+ dsadmin.rm_method(opal, name, type = "aggregate", profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_method(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_method(o, 'foo')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_methods.html b/docs/reference/dsadmin.rm_methods.html
index 2532751f..470d8498 100644
--- a/docs/reference/dsadmin.rm_methods.html
+++ b/docs/reference/dsadmin.rm_methods.html
@@ -69,7 +69,7 @@ Remove DataSHIELD methods.
- dsadmin.rm_methods(opal, type = NULL, profile = NULL)
+ dsadmin.rm_methods(opal, type = NULL, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_methods(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_methods(o)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_option.html b/docs/reference/dsadmin.rm_option.html
index 64995c5f..1b4ed85b 100644
--- a/docs/reference/dsadmin.rm_option.html
+++ b/docs/reference/dsadmin.rm_option.html
@@ -69,7 +69,7 @@ Remove a DataSHIELD option
- dsadmin.rm_option(opal, name, profile = NULL)
+ dsadmin.rm_option(opal, name, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_option(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_option(o, 'foo')
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_options.html b/docs/reference/dsadmin.rm_options.html
index 80414f34..2e4e1b38 100644
--- a/docs/reference/dsadmin.rm_options.html
+++ b/docs/reference/dsadmin.rm_options.html
@@ -69,7 +69,7 @@ Remove all DataSHIELD options
- dsadmin.rm_options(opal, profile = NULL)
+ dsadmin.rm_options(opal, profile = NULL)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_options(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_options(o, 'foo')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_package_methods.html b/docs/reference/dsadmin.rm_package_methods.html
index 26a699ef..f86188d4 100644
--- a/docs/reference/dsadmin.rm_package_methods.html
+++ b/docs/reference/dsadmin.rm_package_methods.html
@@ -69,7 +69,7 @@ Remove DataSHIELD package methods
- dsadmin.rm_package_methods(opal, pkg, type = NULL, profile = NULL)
+ dsadmin.rm_package_methods(opal, pkg, type = NULL, profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_package_methods(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_package_methods(o, 'dsBase')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_method.html b/docs/reference/dsadmin.set_method.html
index ab7bc9ff..a1287cc2 100644
--- a/docs/reference/dsadmin.set_method.html
+++ b/docs/reference/dsadmin.set_method.html
@@ -69,14 +69,14 @@ Set DataSHIELD method
- dsadmin.set_method(
- opal,
- name,
- func = NULL,
- path = NULL,
- type = "aggregate",
- profile = NULL
-)
+ dsadmin.set_method(
+ opal,
+ name,
+ func = NULL,
+ path = NULL,
+ type = "aggregate",
+ profile = NULL
+)
@@ -131,14 +131,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# as a package's function
-dsadmin.set_method(o, 'foo', func = 'base::mean')
-# as a custom function
-dsadmin.set_method(o, 'foo', func = function(x) { base::mean(x) })
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# as a package's function
+dsadmin.set_method(o, 'foo', func = 'base::mean')
+# as a custom function
+dsadmin.set_method(o, 'foo', func = function(x) { base::mean(x) })
+opal.logout(o)
+}
@@ -153,7 +153,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_option.html b/docs/reference/dsadmin.set_option.html
index fa661b5b..af2b415b 100644
--- a/docs/reference/dsadmin.set_option.html
+++ b/docs/reference/dsadmin.set_option.html
@@ -69,7 +69,7 @@ Set DataSHIELD option
- dsadmin.set_option(opal, name, value, profile = NULL)
+ dsadmin.set_option(opal, name, value, profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.set_option(o, 'foo', 'bar')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.set_option(o, 'foo', 'bar')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_package_methods.html b/docs/reference/dsadmin.set_package_methods.html
index 663ff9fd..91a0f0e5 100644
--- a/docs/reference/dsadmin.set_package_methods.html
+++ b/docs/reference/dsadmin.set_package_methods.html
@@ -69,7 +69,7 @@ Set DataSHIELD package methods
- dsadmin.set_package_methods(opal, pkg, type = NULL, profile = NULL)
+ dsadmin.set_package_methods(opal, pkg, type = NULL, profile = NULL)
@@ -122,11 +122,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.set_package_methods(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.set_package_methods(o, 'dsBase')
+opal.logout(o)
+}
@@ -141,7 +141,7 @@ Examples
diff --git a/docs/reference/dsadmin.unpublish_package.html b/docs/reference/dsadmin.unpublish_package.html
index 59177cb6..2f4cb561 100644
--- a/docs/reference/dsadmin.unpublish_package.html
+++ b/docs/reference/dsadmin.unpublish_package.html
@@ -69,7 +69,7 @@ Unpublish DataSHIELD package settings
- dsadmin.unpublish_package(opal, pkg, profile = NULL)
+ dsadmin.unpublish_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.unpublish_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.unpublish_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 7b8fa952..1410bfd7 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -86,6 +86,14 @@ All functions dictionary.inspect()
Inspect the dictionary of a tibble
+
+
+ Get DataSHIELD activity
+
+
+ Get DataSHIELD activity summary
@@ -114,6 +122,10 @@ All functions dsadmin.installed_package()
Check DataSHIELD package
+
+
+ Get DataSHIELD logs
@@ -226,6 +238,14 @@ All functions dsadmin.unpublish_package()
Unpublish DataSHIELD package settings
+
+
+ Get R activity
+
+
+ Get R activity summary
@@ -262,6 +282,18 @@ All functions oadmin.installed_packages()
List installed packages
+
+
+ Get Opal main logs
+
+
+ Get Opal REST API logs
+
+
+ Get Opal SQL API logs
@@ -486,6 +518,10 @@ All functions opal.logout()
Logout from Opal(s)
+
+
+ Get the permissions of a subject
@@ -847,7 +883,7 @@ All functions
diff --git a/docs/reference/oadmin.activity.html b/docs/reference/oadmin.activity.html
new file mode 100644
index 00000000..a11491b6
--- /dev/null
+++ b/docs/reference/oadmin.activity.html
@@ -0,0 +1,146 @@
+
+Get R activity — oadmin.activity • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics.
+
+
+
+ oadmin.activity(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity(o)
+# user and profile specific session metrics
+oadmin.activity(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.activity_summary.html b/docs/reference/oadmin.activity_summary.html
new file mode 100644
index 00000000..a8159421
--- /dev/null
+++ b/docs/reference/oadmin.activity_summary.html
@@ -0,0 +1,146 @@
+
+Get R activity summary — oadmin.activity_summary • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics, grouped by profile and user.
+
+
+
+ oadmin.activity_summary(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity_summary(o)
+# user and profile specific session metrics
+oadmin.activity_summary(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.install_bioconductor_package.html b/docs/reference/oadmin.install_bioconductor_package.html
index adde90ec..2c0551ed 100644
--- a/docs/reference/oadmin.install_bioconductor_package.html
+++ b/docs/reference/oadmin.install_bioconductor_package.html
@@ -69,7 +69,7 @@ Install a package from Bioconductor
- oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
+ oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_bioconductor_package(o, 'GWASTools')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_bioconductor_package(o, 'GWASTools')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.install_cran_package.html b/docs/reference/oadmin.install_cran_package.html
index 3e7e3a18..d229933e 100644
--- a/docs/reference/oadmin.install_cran_package.html
+++ b/docs/reference/oadmin.install_cran_package.html
@@ -69,7 +69,7 @@ Install a package from CRAN
- oadmin.install_cran_package(opal, pkg, profile = NULL)
+ oadmin.install_cran_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_cran_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_cran_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.install_devtools.html b/docs/reference/oadmin.install_devtools.html
index 3f2bc53c..79b175d3 100644
--- a/docs/reference/oadmin.install_devtools.html
+++ b/docs/reference/oadmin.install_devtools.html
@@ -69,7 +69,7 @@ Install devtools package
- oadmin.install_devtools(opal, profile = NULL)
+ oadmin.install_devtools(opal, profile = NULL)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_devtools(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.install_github_package.html b/docs/reference/oadmin.install_github_package.html
index 496f0075..ae130887 100644
--- a/docs/reference/oadmin.install_github_package.html
+++ b/docs/reference/oadmin.install_github_package.html
@@ -69,13 +69,13 @@ Install a package from GitHub
- oadmin.install_github_package(
- opal,
- pkg,
- username = getOption("github.user"),
- ref = "master",
- profile = NULL
-)
+ oadmin.install_github_package(
+ opal,
+ pkg,
+ username = getOption("github.user"),
+ ref = "master",
+ profile = NULL
+)
@@ -117,11 +117,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_github_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_github_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/oadmin.install_local_package.html b/docs/reference/oadmin.install_local_package.html
index 17ddc429..9ddb56c3 100644
--- a/docs/reference/oadmin.install_local_package.html
+++ b/docs/reference/oadmin.install_local_package.html
@@ -71,7 +71,7 @@ Install a package from a local archive file
- oadmin.install_local_package(opal, path, profile = NULL)
+ oadmin.install_local_package(opal, path, profile = NULL)
@@ -105,14 +105,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# install a pre-built local archive file
-oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
-# or build archive file from local package source (in current working folder)
-oadmin.install_local_package(o, devtools::build())
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# install a pre-built local archive file
+oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
+# or build archive file from local package source (in current working folder)
+oadmin.install_local_package(o, devtools::build())
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/oadmin.install_package.html b/docs/reference/oadmin.install_package.html
index 0b2c26c5..7539e7fc 100644
--- a/docs/reference/oadmin.install_package.html
+++ b/docs/reference/oadmin.install_package.html
@@ -69,7 +69,7 @@ Install CRAN package
- oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
+ oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
@@ -113,11 +113,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_package(o, 'xxx')
+opal.logout(o)
+}
@@ -132,7 +132,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_devtools.html b/docs/reference/oadmin.installed_devtools.html
index eaf1b900..a90063c1 100644
--- a/docs/reference/oadmin.installed_devtools.html
+++ b/docs/reference/oadmin.installed_devtools.html
@@ -69,7 +69,7 @@ Check devtools package
- oadmin.installed_devtools(opal, profile = NULL)
+ oadmin.installed_devtools(opal, profile = NULL)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_devtools(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_package.html b/docs/reference/oadmin.installed_package.html
index 604bd8ef..aa802b54 100644
--- a/docs/reference/oadmin.installed_package.html
+++ b/docs/reference/oadmin.installed_package.html
@@ -69,7 +69,7 @@ Check package is installed
- oadmin.installed_package(opal, pkg, profile = NULL)
+ oadmin.installed_package(opal, pkg, profile = NULL)
@@ -109,12 +109,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_package(o, 'xxx')
-oadmin.installed_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_package(o, 'xxx')
+oadmin.installed_package(o, 'stats')
+opal.logout(o)
+}
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_packages.html b/docs/reference/oadmin.installed_packages.html
index 2bc6bfc8..2034f299 100644
--- a/docs/reference/oadmin.installed_packages.html
+++ b/docs/reference/oadmin.installed_packages.html
@@ -69,7 +69,7 @@ List installed packages
- oadmin.installed_packages(opal, profile = NULL)
+ oadmin.installed_packages(opal, profile = NULL)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_packages(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_packages(o)
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/oadmin.log.html b/docs/reference/oadmin.log.html
new file mode 100644
index 00000000..2204fa48
--- /dev/null
+++ b/docs/reference/oadmin.log.html
@@ -0,0 +1,118 @@
+
+Get Opal main logs — oadmin.log • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal main logs
+
+
+
+ oadmin.log(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.log_rest.html b/docs/reference/oadmin.log_rest.html
new file mode 100644
index 00000000..fd2f9ef2
--- /dev/null
+++ b/docs/reference/oadmin.log_rest.html
@@ -0,0 +1,118 @@
+
+Get Opal REST API logs — oadmin.log_rest • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal REST API logs
+
+
+
+ oadmin.log_rest(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_rest(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.log_sql.html b/docs/reference/oadmin.log_sql.html
new file mode 100644
index 00000000..0dc4fae5
--- /dev/null
+++ b/docs/reference/oadmin.log_sql.html
@@ -0,0 +1,118 @@
+
+Get Opal SQL API logs — oadmin.log_sql • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal SQL API logs
+
+
+
+ oadmin.log_sql(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_sql(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.package_description.html b/docs/reference/oadmin.package_description.html
index d07d871e..d402b336 100644
--- a/docs/reference/oadmin.package_description.html
+++ b/docs/reference/oadmin.package_description.html
@@ -69,7 +69,7 @@ Get package description
- oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
+ oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.package_description(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.package_description(o, 'stats')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/oadmin.perm.html b/docs/reference/oadmin.perm.html
index b61d3e13..20a30ecc 100644
--- a/docs/reference/oadmin.perm.html
+++ b/docs/reference/oadmin.perm.html
@@ -69,7 +69,7 @@ Get the R permissions (deprecated)
- oadmin.perm(opal)
+ oadmin.perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.perm_add.html b/docs/reference/oadmin.perm_add.html
index b3a39610..df43a7c7 100644
--- a/docs/reference/oadmin.perm_add.html
+++ b/docs/reference/oadmin.perm_add.html
@@ -69,7 +69,7 @@ Add or update a R permission (deprecated)
- oadmin.perm_add(opal, subject, type = "user", permission)
+ oadmin.perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.perm_delete.html b/docs/reference/oadmin.perm_delete.html
index f629e6fc..fa8fa4de 100644
--- a/docs/reference/oadmin.perm_delete.html
+++ b/docs/reference/oadmin.perm_delete.html
@@ -69,7 +69,7 @@ Delete a R permission (deprecated)
- oadmin.perm_delete(opal, subject, type = "user")
+ oadmin.perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm.html b/docs/reference/oadmin.r_perm.html
index 4bae064d..12b32d20 100644
--- a/docs/reference/oadmin.r_perm.html
+++ b/docs/reference/oadmin.r_perm.html
@@ -69,7 +69,7 @@ Get the R permissions
- oadmin.r_perm(opal)
+ oadmin.r_perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm_add.html b/docs/reference/oadmin.r_perm_add.html
index 06ec844e..fc74abf1 100644
--- a/docs/reference/oadmin.r_perm_add.html
+++ b/docs/reference/oadmin.r_perm_add.html
@@ -69,7 +69,7 @@ Add or update a R permission
- oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
+ oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm_delete.html b/docs/reference/oadmin.r_perm_delete.html
index c68d1ff5..01177602 100644
--- a/docs/reference/oadmin.r_perm_delete.html
+++ b/docs/reference/oadmin.r_perm_delete.html
@@ -69,7 +69,7 @@ Delete a R permission
- oadmin.r_perm_delete(opal, subject, type = "user")
+ oadmin.r_perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.remove_package.html b/docs/reference/oadmin.remove_package.html
index 7d9fd447..0953b827 100644
--- a/docs/reference/oadmin.remove_package.html
+++ b/docs/reference/oadmin.remove_package.html
@@ -69,7 +69,7 @@ Remove package
- oadmin.remove_package(opal, pkg, profile = NULL)
+ oadmin.remove_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.remove_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.remove_package(o, 'xxx')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.system_metrics.html b/docs/reference/oadmin.system_metrics.html
index 4e5ba20e..9eb7d54a 100644
--- a/docs/reference/oadmin.system_metrics.html
+++ b/docs/reference/oadmin.system_metrics.html
@@ -81,7 +81,7 @@ Get system metrics
- oadmin.system_metrics(opal)
+ oadmin.system_metrics(opal)
@@ -93,11 +93,11 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_metrics(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_metrics(o)
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm.html b/docs/reference/oadmin.system_perm.html
index a858025b..5cc5a542 100644
--- a/docs/reference/oadmin.system_perm.html
+++ b/docs/reference/oadmin.system_perm.html
@@ -69,7 +69,7 @@ Get the System permissions
- oadmin.system_perm(opal)
+ oadmin.system_perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm_add.html b/docs/reference/oadmin.system_perm_add.html
index 8b06fd5e..ecc56a90 100644
--- a/docs/reference/oadmin.system_perm_add.html
+++ b/docs/reference/oadmin.system_perm_add.html
@@ -69,7 +69,7 @@ Add or update a System permission
- oadmin.system_perm_add(opal, subject, type = "user", permission)
+ oadmin.system_perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm_delete.html b/docs/reference/oadmin.system_perm_delete.html
index c78fc7d4..5268feec 100644
--- a/docs/reference/oadmin.system_perm_delete.html
+++ b/docs/reference/oadmin.system_perm_delete.html
@@ -69,7 +69,7 @@ Delete a System permission
- oadmin.system_perm_delete(opal, subject, type = "user")
+ oadmin.system_perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.user_add.html b/docs/reference/oadmin.user_add.html
index e5a58e5b..1b82c9b6 100644
--- a/docs/reference/oadmin.user_add.html
+++ b/docs/reference/oadmin.user_add.html
@@ -69,7 +69,7 @@ Add a user
- oadmin.user_add(opal, name, groups = NULL, password = NULL)
+ oadmin.user_add(opal, name, groups = NULL, password = NULL)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/oadmin.user_delete.html b/docs/reference/oadmin.user_delete.html
index 123be6e5..1ae1cb20 100644
--- a/docs/reference/oadmin.user_delete.html
+++ b/docs/reference/oadmin.user_delete.html
@@ -69,7 +69,7 @@ Delete a user
- oadmin.user_delete(opal, name)
+ oadmin.user_delete(opal, name)
@@ -96,12 +96,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_delete(o, "foo")
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/oadmin.user_enable.html b/docs/reference/oadmin.user_enable.html
index 1b531f3a..5b480d04 100644
--- a/docs/reference/oadmin.user_enable.html
+++ b/docs/reference/oadmin.user_enable.html
@@ -69,7 +69,7 @@ Enable a user
- oadmin.user_enable(opal, name, enabled = TRUE)
+ oadmin.user_enable(opal, name, enabled = TRUE)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_enable(o, "foo", enabled = FALSE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_enable(o, "foo", enabled = FALSE)
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/oadmin.user_exists.html b/docs/reference/oadmin.user_exists.html
index e05a1f79..fad76e33 100644
--- a/docs/reference/oadmin.user_exists.html
+++ b/docs/reference/oadmin.user_exists.html
@@ -71,7 +71,7 @@ Check user exists
- oadmin.user_exists(opal, name)
+ oadmin.user_exists(opal, name)
@@ -98,12 +98,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-if (!oadmin.user_exists(o, "foo"))
- oadmin.user_add(o, "foo", password = "bar123")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+if (!oadmin.user_exists(o, "foo"))
+ oadmin.user_add(o, "foo", password = "bar123")
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.user_profile_delete.html b/docs/reference/oadmin.user_profile_delete.html
index e1aab115..2e585266 100644
--- a/docs/reference/oadmin.user_profile_delete.html
+++ b/docs/reference/oadmin.user_profile_delete.html
@@ -75,7 +75,7 @@ Delete a user profile
- oadmin.user_profile_delete(opal, name)
+ oadmin.user_profile_delete(opal, name)
@@ -102,12 +102,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_profile_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_profile_delete(o, "foo")
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.user_profiles.html b/docs/reference/oadmin.user_profiles.html
index 2c1e5a94..f23f1669 100644
--- a/docs/reference/oadmin.user_profiles.html
+++ b/docs/reference/oadmin.user_profiles.html
@@ -71,7 +71,7 @@ Get user profiles
- oadmin.user_profiles(opal, df = TRUE)
+ oadmin.user_profiles(opal, df = TRUE)
@@ -98,11 +98,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.user_profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.user_profiles(o)
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/oadmin.user_reset_password.html b/docs/reference/oadmin.user_reset_password.html
index 7bc446ae..75e27675 100644
--- a/docs/reference/oadmin.user_reset_password.html
+++ b/docs/reference/oadmin.user_reset_password.html
@@ -69,7 +69,7 @@ Reset user password
- oadmin.user_reset_password(opal, name, password = NULL)
+ oadmin.user_reset_password(opal, name, password = NULL)
@@ -100,13 +100,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_reset_password(o, "foo", password = "password1234")
-oadmin.user_rm(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_reset_password(o, "foo", password = "password1234")
+oadmin.user_rm(o, "foo")
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/oadmin.users.html b/docs/reference/oadmin.users.html
index e16383d7..f7a3388e 100644
--- a/docs/reference/oadmin.users.html
+++ b/docs/reference/oadmin.users.html
@@ -69,7 +69,7 @@ Get the users
- oadmin.users(opal, df = TRUE)
+ oadmin.users(opal, df = TRUE)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.users(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.users(o)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.annotate.html b/docs/reference/opal.annotate.html
index f8b0529c..d0970046 100644
--- a/docs/reference/opal.annotate.html
+++ b/docs/reference/opal.annotate.html
@@ -71,7 +71,7 @@ Apply the annotations to a Opal table
- opal.annotate(opal, datasource, table, annotations)
+ opal.annotate(opal, datasource, table, annotations)
@@ -111,12 +111,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/opal.annotations.html b/docs/reference/opal.annotations.html
index 54727239..9f6b17eb 100644
--- a/docs/reference/opal.annotations.html
+++ b/docs/reference/opal.annotations.html
@@ -69,7 +69,7 @@ Get the annotations of a Opal table
- opal.annotations(opal, datasource, table)
+ opal.annotations(opal, datasource, table)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.as_md_table.html b/docs/reference/opal.as_md_table.html
index e37dd66e..b6b4c121 100644
--- a/docs/reference/opal.as_md_table.html
+++ b/docs/reference/opal.as_md_table.html
@@ -69,14 +69,14 @@ Array to Markdown
-
+
@@ -108,11 +108,11 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/opal.assign.data.html b/docs/reference/opal.assign.data.html
index e7b39e90..2be27522 100644
--- a/docs/reference/opal.assign.data.html
+++ b/docs/reference/opal.assign.data.html
@@ -69,7 +69,7 @@ Data assignment
- opal.assign.data(opal, symbol, value, async = FALSE)
+ opal.assign.data(opal, symbol, value, async = FALSE)
@@ -102,16 +102,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# push an arbitrary data frame to the R server
-opal.assign.data(o, "D", mtcars)
-# push an arbitrary vector to the R server
-opal.assign.data(o, "C", mtcars$cyl)
-# push a string
-opal.assign.data(o, "S", "Hello!")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# push an arbitrary data frame to the R server
+opal.assign.data(o, "D", mtcars)
+# push an arbitrary vector to the R server
+opal.assign.data(o, "C", mtcars$cyl)
+# push a string
+opal.assign.data(o, "S", "Hello!")
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.assign.html b/docs/reference/opal.assign.html
index c0c14727..83bab276 100644
--- a/docs/reference/opal.assign.html
+++ b/docs/reference/opal.assign.html
@@ -69,17 +69,17 @@ Data or expression assignment
- opal.assign(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- async = FALSE
-)
+ opal.assign(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ async = FALSE
+)
@@ -132,21 +132,21 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-# push an arbitrary data frame to the R server
-#opal.assign(o, "D", mtcars)
-# push an arbitrary vector to the R server
-#opal.assign(o, "C", mtcars$cyl)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+# push an arbitrary data frame to the R server
+#opal.assign(o, "D", mtcars)
+# push an arbitrary vector to the R server
+#opal.assign(o, "C", mtcars$cyl)
+opal.logout(o)
+}
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/opal.assign.resource.html b/docs/reference/opal.assign.resource.html
index 649d475e..b06c3fee 100644
--- a/docs/reference/opal.assign.resource.html
+++ b/docs/reference/opal.assign.resource.html
@@ -69,7 +69,7 @@ Resource assignment
- opal.assign.resource(opal, symbol, value, async = FALSE)
+ opal.assign.resource(opal, symbol, value, async = FALSE)
@@ -102,13 +102,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a resource and make some operation on it
-opal.assign.resource(o, "D", "datashield.cram1")
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a resource and make some operation on it
+opal.assign.resource(o, "D", "datashield.cram1")
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.assign.script.html b/docs/reference/opal.assign.script.html
index ce2ee8a8..4826146e 100644
--- a/docs/reference/opal.assign.script.html
+++ b/docs/reference/opal.assign.script.html
@@ -69,7 +69,7 @@ R script assignment
- opal.assign.script(opal, symbol, value, async = FALSE)
+ opal.assign.script(opal, symbol, value, async = FALSE)
@@ -102,13 +102,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.assign.table.html b/docs/reference/opal.assign.table.html
index f23b63b9..b853219b 100644
--- a/docs/reference/opal.assign.table.html
+++ b/docs/reference/opal.assign.table.html
@@ -69,18 +69,18 @@ Data assignment to a data.frame
- opal.assign.table(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- class = "data.frame",
- async = FALSE
-)
+ opal.assign.table(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ class = "data.frame",
+ async = FALSE
+)
@@ -137,19 +137,19 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-opal.execute(o, "colnames(D)")
-# assign a table CNSIM1 with a identifiers column
-opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
-opal.execute(o, "colnames(H)")
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-opal.execute(o, "colnames(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+opal.execute(o, "colnames(D)")
+# assign a table CNSIM1 with a identifiers column
+opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
+opal.execute(o, "colnames(H)")
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+opal.execute(o, "colnames(D)")
+opal.logout(o)
+}
@@ -164,7 +164,7 @@ Examples
diff --git a/docs/reference/opal.assign.table.tibble.html b/docs/reference/opal.assign.table.tibble.html
index 95dc04a3..e508e729 100644
--- a/docs/reference/opal.assign.table.tibble.html
+++ b/docs/reference/opal.assign.table.tibble.html
@@ -69,18 +69,18 @@ Data assignment to a tibble
- opal.assign.table.tibble(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = "id",
- with.factors = FALSE,
- updated.name = NULL,
- async = FALSE
-)
+ opal.assign.table.tibble(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = "id",
+ with.factors = FALSE,
+ updated.name = NULL,
+ async = FALSE
+)
@@ -137,13 +137,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a table and make some operation on it
-opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a table and make some operation on it
+opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
@@ -158,7 +158,7 @@ Examples
diff --git a/docs/reference/opal.attribute_values.html b/docs/reference/opal.attribute_values.html
index dd1b1537..98a94106 100644
--- a/docs/reference/opal.attribute_values.html
+++ b/docs/reference/opal.attribute_values.html
@@ -69,7 +69,7 @@ Get a vector of attribute values
- opal.attribute_values(attributes, namespace = NULL, name = "label")
+ opal.attribute_values(attributes, namespace = NULL, name = "label")
@@ -103,12 +103,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.attribute_values(var$attributes)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.attribute_values(var$attributes)
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.command.html b/docs/reference/opal.command.html
index 0f88509d..4f419a6e 100644
--- a/docs/reference/opal.command.html
+++ b/docs/reference/opal.command.html
@@ -69,7 +69,7 @@ Get an asynchronous command
- opal.command(opal, id, wait = FALSE)
+ opal.command(opal, id, wait = FALSE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command(o, '1234')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.command_result.html b/docs/reference/opal.command_result.html
index 5289b55a..35bc7964 100644
--- a/docs/reference/opal.command_result.html
+++ b/docs/reference/opal.command_result.html
@@ -71,7 +71,7 @@ Get result of an asynchronous command
- opal.command_result(opal, id, wait = FALSE)
+ opal.command_result(opal, id, wait = FALSE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_result(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_result(o, '1234')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.command_rm.html b/docs/reference/opal.command_rm.html
index c43351fa..e7fea6bb 100644
--- a/docs/reference/opal.command_rm.html
+++ b/docs/reference/opal.command_rm.html
@@ -69,7 +69,7 @@ Remove an asynchronous command
- opal.command_rm(opal, id)
+ opal.command_rm(opal, id)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_rm(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_rm(o, '1234')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.commands.html b/docs/reference/opal.commands.html
index f184c2a2..e5067c0f 100644
--- a/docs/reference/opal.commands.html
+++ b/docs/reference/opal.commands.html
@@ -69,7 +69,7 @@ List the asynchronous commands
- opal.commands(opal, df = TRUE)
+ opal.commands(opal, df = TRUE)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands(o)
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.commands_rm.html b/docs/reference/opal.commands_rm.html
index a79be20b..dad19270 100644
--- a/docs/reference/opal.commands_rm.html
+++ b/docs/reference/opal.commands_rm.html
@@ -69,7 +69,7 @@ Remove all asynchronous commands
- opal.commands_rm(opal)
+ opal.commands_rm(opal)
@@ -89,11 +89,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands_rm(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands_rm(o)
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/opal.datasource.html b/docs/reference/opal.datasource.html
index db4e3140..18ec94fc 100644
--- a/docs/reference/opal.datasource.html
+++ b/docs/reference/opal.datasource.html
@@ -69,7 +69,7 @@ Get a datasource
- opal.datasource(opal, datasource)
+ opal.datasource(opal, datasource)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasource(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasource(o, 'CNSIM')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.datasources.html b/docs/reference/opal.datasources.html
index 2c0c3136..b541b556 100644
--- a/docs/reference/opal.datasources.html
+++ b/docs/reference/opal.datasources.html
@@ -69,7 +69,7 @@ Get datasources
- opal.datasources(opal, df = TRUE)
+ opal.datasources(opal, df = TRUE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasources(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasources(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.delete.html b/docs/reference/opal.delete.html
index 9acf1da1..97b75ae3 100644
--- a/docs/reference/opal.delete.html
+++ b/docs/reference/opal.delete.html
@@ -69,7 +69,7 @@ Generic REST resource deletion.
- opal.delete(opal, ..., query = list(), callback = NULL)
+ opal.delete(opal, ..., query = list(), callback = NULL)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.delete(o, 'some', 'resource')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.delete(o, 'some', 'resource')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.execute.html b/docs/reference/opal.execute.html
index 244ade02..f91dcca6 100644
--- a/docs/reference/opal.execute.html
+++ b/docs/reference/opal.execute.html
@@ -69,7 +69,7 @@ Execute a R script
- opal.execute(opal, script, async = FALSE)
+ opal.execute(opal, script, async = FALSE)
@@ -97,12 +97,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute(o, "x <- 'foo'")
-opal.execute(o, "ls()")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute(o, "x <- 'foo'")
+opal.execute(o, "ls()")
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/opal.execute.source.html b/docs/reference/opal.execute.source.html
index 9ad4eef0..f512ffb2 100644
--- a/docs/reference/opal.execute.source.html
+++ b/docs/reference/opal.execute.source.html
@@ -69,7 +69,7 @@ Execute a R file script
- opal.execute.source(opal, path, async = FALSE)
+ opal.execute.source(opal, path, async = FALSE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute.source(o, "myscript.R")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute.source(o, "myscript.R")
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.file.html b/docs/reference/opal.file.html
index 074023d1..72a13d97 100644
--- a/docs/reference/opal.file.html
+++ b/docs/reference/opal.file.html
@@ -69,7 +69,7 @@ Get file content
- opal.file(opal, path, key = NULL)
+ opal.file(opal, path, key = NULL)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.file(o, '/home/administrator/joins/join-src-3.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.file(o, '/home/administrator/joins/join-src-3.csv')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.file_cp.html b/docs/reference/opal.file_cp.html
index c895e41c..33bb18fd 100644
--- a/docs/reference/opal.file_cp.html
+++ b/docs/reference/opal.file_cp.html
@@ -69,7 +69,7 @@ Copy a file
- opal.file_cp(opal, source, destination)
+ opal.file_cp(opal, source, destination)
@@ -104,14 +104,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# copy a file to another folder
-opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# copy recursively a folder to another folder
-opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# copy a file to another folder
+opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# copy recursively a folder to another folder
+opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.file_download.html b/docs/reference/opal.file_download.html
index dde0cba7..e6770678 100644
--- a/docs/reference/opal.file_download.html
+++ b/docs/reference/opal.file_download.html
@@ -69,7 +69,7 @@ Download a file
- opal.file_download(opal, source, destination = NULL, key = NULL)
+ opal.file_download(opal, source, destination = NULL, key = NULL)
@@ -108,19 +108,19 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# download a file
-opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
-# download a file encrypted by a key: resulting file is a zip with an encrypted content
-opal.file_download(o, '/home/administrator/export/some-data.csv',
- destination='some-data.zip', key='AZF57893FBDE')
-# download, create destination folder and rename file
-opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
-# download a folder
-opal.file_download(o, '/home/administrator/export', 'export.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# download a file
+opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
+# download a file encrypted by a key: resulting file is a zip with an encrypted content
+opal.file_download(o, '/home/administrator/export/some-data.csv',
+ destination='some-data.zip', key='AZF57893FBDE')
+# download, create destination folder and rename file
+opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
+# download a folder
+opal.file_download(o, '/home/administrator/export', 'export.zip')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.file_ls.html b/docs/reference/opal.file_ls.html
index c57e02da..8664df11 100644
--- a/docs/reference/opal.file_ls.html
+++ b/docs/reference/opal.file_ls.html
@@ -69,7 +69,7 @@ List content of a folder
- opal.file_ls(opal, path)
+ opal.file_ls(opal, path)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# list content of a folder
-opal.file_ls(o, '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# list content of a folder
+opal.file_ls(o, '/home/administrator')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.file_mkdir.html b/docs/reference/opal.file_mkdir.html
index 0ed72ad7..d15743df 100644
--- a/docs/reference/opal.file_mkdir.html
+++ b/docs/reference/opal.file_mkdir.html
@@ -71,7 +71,7 @@ Make a folder
- opal.file_mkdir(opal, path, parents = FALSE)
+ opal.file_mkdir(opal, path, parents = FALSE)
@@ -106,12 +106,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.file_mkdir_tmp.html b/docs/reference/opal.file_mkdir_tmp.html
index 396c04ff..8e187fcb 100644
--- a/docs/reference/opal.file_mkdir_tmp.html
+++ b/docs/reference/opal.file_mkdir_tmp.html
@@ -69,7 +69,7 @@ Make a temporary folder
- opal.file_mkdir_tmp(opal)
+ opal.file_mkdir_tmp(opal)
@@ -102,12 +102,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-path <- opal.file_mkdir_tmp(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+path <- opal.file_mkdir_tmp(o)
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/opal.file_mv.html b/docs/reference/opal.file_mv.html
index fc322297..1d6874df 100644
--- a/docs/reference/opal.file_mv.html
+++ b/docs/reference/opal.file_mv.html
@@ -69,7 +69,7 @@ Move and/or rename a file
- opal.file_mv(opal, source, destination)
+ opal.file_mv(opal, source, destination)
@@ -104,18 +104,18 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# move a file to another folder
-opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/administrator/export/some-data.csv')
-# move and rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/userx/deliverables/some-data.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# move a file to another folder
+opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/administrator/export/some-data.csv')
+# move and rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/userx/deliverables/some-data.csv')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.file_read.html b/docs/reference/opal.file_read.html
index 64f4982d..1807b28c 100644
--- a/docs/reference/opal.file_read.html
+++ b/docs/reference/opal.file_read.html
@@ -69,7 +69,7 @@ Read a file
- opal.file_read(opal, source, destination)
+ opal.file_read(opal, source, destination)
@@ -104,16 +104,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# read into folder
-opal.file_read(o,"DatabaseTest.sav", "/tmp")
-# read and rename
-opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
-# user home expansion
-opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# read into folder
+opal.file_read(o,"DatabaseTest.sav", "/tmp")
+# read and rename
+opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
+# user home expansion
+opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.file_rm.html b/docs/reference/opal.file_rm.html
index a23dee2e..5d79795c 100644
--- a/docs/reference/opal.file_rm.html
+++ b/docs/reference/opal.file_rm.html
@@ -69,7 +69,7 @@ Remove a file
- opal.file_rm(opal, path)
+ opal.file_rm(opal, path)
@@ -100,14 +100,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# remove a file
-opal.file_rm(o, '/home/administrator/export/some-data.csv')
-# remove recursively a folder
-opal.file_rm(o, '/home/administrator/export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# remove a file
+opal.file_rm(o, '/home/administrator/export/some-data.csv')
+# remove recursively a folder
+opal.file_rm(o, '/home/administrator/export')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/opal.file_unzip.html b/docs/reference/opal.file_unzip.html
index 66eaea32..a695dfec 100644
--- a/docs/reference/opal.file_unzip.html
+++ b/docs/reference/opal.file_unzip.html
@@ -69,7 +69,7 @@ Unzip a zip archive file
- opal.file_unzip(opal, source, destination, key = NULL)
+ opal.file_unzip(opal, source, destination, key = NULL)
@@ -114,12 +114,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# unzip
-path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# unzip
+path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.file_upload.html b/docs/reference/opal.file_upload.html
index 83a6426c..70c2faea 100644
--- a/docs/reference/opal.file_upload.html
+++ b/docs/reference/opal.file_upload.html
@@ -71,7 +71,7 @@ Upload a file or a folder
- opal.file_upload(opal, source, destination, all.files = TRUE)
+ opal.file_upload(opal, source, destination, all.files = TRUE)
@@ -111,14 +111,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# upload a file
-opal.file_upload(o, 'some_data.csv', '/home/administrator')
-# upload a folder
-opal.file_upload(o, 'some_data', '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# upload a file
+opal.file_upload(o, 'some_data.csv', '/home/administrator')
+# upload a folder
+opal.file_upload(o, 'some_data', '/home/administrator')
+opal.logout(o)
+}
@@ -133,7 +133,7 @@ Examples
diff --git a/docs/reference/opal.file_write.html b/docs/reference/opal.file_write.html
index a1bfb19d..f0835d11 100644
--- a/docs/reference/opal.file_write.html
+++ b/docs/reference/opal.file_write.html
@@ -69,7 +69,7 @@ Write a file
- opal.file_write(opal, source, destination = NULL)
+ opal.file_write(opal, source, destination = NULL)
@@ -104,16 +104,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# user home expansion
-opal.file_write(o, "~/spss/DatabaseTest.sav")
-# rename file
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
-# create sub-folder
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# user home expansion
+opal.file_write(o, "~/spss/DatabaseTest.sav")
+# rename file
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
+# create sub-folder
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.get.html b/docs/reference/opal.get.html
index 19e0f260..f83d5cb9 100644
--- a/docs/reference/opal.get.html
+++ b/docs/reference/opal.get.html
@@ -69,14 +69,14 @@ Generic REST resource getter.
- opal.get(
- opal,
- ...,
- query = list(),
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)
+ opal.get(
+ opal,
+ ...,
+ query = list(),
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)
@@ -115,11 +115,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.get(o, 'project', 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.get(o, 'project', 'CNSIM')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.load_package.html b/docs/reference/opal.load_package.html
index 15e9967f..cba05243 100644
--- a/docs/reference/opal.load_package.html
+++ b/docs/reference/opal.load_package.html
@@ -69,7 +69,7 @@ Load package
- opal.load_package(opal, pkg)
+ opal.load_package(opal, pkg)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.load_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.load_package(o, 'stats')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.login.html b/docs/reference/opal.login.html
index f9523698..549cdc71 100644
--- a/docs/reference/opal.login.html
+++ b/docs/reference/opal.login.html
@@ -73,15 +73,15 @@ Opal login
-
+
@@ -132,44 +132,44 @@ See also
Examples
- if (FALSE) {
-#### The below examples illustrate the different ways to login in opal ####
-
-# explicite username/password login
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
- # explicite personal access token login
-o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login using options and user credentials
-options(opal.username = 'administrator',
- opal.password = 'password',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using options and personal access token
-options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using ssl key pair
-options(opal.opts = list(
- sslcert = 'my-publickey.pem',
- sslkey = 'my-privatekey.pem'))
-o <- opal.login(url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login with a R server profile
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org', profile = 'default')
-opal.logout(o)
-}
+ if (FALSE) {
+#### The below examples illustrate the different ways to login in opal ####
+
+# explicite username/password login
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+ # explicite personal access token login
+o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login using options and user credentials
+options(opal.username = 'administrator',
+ opal.password = 'password',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using options and personal access token
+options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using ssl key pair
+options(opal.opts = list(
+ sslcert = 'my-publickey.pem',
+ sslkey = 'my-privatekey.pem'))
+o <- opal.login(url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login with a R server profile
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org', profile = 'default')
+opal.logout(o)
+}
@@ -184,7 +184,7 @@ Examples
diff --git a/docs/reference/opal.logout.html b/docs/reference/opal.logout.html
index e64f3e86..b91868aa 100644
--- a/docs/reference/opal.logout.html
+++ b/docs/reference/opal.logout.html
@@ -69,7 +69,7 @@ Logout from Opal(s)
- opal.logout(opal, save = FALSE)
+ opal.logout(opal, save = FALSE)
@@ -91,10 +91,10 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+}
@@ -109,7 +109,7 @@ Examples
diff --git a/docs/reference/opal.perms.html b/docs/reference/opal.perms.html
new file mode 100644
index 00000000..aab233ff
--- /dev/null
+++ b/docs/reference/opal.perms.html
@@ -0,0 +1,154 @@
+
+Get the permissions of a subject — opal.perms • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the permissions of a subject. If the subject is a user, the permissions of
+the groups to which the user belongs are also added to the result.
+
+
+
+ opal.perms(opal, subject, type = "user")
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- subject
+A subject identifier: user or group name.
- type
+The type of subject: user (default) or group.
+
+ Value
+
+
+A data.frame with columns: subject, type, target (path to the opal object to which
+the permission applies), target_type and perm (the permission name)
+
+
+ See also
+ Other table functions:
+opal.resource_view_create(),
+opal.resource_view_reconnect(),
+opal.table_create(),
+opal.table_delete(),
+opal.table_dictionary_get(),
+opal.table_dictionary_update(),
+opal.table_exists(),
+opal.table_export(),
+opal.table_get(),
+opal.table_import(),
+opal.table_perm_add(),
+opal.table_perm_delete(),
+opal.table_perm(),
+opal.table_save(),
+opal.table_truncate(),
+opal.table_view_create(),
+opal.table_view_update()
+
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.perms(o, 'andrei')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/opal.post.html b/docs/reference/opal.post.html
index d93bb6bf..f7d80068 100644
--- a/docs/reference/opal.post.html
+++ b/docs/reference/opal.post.html
@@ -69,16 +69,16 @@ Generic REST resource creation.
- opal.post(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)
+ opal.post(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)
@@ -125,11 +125,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.post(o, 'some', 'resources', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.post(o, 'some', 'resources', body = '{"some":"value"}')
+opal.logout(o)
+}
@@ -144,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.profiles.html b/docs/reference/opal.profiles.html
index 067273c2..1e96f85c 100644
--- a/docs/reference/opal.profiles.html
+++ b/docs/reference/opal.profiles.html
@@ -71,7 +71,7 @@ List R profiles
- opal.profiles(opal, df = TRUE)
+ opal.profiles(opal, df = TRUE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.profiles(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.project.html b/docs/reference/opal.project.html
index cd3a4f68..3e6b4a16 100644
--- a/docs/reference/opal.project.html
+++ b/docs/reference/opal.project.html
@@ -69,7 +69,7 @@ Get a project
- opal.project(opal, project)
+ opal.project(opal, project)
@@ -94,11 +94,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project(o, 'datashield')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project(o, 'datashield')
+opal.logout(o)
+}
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/opal.project_backup.html b/docs/reference/opal.project_backup.html
index 9fe7543f..58bf4b6e 100644
--- a/docs/reference/opal.project_backup.html
+++ b/docs/reference/opal.project_backup.html
@@ -75,14 +75,14 @@ Backup a project
- opal.project_backup(
- opal,
- project,
- archive,
- viewsAsTables = FALSE,
- override = TRUE,
- wait = TRUE
-)
+ opal.project_backup(
+ opal,
+ project,
+ archive,
+ viewsAsTables = FALSE,
+ override = TRUE,
+ wait = TRUE
+)
@@ -120,12 +120,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
-opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
+opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
+opal.logout(o)
+}
@@ -140,7 +140,7 @@ Examples
diff --git a/docs/reference/opal.project_command.html b/docs/reference/opal.project_command.html
index 13740837..9e6c5e62 100644
--- a/docs/reference/opal.project_command.html
+++ b/docs/reference/opal.project_command.html
@@ -69,7 +69,7 @@ Get project task
- opal.project_command(opal, project, id)
+ opal.project_command(opal, project, id)
@@ -95,12 +95,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
-opal.project_command(opal, 'GREENSPACE', id)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
+opal.project_command(opal, 'GREENSPACE', id)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.project_create.html b/docs/reference/opal.project_create.html
index 2524037d..d1eb8488 100644
--- a/docs/reference/opal.project_create.html
+++ b/docs/reference/opal.project_create.html
@@ -69,15 +69,15 @@ Create a project
- opal.project_create(
- opal,
- project,
- database = NULL,
- title = NULL,
- description = NULL,
- tags = NULL,
- exportFolder = NULL
-)
+ opal.project_create(
+ opal,
+ project,
+ database = NULL,
+ title = NULL,
+ description = NULL,
+ tags = NULL,
+ exportFolder = NULL
+)
@@ -124,16 +124,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with named database
-opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
-# with default database
-opal.project_create(o, 'test_default_db', database = TRUE)
-# no database, for views and resources only
-opal.project_create(o, 'test_no_db')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with named database
+opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
+# with default database
+opal.project_create(o, 'test_default_db', database = TRUE)
+# no database, for views and resources only
+opal.project_create(o, 'test_no_db')
+opal.logout(o)
+}
@@ -148,7 +148,7 @@ Examples
diff --git a/docs/reference/opal.project_delete.html b/docs/reference/opal.project_delete.html
index 0975b5d4..249dfdd3 100644
--- a/docs/reference/opal.project_delete.html
+++ b/docs/reference/opal.project_delete.html
@@ -69,7 +69,7 @@ Delete a project
- opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
+ opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
@@ -102,11 +102,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_delete(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_delete(o, 'test')
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/opal.project_exists.html b/docs/reference/opal.project_exists.html
index 2d217cab..10266208 100644
--- a/docs/reference/opal.project_exists.html
+++ b/docs/reference/opal.project_exists.html
@@ -69,7 +69,7 @@ Check a project exists
- opal.project_exists(opal, project)
+ opal.project_exists(opal, project)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_exists(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_exists(o, 'test')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.project_perm.html b/docs/reference/opal.project_perm.html
index 07a974c3..abba6946 100644
--- a/docs/reference/opal.project_perm.html
+++ b/docs/reference/opal.project_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a project
- opal.project_perm(opal, project)
+ opal.project_perm(opal, project)
@@ -91,13 +91,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.project_perm_add.html b/docs/reference/opal.project_perm_add.html
index 1fd19072..e134d7b0 100644
--- a/docs/reference/opal.project_perm_add.html
+++ b/docs/reference/opal.project_perm_add.html
@@ -69,13 +69,13 @@ Add or update a permission on a project
- opal.project_perm_add(
- opal,
- project,
- subject,
- type = "user",
- permission = "administrate"
-)
+ opal.project_perm_add(
+ opal,
+ project,
+ subject,
+ type = "user",
+ permission = "administrate"
+)
@@ -103,13 +103,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.project_perm_delete.html b/docs/reference/opal.project_perm_delete.html
index 8a290c35..885e9c53 100644
--- a/docs/reference/opal.project_perm_delete.html
+++ b/docs/reference/opal.project_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a project
- opal.project_perm_delete(opal, project, subject, type = "user")
+ opal.project_perm_delete(opal, project, subject, type = "user")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/opal.project_restore.html b/docs/reference/opal.project_restore.html
index 76c5f138..8f4c0d05 100644
--- a/docs/reference/opal.project_restore.html
+++ b/docs/reference/opal.project_restore.html
@@ -75,14 +75,14 @@ Restore a project
- opal.project_restore(
- opal,
- project,
- archive,
- key = NULL,
- override = TRUE,
- wait = TRUE
-)
+ opal.project_restore(
+ opal,
+ project,
+ archive,
+ key = NULL,
+ override = TRUE,
+ wait = TRUE
+)
@@ -120,15 +120,15 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# create the project to restore, with the default database (to store tables)
-opal.project_create(o, 'GREENSPACE2', database = TRUE)
-# upload backup zip and launch restore task
-opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
-opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# create the project to restore, with the default database (to store tables)
+opal.project_create(o, 'GREENSPACE2', database = TRUE)
+# upload backup zip and launch restore task
+opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
+opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
+opal.logout(o)
+}
@@ -143,7 +143,7 @@ Examples
diff --git a/docs/reference/opal.projects.html b/docs/reference/opal.projects.html
index e8d51a41..73e9e973 100644
--- a/docs/reference/opal.projects.html
+++ b/docs/reference/opal.projects.html
@@ -69,7 +69,7 @@ Get projects
- opal.projects(opal, df = TRUE)
+ opal.projects(opal, df = TRUE)
@@ -94,11 +94,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects(o)
+opal.logout(o)
+}
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/opal.projects_databases.html b/docs/reference/opal.projects_databases.html
index 45f818b3..2a9dc9f0 100644
--- a/docs/reference/opal.projects_databases.html
+++ b/docs/reference/opal.projects_databases.html
@@ -69,7 +69,7 @@ Get projects databases
- opal.projects_databases(opal)
+ opal.projects_databases(opal)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects_databases(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects_databases(o)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.put.html b/docs/reference/opal.put.html
index de59ef78..1622010c 100644
--- a/docs/reference/opal.put.html
+++ b/docs/reference/opal.put.html
@@ -69,14 +69,14 @@ Generic REST resource update.
- opal.put(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- callback = NULL
-)
+ opal.put(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ callback = NULL
+)
@@ -115,11 +115,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.report.html b/docs/reference/opal.report.html
index eaf6c399..efc8d7c1 100644
--- a/docs/reference/opal.report.html
+++ b/docs/reference/opal.report.html
@@ -69,13 +69,13 @@ Opal report
- opal.report(
- input,
- output = NULL,
- progress = FALSE,
- verbose = FALSE,
- boot_style = NULL
-)
+ opal.report(
+ input,
+ output = NULL,
+ progress = FALSE,
+ verbose = FALSE,
+ boot_style = NULL
+)
@@ -103,9 +103,9 @@ Arguments
Examples
- if (FALSE) {
-opal.report('input.Rmd', 'report', progress=TRUE)
-}
+ if (FALSE) {
+opal.report('input.Rmd', 'report', progress=TRUE)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.report_md.html b/docs/reference/opal.report_md.html
index ad0cadd5..50a44df1 100644
--- a/docs/reference/opal.report_md.html
+++ b/docs/reference/opal.report_md.html
@@ -69,7 +69,7 @@ Turn a R markdown file to html.
- opal.report_md(inputFile, progress, verbose)
+ opal.report_md(inputFile, progress, verbose)
@@ -85,7 +85,7 @@ Turn a R markdown file to html.
diff --git a/docs/reference/opal.resource.html b/docs/reference/opal.resource.html
index 8040add0..128ece62 100644
--- a/docs/reference/opal.resource.html
+++ b/docs/reference/opal.resource.html
@@ -69,7 +69,7 @@ Get a resource reference of a project
- opal.resource(opal, project, resource)
+ opal.resource(opal, project, resource)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.resource_create.html b/docs/reference/opal.resource_create.html
index a7f47634..9ed343f2 100644
--- a/docs/reference/opal.resource_create.html
+++ b/docs/reference/opal.resource_create.html
@@ -69,17 +69,17 @@ Create a resource reference in a project
- opal.resource_create(
- opal,
- project,
- name,
- url,
- description = NULL,
- format = NULL,
- package = NULL,
- identity = NULL,
- secret = NULL
-)
+ opal.resource_create(
+ opal,
+ project,
+ name,
+ url,
+ description = NULL,
+ format = NULL,
+ package = NULL,
+ identity = NULL,
+ secret = NULL
+)
@@ -139,13 +139,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_create(o, 'RSRC', 'CNSIM4',
- url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
- format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_create(o, 'RSRC', 'CNSIM4',
+ url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
+ format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
+opal.logout(o)
+}
@@ -160,7 +160,7 @@ Examples
diff --git a/docs/reference/opal.resource_delete.html b/docs/reference/opal.resource_delete.html
index 41eee541..a3e48fb8 100644
--- a/docs/reference/opal.resource_delete.html
+++ b/docs/reference/opal.resource_delete.html
@@ -69,7 +69,7 @@ Delete a resource reference
- opal.resource_delete(opal, project, resource, silent = TRUE)
+ opal.resource_delete(opal, project, resource, silent = TRUE)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_delete(o, "RSRC", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_delete(o, "RSRC", "CNSIM4")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.resource_exists.html b/docs/reference/opal.resource_exists.html
index 7a5852e1..700fd693 100644
--- a/docs/reference/opal.resource_exists.html
+++ b/docs/reference/opal.resource_exists.html
@@ -69,7 +69,7 @@ Check a resource reference exists
- opal.resource_exists(opal, project, resource)
+ opal.resource_exists(opal, project, resource)
@@ -111,11 +111,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_exists(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_exists(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.resource_extension_create.html b/docs/reference/opal.resource_extension_create.html
index c0a045fe..1c8013c4 100644
--- a/docs/reference/opal.resource_extension_create.html
+++ b/docs/reference/opal.resource_extension_create.html
@@ -69,16 +69,16 @@ Create an extended resource reference in a project
- opal.resource_extension_create(
- opal,
- project,
- name,
- provider,
- factory,
- parameters,
- description = NULL,
- credentials = NULL
-)
+ opal.resource_extension_create(
+ opal,
+ project,
+ name,
+ provider,
+ factory,
+ parameters,
+ description = NULL,
+ credentials = NULL
+)
@@ -134,21 +134,21 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
- provider = 'dsOmics', factory = 'ga4gh-htsget',
- parameters = list(
- host = 'https://htsget.ga4gh.org',
- sample = '1000genomes.phase1.chr1',
- reference = '1',
- start = '1',
- end = '100000',
- format = 'GA4GHVCF'
- )
-)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
+ provider = 'dsOmics', factory = 'ga4gh-htsget',
+ parameters = list(
+ host = 'https://htsget.ga4gh.org',
+ sample = '1000genomes.phase1.chr1',
+ reference = '1',
+ start = '1',
+ end = '100000',
+ format = 'GA4GHVCF'
+ )
+)
+opal.logout(o)
+}
@@ -163,7 +163,7 @@ Examples
diff --git a/docs/reference/opal.resource_get.html b/docs/reference/opal.resource_get.html
index ae00707a..80a02871 100644
--- a/docs/reference/opal.resource_get.html
+++ b/docs/reference/opal.resource_get.html
@@ -69,7 +69,7 @@ Get the resource object of a project
- opal.resource_get(opal, project, resource)
+ opal.resource_get(opal, project, resource)
@@ -105,17 +105,17 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
-# then interpret locally the resource object (load the appropriate R packages)
-library(resourcer)
-# coerce to a data.frame
-as.data.frame(res)
-# or get the resource client object for low-level interactions
-rescli <- resourcer::newResourceClient(res)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
+# then interpret locally the resource object (load the appropriate R packages)
+library(resourcer)
+# coerce to a data.frame
+as.data.frame(res)
+# or get the resource client object for low-level interactions
+rescli <- resourcer::newResourceClient(res)
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm.html b/docs/reference/opal.resource_perm.html
index e6856cab..d97e7fef 100644
--- a/docs/reference/opal.resource_perm.html
+++ b/docs/reference/opal.resource_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a resource
- opal.resource_perm(opal, project, resource)
+ opal.resource_perm(opal, project, resource)
@@ -111,13 +111,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -132,7 +132,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm_add.html b/docs/reference/opal.resource_perm_add.html
index 9c3d1438..6ad84919 100644
--- a/docs/reference/opal.resource_perm_add.html
+++ b/docs/reference/opal.resource_perm_add.html
@@ -69,14 +69,14 @@ Add or update a permission on a resource
- opal.resource_perm_add(
- opal,
- project,
- resource,
- subject,
- type = "user",
- permission
-)
+ opal.resource_perm_add(
+ opal,
+ project,
+ resource,
+ subject,
+ type = "user",
+ permission
+)
@@ -125,13 +125,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -146,7 +146,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm_delete.html b/docs/reference/opal.resource_perm_delete.html
index df299ed2..541396ce 100644
--- a/docs/reference/opal.resource_perm_delete.html
+++ b/docs/reference/opal.resource_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a resource
- opal.resource_perm_delete(opal, project, resource, subject, type = "user")
+ opal.resource_perm_delete(opal, project, resource, subject, type = "user")
@@ -113,13 +113,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.resource_view_create.html b/docs/reference/opal.resource_view_create.html
index d653a1cf..f3a7a1f2 100644
--- a/docs/reference/opal.resource_view_create.html
+++ b/docs/reference/opal.resource_view_create.html
@@ -73,15 +73,15 @@ Create an Opal view over a resource reference
- opal.resource_view_create(
- opal,
- project,
- table,
- resource,
- type = "Participant",
- idColumn = NULL,
- profile = NULL
-)
+ opal.resource_view_create(
+ opal,
+ project,
+ table,
+ resource,
+ type = "Participant",
+ idColumn = NULL,
+ profile = NULL
+)
@@ -119,6 +119,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
@@ -139,14 +140,14 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
- resource = "RSRC.FEMALE_2439", idColumn = "Name")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
+ resource = "RSRC.FEMALE_2439", idColumn = "Name")
+opal.logout(o)
+}
@@ -161,7 +162,7 @@ Examples
diff --git a/docs/reference/opal.resource_view_reconnect.html b/docs/reference/opal.resource_view_reconnect.html
index e8650b92..06f03a44 100644
--- a/docs/reference/opal.resource_view_reconnect.html
+++ b/docs/reference/opal.resource_view_reconnect.html
@@ -73,7 +73,7 @@ Reconnect an Opal view to its underlying resource
- opal.resource_view_reconnect(opal, project, table)
+ opal.resource_view_reconnect(opal, project, table)
@@ -93,6 +93,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.table_create(),
opal.table_delete(),
@@ -113,14 +114,14 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-# re-initialize the view's connection to the resource
-opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+# re-initialize the view's connection to the resource
+opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
+opal.logout(o)
+}
@@ -135,7 +136,7 @@ Examples
diff --git a/docs/reference/opal.resources.html b/docs/reference/opal.resources.html
index 305236d9..1219e1b9 100644
--- a/docs/reference/opal.resources.html
+++ b/docs/reference/opal.resources.html
@@ -69,7 +69,7 @@ Get the resource references of a project
- opal.resources(opal, project, df = TRUE)
+ opal.resources(opal, project, df = TRUE)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources(o, 'RSRC')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources(o, 'RSRC')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm.html b/docs/reference/opal.resources_perm.html
index ba3302b2..c53289ba 100644
--- a/docs/reference/opal.resources_perm.html
+++ b/docs/reference/opal.resources_perm.html
@@ -69,7 +69,7 @@ Get the permissions on any resource
- opal.resources_perm(opal, project)
+ opal.resources_perm(opal, project)
@@ -107,13 +107,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm_add.html b/docs/reference/opal.resources_perm_add.html
index 1a4a38e2..f1c870b4 100644
--- a/docs/reference/opal.resources_perm_add.html
+++ b/docs/reference/opal.resources_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on any resource
- opal.resources_perm_add(opal, project, subject, type = "user", permission)
+ opal.resources_perm_add(opal, project, subject, type = "user", permission)
@@ -114,13 +114,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm_delete.html b/docs/reference/opal.resources_perm_delete.html
index e7c09535..5c093566 100644
--- a/docs/reference/opal.resources_perm_delete.html
+++ b/docs/reference/opal.resources_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from any resource
- opal.resources_perm_delete(opal, project, subject, type = "user")
+ opal.resources_perm_delete(opal, project, subject, type = "user")
@@ -109,13 +109,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM', 'CNSIM1')
-opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM', 'CNSIM1')
+opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.rm.html b/docs/reference/opal.rm.html
index f444e41c..728ec6d4 100644
--- a/docs/reference/opal.rm.html
+++ b/docs/reference/opal.rm.html
@@ -69,7 +69,7 @@ Remove a R symbol (deprecated)
- opal.rm(opal, symbol)
+ opal.rm(opal, symbol)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.rm(o, 'D')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.sql.html b/docs/reference/opal.sql.html
index 41f13417..5fa1f9b8 100644
--- a/docs/reference/opal.sql.html
+++ b/docs/reference/opal.sql.html
@@ -75,7 +75,7 @@ Execute a SQL query on tables
- opal.sql(opal, query, project = NULL, id.name = "_id")
+ opal.sql(opal, query, project = NULL, id.name = "_id")
@@ -106,23 +106,23 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from CNSIM1
- where LAB_HDL is not null
- group by GENDER',
- 'CNSIM')
-# without project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from `CNSIM.CNSIM1`
- where LAB_HDL is not null
- group by GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from CNSIM1
+ where LAB_HDL is not null
+ group by GENDER',
+ 'CNSIM')
+# without project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from `CNSIM.CNSIM1`
+ where LAB_HDL is not null
+ group by GENDER')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/opal.sql_history.html b/docs/reference/opal.sql_history.html
index ff53d0db..1bd338f2 100644
--- a/docs/reference/opal.sql_history.html
+++ b/docs/reference/opal.sql_history.html
@@ -71,14 +71,14 @@ SQL query execution history
- opal.sql_history(
- opal,
- project = NULL,
- offset = 0,
- limit = 100,
- user = NULL,
- df = TRUE
-)
+ opal.sql_history(
+ opal,
+ project = NULL,
+ offset = 0,
+ limit = 100,
+ user = NULL,
+ df = TRUE
+)
@@ -118,16 +118,16 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql_history(o, 'CNSIM')
-# without project context
-opal.sql_history(o, NA)
-# with or without project context
-opal.sql_history(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql_history(o, 'CNSIM')
+# without project context
+opal.sql_history(o, NA)
+# with or without project context
+opal.sql_history(o)
+opal.logout(o)
+}
@@ -142,7 +142,7 @@ Examples
diff --git a/docs/reference/opal.symbol_import.html b/docs/reference/opal.symbol_import.html
index ae50bd82..5ee219a5 100644
--- a/docs/reference/opal.symbol_import.html
+++ b/docs/reference/opal.symbol_import.html
@@ -71,16 +71,16 @@ Import a tibble
- opal.symbol_import(
- opal,
- symbol,
- project,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)
+ opal.symbol_import(
+ opal,
+ symbol,
+ project,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)
@@ -128,11 +128,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_import(o, 'D', 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_import(o, 'D', 'test')
+opal.logout(o)
+}
@@ -147,7 +147,7 @@ Examples
diff --git a/docs/reference/opal.symbol_rm.html b/docs/reference/opal.symbol_rm.html
index d0cfd696..6d16a689 100644
--- a/docs/reference/opal.symbol_rm.html
+++ b/docs/reference/opal.symbol_rm.html
@@ -69,7 +69,7 @@ Remove a R symbol
- opal.symbol_rm(opal, symbol)
+ opal.symbol_rm(opal, symbol)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_rm(o, 'D')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.symbol_save.html b/docs/reference/opal.symbol_save.html
index f2a900f1..79035aa9 100644
--- a/docs/reference/opal.symbol_save.html
+++ b/docs/reference/opal.symbol_save.html
@@ -69,7 +69,7 @@ Save a tibble
- opal.symbol_save(opal, symbol, destination)
+ opal.symbol_save(opal, symbol, destination)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_save(o, 'D', 'test.sav')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_save(o, 'D', 'test.sav')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.symbols.html b/docs/reference/opal.symbols.html
index bb88de70..1b7894c4 100644
--- a/docs/reference/opal.symbols.html
+++ b/docs/reference/opal.symbols.html
@@ -69,7 +69,7 @@ List R symbols
- opal.symbols(opal)
+ opal.symbols(opal)
@@ -89,11 +89,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbols(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbols(o)
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/opal.table.html b/docs/reference/opal.table.html
index b4d05790..be03e321 100644
--- a/docs/reference/opal.table.html
+++ b/docs/reference/opal.table.html
@@ -69,7 +69,7 @@ Get a table of a datasource
- opal.table(opal, datasource, table, counts = FALSE)
+ opal.table(opal, datasource, table, counts = FALSE)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.table_create.html b/docs/reference/opal.table_create.html
index 44e433ba..46cf045b 100644
--- a/docs/reference/opal.table_create.html
+++ b/docs/reference/opal.table_create.html
@@ -73,7 +73,7 @@ Create an Opal table or view
- opal.table_create(opal, project, table, type = "Participant", tables = NULL)
+ opal.table_create(opal, project, table, type = "Participant", tables = NULL)
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_delete(),
@@ -122,15 +123,15 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a raw table
-opal.table_create(o, "CNSIM", "CNSIM4")
-# make a view
-opal.table_create(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a raw table
+opal.table_create(o, "CNSIM", "CNSIM4")
+# make a view
+opal.table_create(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
@@ -145,7 +146,7 @@ Examples
diff --git a/docs/reference/opal.table_delete.html b/docs/reference/opal.table_delete.html
index 778f2343..cba12a39 100644
--- a/docs/reference/opal.table_delete.html
+++ b/docs/reference/opal.table_delete.html
@@ -71,7 +71,7 @@ Delete a Opal table
- opal.table_delete(opal, project, table, silent = TRUE)
+ opal.table_delete(opal, project, table, silent = TRUE)
@@ -95,6 +95,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,11 +116,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_delete(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_delete(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -134,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.table_dictionary_get.html b/docs/reference/opal.table_dictionary_get.html
index 95a5c21a..59126cc2 100644
--- a/docs/reference/opal.table_dictionary_get.html
+++ b/docs/reference/opal.table_dictionary_get.html
@@ -69,7 +69,7 @@ Get the dictionary of a Opal table
- opal.table_dictionary_get(opal, project, table)
+ opal.table_dictionary_get(opal, project, table)
@@ -89,6 +89,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -109,11 +110,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -128,7 +129,7 @@ Examples
diff --git a/docs/reference/opal.table_dictionary_update.html b/docs/reference/opal.table_dictionary_update.html
index c2e5bfc5..090a7d91 100644
--- a/docs/reference/opal.table_dictionary_update.html
+++ b/docs/reference/opal.table_dictionary_update.html
@@ -69,13 +69,13 @@ Update the dictionary of a Opal table
- opal.table_dictionary_update(
- opal,
- project,
- table,
- variables,
- categories = NULL
-)
+ opal.table_dictionary_update(
+ opal,
+ project,
+ table,
+ variables,
+ categories = NULL
+)
@@ -104,6 +104,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -124,23 +125,23 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-variables <- tibble::tribble(
- ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
- "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
- "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
- "disp", "decimal", "Disp label", NA, NA, 1, 3
-)
-categories <- tibble::tribble(
- ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
- "cyl", "4", 0, "Four", "Quatre",
- "cyl", "6", 0, "Six", "Six",
- "cyl", "8", 1, "Height", "Huit"
-)
-opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+variables <- tibble::tribble(
+ ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
+ "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
+ "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
+ "disp", "decimal", "Disp label", NA, NA, 1, 3
+)
+categories <- tibble::tribble(
+ ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
+ "cyl", "4", 0, "Four", "Quatre",
+ "cyl", "6", 0, "Six", "Six",
+ "cyl", "8", 1, "Height", "Huit"
+)
+opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
+opal.logout(o)
+}
@@ -155,7 +156,7 @@ Examples
diff --git a/docs/reference/opal.table_exists.html b/docs/reference/opal.table_exists.html
index 10649da8..e4ac20bb 100644
--- a/docs/reference/opal.table_exists.html
+++ b/docs/reference/opal.table_exists.html
@@ -71,7 +71,7 @@ Check a Opal table exists
- opal.table_exists(opal, project, table, view = NA)
+ opal.table_exists(opal, project, table, view = NA)
@@ -96,6 +96,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -116,16 +117,16 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# check table exists
-opal.table_exists(o, "CNSIM", "CNSIM1")
-# check table exists AND is a NOT a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
-# check table exists AND is a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# check table exists
+opal.table_exists(o, "CNSIM", "CNSIM1")
+# check table exists AND is a NOT a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
+# check table exists AND is a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
+opal.logout(o)
+}
@@ -140,7 +141,7 @@ Examples
diff --git a/docs/reference/opal.table_export.html b/docs/reference/opal.table_export.html
index f5eb8c76..5110bb07 100644
--- a/docs/reference/opal.table_export.html
+++ b/docs/reference/opal.table_export.html
@@ -73,15 +73,15 @@ Export a table as a file
- opal.table_export(
- opal,
- project,
- table,
- file,
- identifiers = NULL,
- id.name = "id",
- wait = TRUE
-)
+ opal.table_export(
+ opal,
+ project,
+ table,
+ file,
+ identifiers = NULL,
+ id.name = "id",
+ wait = TRUE
+)
@@ -120,6 +120,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -140,12 +141,12 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
- file = "/home/administrator/cnsim1.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
+ file = "/home/administrator/cnsim1.sav")
+opal.logout(o)
+}
@@ -160,7 +161,7 @@ Examples
diff --git a/docs/reference/opal.table_get.html b/docs/reference/opal.table_get.html
index 8a695e18..50b31621 100644
--- a/docs/reference/opal.table_get.html
+++ b/docs/reference/opal.table_get.html
@@ -73,14 +73,14 @@ Get a Opal table as a tibble
- opal.table_get(
- opal,
- project,
- table,
- id.name = "id",
- variables = NULL,
- missings = TRUE
-)
+ opal.table_get(
+ opal,
+ project,
+ table,
+ id.name = "id",
+ variables = NULL,
+ missings = TRUE
+)
@@ -112,6 +112,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -132,11 +133,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+opal.logout(o)
+}
@@ -151,7 +152,7 @@ Examples
diff --git a/docs/reference/opal.table_import.html b/docs/reference/opal.table_import.html
index e7a050a5..587ba457 100644
--- a/docs/reference/opal.table_import.html
+++ b/docs/reference/opal.table_import.html
@@ -77,17 +77,17 @@ Import a file as table
- opal.table_import(
- opal,
- file,
- project,
- table,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)
+ opal.table_import(
+ opal,
+ file,
+ project,
+ table,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)
@@ -131,6 +131,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -151,11 +152,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
+opal.logout(o)
+}
@@ -170,7 +171,7 @@ Examples
diff --git a/docs/reference/opal.table_perm.html b/docs/reference/opal.table_perm.html
index d6ebf2a3..b007ebba 100644
--- a/docs/reference/opal.table_perm.html
+++ b/docs/reference/opal.table_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a table
- opal.table_perm(opal, project, table)
+ opal.table_perm(opal, project, table)
@@ -95,6 +95,7 @@ Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,13 +116,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -136,7 +137,7 @@ Examples
diff --git a/docs/reference/opal.table_perm_add.html b/docs/reference/opal.table_perm_add.html
index dcd7c7bc..0a6d3975 100644
--- a/docs/reference/opal.table_perm_add.html
+++ b/docs/reference/opal.table_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on a table
- opal.table_perm_add(opal, project, table, subject, type = "user", permission)
+ opal.table_perm_add(opal, project, table, subject, type = "user", permission)
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -143,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.table_perm_delete.html b/docs/reference/opal.table_perm_delete.html
index 8b9b72de..940dd6c6 100644
--- a/docs/reference/opal.table_perm_delete.html
+++ b/docs/reference/opal.table_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a table
- opal.table_perm_delete(opal, project, table, subject, type = "user")
+ opal.table_perm_delete(opal, project, table, subject, type = "user")
@@ -97,6 +97,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -117,13 +118,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -138,7 +139,7 @@ Examples
diff --git a/docs/reference/opal.table_save.html b/docs/reference/opal.table_save.html
index 99d85274..b60ae4ab 100644
--- a/docs/reference/opal.table_save.html
+++ b/docs/reference/opal.table_save.html
@@ -71,18 +71,18 @@ Save a local tibble as a Opal table
- opal.table_save(
- opal,
- tibble,
- project,
- table,
- overwrite = TRUE,
- force = FALSE,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant"
-)
+ opal.table_save(
+ opal,
+ tibble,
+ project,
+ table,
+ overwrite = TRUE,
+ force = FALSE,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant"
+)
@@ -142,6 +142,7 @@ Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -162,15 +163,15 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-# do some (meta)data transformations, then save in opal's database
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
-# or overwrite data only (keep original data dictionary)
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+# do some (meta)data transformations, then save in opal's database
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
+# or overwrite data only (keep original data dictionary)
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
+opal.logout(o)
+}
@@ -185,7 +186,7 @@ Examples
diff --git a/docs/reference/opal.table_truncate.html b/docs/reference/opal.table_truncate.html
index 13487c0d..41394336 100644
--- a/docs/reference/opal.table_truncate.html
+++ b/docs/reference/opal.table_truncate.html
@@ -71,7 +71,7 @@ Truncate a Opal table
- opal.table_truncate(opal, project, table)
+ opal.table_truncate(opal, project, table)
@@ -91,6 +91,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -111,11 +112,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_truncate(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_truncate(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -130,7 +131,7 @@ Examples
diff --git a/docs/reference/opal.table_view_create.html b/docs/reference/opal.table_view_create.html
index 9b40db41..704d8e1c 100644
--- a/docs/reference/opal.table_view_create.html
+++ b/docs/reference/opal.table_view_create.html
@@ -73,7 +73,7 @@ Create an Opal view over tables
- opal.table_view_create(opal, project, table, tables, type = "Participant")
+ opal.table_view_create(opal, project, table, tables, type = "Participant")
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
@@ -143,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.table_view_update.html b/docs/reference/opal.table_view_update.html
index c4892e57..edf8750f 100644
--- a/docs/reference/opal.table_view_update.html
+++ b/docs/reference/opal.table_view_update.html
@@ -73,7 +73,7 @@ Update the table references and the entity filter of an Opal view
- opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
+ opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
@@ -101,6 +101,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -121,28 +122,28 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1"))
-
-# update the table references
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-
-# update the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
-
-# remove the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
-
-# update both the table references and the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
- where = "$('LAB_TSC').ge(5)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1"))
+
+# update the table references
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+
+# update the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
+
+# remove the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
+
+# update both the table references and the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
+ where = "$('LAB_TSC').ge(5)")
+opal.logout(o)
+}
@@ -157,7 +158,7 @@ Examples
diff --git a/docs/reference/opal.tables.html b/docs/reference/opal.tables.html
index da771ccc..3523f1ce 100644
--- a/docs/reference/opal.tables.html
+++ b/docs/reference/opal.tables.html
@@ -69,7 +69,7 @@ Get tables of a datasource
- opal.tables(opal, datasource, counts = FALSE, df = TRUE)
+ opal.tables(opal, datasource, counts = FALSE, df = TRUE)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables(o, 'CNSIM')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm.html b/docs/reference/opal.tables_perm.html
index e401969e..eaf76e27 100644
--- a/docs/reference/opal.tables_perm.html
+++ b/docs/reference/opal.tables_perm.html
@@ -69,7 +69,7 @@ Get the permissions on any table of a project
- opal.tables_perm(opal, project)
+ opal.tables_perm(opal, project)
@@ -91,13 +91,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm_add.html b/docs/reference/opal.tables_perm_add.html
index f9f318fe..34f1092b 100644
--- a/docs/reference/opal.tables_perm_add.html
+++ b/docs/reference/opal.tables_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on any table of a project
- opal.tables_perm_add(opal, project, subject, type = "user", permission)
+ opal.tables_perm_add(opal, project, subject, type = "user", permission)
@@ -97,13 +97,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm_delete.html b/docs/reference/opal.tables_perm_delete.html
index 58317fa1..c6c2bbb4 100644
--- a/docs/reference/opal.tables_perm_delete.html
+++ b/docs/reference/opal.tables_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from any table of a project
- opal.tables_perm_delete(opal, project, subject, type = "user")
+ opal.tables_perm_delete(opal, project, subject, type = "user")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/opal.task.html b/docs/reference/opal.task.html
index 5f63c0bb..9f2abe58 100644
--- a/docs/reference/opal.task.html
+++ b/docs/reference/opal.task.html
@@ -69,7 +69,7 @@ Get a task
- opal.task(opal, id)
+ opal.task(opal, id)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task(o, '1')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.task_cancel.html b/docs/reference/opal.task_cancel.html
index 4d2f68ff..a6d3af66 100644
--- a/docs/reference/opal.task_cancel.html
+++ b/docs/reference/opal.task_cancel.html
@@ -69,7 +69,7 @@ Cancel a task
- opal.task_cancel(opal, id)
+ opal.task_cancel(opal, id)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_cancel(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_cancel(o, '1')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.task_wait.html b/docs/reference/opal.task_wait.html
index e46c9ad1..c75baf8d 100644
--- a/docs/reference/opal.task_wait.html
+++ b/docs/reference/opal.task_wait.html
@@ -69,7 +69,7 @@ Wait for a task to complete.
- opal.task_wait(opal, id, max = NULL)
+ opal.task_wait(opal, id, max = NULL)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_wait(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_wait(o, '1')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.tasks.html b/docs/reference/opal.tasks.html
index b03cca25..bbc1909c 100644
--- a/docs/reference/opal.tasks.html
+++ b/docs/reference/opal.tasks.html
@@ -69,7 +69,7 @@ Get the tasks
- opal.tasks(opal, df = TRUE)
+ opal.tasks(opal, df = TRUE)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tasks(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tasks(o)
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.taxonomies.html b/docs/reference/opal.taxonomies.html
index 6eb7c9fc..7fdeb65c 100644
--- a/docs/reference/opal.taxonomies.html
+++ b/docs/reference/opal.taxonomies.html
@@ -71,7 +71,7 @@ Get taxonomies
- opal.taxonomies(opal, locale = "en", df = TRUE)
+ opal.taxonomies(opal, locale = "en", df = TRUE)
@@ -102,11 +102,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomies(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomies(o)
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy.html b/docs/reference/opal.taxonomy.html
index 588356cb..830f2f20 100644
--- a/docs/reference/opal.taxonomy.html
+++ b/docs/reference/opal.taxonomy.html
@@ -69,7 +69,7 @@ Get a taxonomy
- opal.taxonomy(opal, taxonomy)
+ opal.taxonomy(opal, taxonomy)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_delete.html b/docs/reference/opal.taxonomy_delete.html
index 56a28d51..16c5fe75 100644
--- a/docs/reference/opal.taxonomy_delete.html
+++ b/docs/reference/opal.taxonomy_delete.html
@@ -69,7 +69,7 @@ Delete a taxonomy
- opal.taxonomy_delete(opal, taxonomy)
+ opal.taxonomy_delete(opal, taxonomy)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_delete(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_delete(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_download.html b/docs/reference/opal.taxonomy_download.html
index bde9b7cc..72ddba73 100644
--- a/docs/reference/opal.taxonomy_download.html
+++ b/docs/reference/opal.taxonomy_download.html
@@ -69,7 +69,7 @@ Download a taxonomy file
- opal.taxonomy_download(opal, taxonomy, destination = NULL)
+ opal.taxonomy_download(opal, taxonomy, destination = NULL)
@@ -101,11 +101,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_upload.html b/docs/reference/opal.taxonomy_upload.html
index f64a1c9c..33aa2918 100644
--- a/docs/reference/opal.taxonomy_upload.html
+++ b/docs/reference/opal.taxonomy_upload.html
@@ -71,7 +71,7 @@ Upload a taxonomy file
- opal.taxonomy_upload(opal, path)
+ opal.taxonomy_upload(opal, path)
@@ -98,11 +98,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/opal.terms.html b/docs/reference/opal.terms.html
index 42d3ba1c..4514444d 100644
--- a/docs/reference/opal.terms.html
+++ b/docs/reference/opal.terms.html
@@ -69,7 +69,7 @@ Get the terms of a vocabulary
- opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
+ opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/opal.token.html b/docs/reference/opal.token.html
index 139cfb7f..2b23254c 100644
--- a/docs/reference/opal.token.html
+++ b/docs/reference/opal.token.html
@@ -71,7 +71,7 @@ Get a personal access token
- opal.token(opal, name)
+ opal.token(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_datashield_create.html b/docs/reference/opal.token_datashield_create.html
index 3eb7cd13..2f127a6b 100644
--- a/docs/reference/opal.token_datashield_create.html
+++ b/docs/reference/opal.token_datashield_create.html
@@ -71,7 +71,7 @@ Create a personal access token for Datashield usage
- opal.token_datashield_create(opal, name, projects = NULL)
+ opal.token_datashield_create(opal, name, projects = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_datashield_create(o, 'ds-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_datashield_create(o, 'ds-1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.token_delete.html b/docs/reference/opal.token_delete.html
index 780eb5ed..402a3d26 100644
--- a/docs/reference/opal.token_delete.html
+++ b/docs/reference/opal.token_delete.html
@@ -71,7 +71,7 @@ Delete a personal access token
- opal.token_delete(opal, name)
+ opal.token_delete(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_delete(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_delete(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_r_create.html b/docs/reference/opal.token_r_create.html
index b0b36787..c8222189 100644
--- a/docs/reference/opal.token_r_create.html
+++ b/docs/reference/opal.token_r_create.html
@@ -71,13 +71,13 @@ Create a personal access token for R usage
- opal.token_r_create(
- opal,
- name,
- projects = NULL,
- access = NULL,
- commands = c("export")
-)
+ opal.token_r_create(
+ opal,
+ name,
+ projects = NULL,
+ access = NULL,
+ commands = c("export")
+)
@@ -121,11 +121,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
+opal.logout(o)
+}
@@ -140,7 +140,7 @@ Examples
diff --git a/docs/reference/opal.token_renew.html b/docs/reference/opal.token_renew.html
index 72208339..e11a4f33 100644
--- a/docs/reference/opal.token_renew.html
+++ b/docs/reference/opal.token_renew.html
@@ -71,7 +71,7 @@ Renew an inactive personal access token
- opal.token_renew(opal, name)
+ opal.token_renew(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_renew(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_renew(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_sql_create.html b/docs/reference/opal.token_sql_create.html
index b618980e..d65e177c 100644
--- a/docs/reference/opal.token_sql_create.html
+++ b/docs/reference/opal.token_sql_create.html
@@ -71,7 +71,7 @@ Create a personal access token for SQL usage
- opal.token_sql_create(opal, name, projects = NULL)
+ opal.token_sql_create(opal, name, projects = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_sql_create(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_sql_create(o, 'sql-1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.tokens.html b/docs/reference/opal.tokens.html
index 59d4edfa..703771e5 100644
--- a/docs/reference/opal.tokens.html
+++ b/docs/reference/opal.tokens.html
@@ -71,7 +71,7 @@ Get the personal access tokens
- opal.tokens(opal, df = TRUE)
+ opal.tokens(opal, df = TRUE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tokens(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tokens(o)
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.unload_package.html b/docs/reference/opal.unload_package.html
index cb7ded42..6b5ebac0 100644
--- a/docs/reference/opal.unload_package.html
+++ b/docs/reference/opal.unload_package.html
@@ -69,7 +69,7 @@ Unload package
- opal.unload_package(opal, pkg)
+ opal.unload_package(opal, pkg)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.unload_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.unload_package(o, 'stats')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.valueset.html b/docs/reference/opal.valueset.html
index 7bbd50a4..d0c5c00a 100644
--- a/docs/reference/opal.valueset.html
+++ b/docs/reference/opal.valueset.html
@@ -69,7 +69,7 @@ Get the values of an entity
- opal.valueset(opal, datasource, table, identifier)
+ opal.valueset(opal, datasource, table, identifier)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.variable.html b/docs/reference/opal.variable.html
index 3e2e9155..2269ea5d 100644
--- a/docs/reference/opal.variable.html
+++ b/docs/reference/opal.variable.html
@@ -69,7 +69,7 @@ Get a variable of a table
- opal.variable(opal, datasource, table, variable)
+ opal.variable(opal, datasource, table, variable)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.variable_summary.html b/docs/reference/opal.variable_summary.html
index 75fda252..5686692d 100644
--- a/docs/reference/opal.variable_summary.html
+++ b/docs/reference/opal.variable_summary.html
@@ -69,14 +69,14 @@ Get summary statistics of a variable of a table
- opal.variable_summary(
- opal,
- datasource,
- table,
- variable,
- cached = TRUE,
- nature = NULL
-)
+ opal.variable_summary(
+ opal,
+ datasource,
+ table,
+ variable,
+ cached = TRUE,
+ nature = NULL
+)
@@ -124,11 +124,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
@@ -143,7 +143,7 @@ Examples
diff --git a/docs/reference/opal.variables.html b/docs/reference/opal.variables.html
index e1072df8..3ea90c87 100644
--- a/docs/reference/opal.variables.html
+++ b/docs/reference/opal.variables.html
@@ -69,7 +69,7 @@ Get variables of a table
- opal.variables(opal, datasource, table, locale = "en", df = TRUE)
+ opal.variables(opal, datasource, table, locale = "en", df = TRUE)
@@ -111,11 +111,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variables(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variables(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.version_compare.html b/docs/reference/opal.version_compare.html
index f9a8bc44..b8a11b96 100644
--- a/docs/reference/opal.version_compare.html
+++ b/docs/reference/opal.version_compare.html
@@ -71,7 +71,7 @@ Compare
- opal.version_compare(opal, version)
+ opal.version_compare(opal, version)
@@ -93,11 +93,11 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.version_compare(o, "2.6.0")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.version_compare(o, "2.6.0")
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.vocabularies.html b/docs/reference/opal.vocabularies.html
index 2a4ae4ac..edaf165e 100644
--- a/docs/reference/opal.vocabularies.html
+++ b/docs/reference/opal.vocabularies.html
@@ -69,7 +69,7 @@ Get the vocabularies of a taxonomy
- opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
+ opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabularies(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabularies(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.vocabulary.html b/docs/reference/opal.vocabulary.html
index 8dd847d4..18c471f7 100644
--- a/docs/reference/opal.vocabulary.html
+++ b/docs/reference/opal.vocabulary.html
@@ -69,7 +69,7 @@ Get a taxonomy vocabulary
- opal.vocabulary(opal, taxonomy, vocabulary)
+ opal.vocabulary(opal, taxonomy, vocabulary)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.workspace_restore.html b/docs/reference/opal.workspace_restore.html
index 192c945b..705b823a 100644
--- a/docs/reference/opal.workspace_restore.html
+++ b/docs/reference/opal.workspace_restore.html
@@ -69,7 +69,7 @@ Restore a R workspace from a opal.
- opal.workspace_restore(opal, ws)
+ opal.workspace_restore(opal, ws)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_restore(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_restore(o, 'test')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.workspace_rm.html b/docs/reference/opal.workspace_rm.html
index e33cf1d2..4bce81f9 100644
--- a/docs/reference/opal.workspace_rm.html
+++ b/docs/reference/opal.workspace_rm.html
@@ -69,7 +69,7 @@ Remove a R workspace from a opal.
- opal.workspace_rm(opal, ws, user = NULL)
+ opal.workspace_rm(opal, ws, user = NULL)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_rm(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_rm(o, 'test')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.workspace_save.html b/docs/reference/opal.workspace_save.html
index 074274e0..aa974933 100644
--- a/docs/reference/opal.workspace_save.html
+++ b/docs/reference/opal.workspace_save.html
@@ -69,7 +69,7 @@ Save the current session in a opal R workspace.
- opal.workspace_save(opal, save = TRUE)
+ opal.workspace_save(opal, save = TRUE)
@@ -98,14 +98,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# provide a workspace ID
-opal.workspace_save(o, 'test')
-# or use default one
-id <- opal.workspace_save(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# provide a workspace ID
+opal.workspace_save(o, 'test')
+# or use default one
+id <- opal.workspace_save(o)
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.workspaces.html b/docs/reference/opal.workspaces.html
index 83f92fdc..f4b0c155 100644
--- a/docs/reference/opal.workspaces.html
+++ b/docs/reference/opal.workspaces.html
@@ -69,7 +69,7 @@ Get the R workspaces from a opal.
- opal.workspaces(opal)
+ opal.workspaces(opal)
@@ -88,11 +88,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspaces(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspaces(o)
+opal.logout(o)
+}
@@ -107,7 +107,7 @@ Examples
diff --git a/docs/reference/opalr-package.html b/docs/reference/opalr-package.html
index acf0539c..7a3957ef 100644
--- a/docs/reference/opalr-package.html
+++ b/docs/reference/opalr-package.html
@@ -99,7 +99,7 @@ Author
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index db0185af..5d5b6ce2 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -123,6 +123,12 @@
/reference/dot-verbose.html
+
+ /reference/dsadmin.activity.html
+
+
+ /reference/dsadmin.activity_summary.html
+
/reference/dsadmin.get_method.html
@@ -144,6 +150,9 @@
/reference/dsadmin.installed_package.html
+
+ /reference/dsadmin.log.html
+
/reference/dsadmin.package_description.html
@@ -231,6 +240,12 @@
/reference/index.html
+
+ /reference/oadmin.activity.html
+
+
+ /reference/oadmin.activity_summary.html
+
/reference/oadmin.install_bioconductor_package.html
@@ -258,6 +273,15 @@
/reference/oadmin.installed_packages.html
+
+ /reference/oadmin.log.html
+
+
+ /reference/oadmin.log_rest.html
+
+
+ /reference/oadmin.log_sql.html
+
/reference/oadmin.package_description.html
@@ -426,6 +450,9 @@
/reference/opal.logout.html
+
+ /reference/opal.perms.html
+
/reference/opal.post.html
opal-rsession.Rmd
-library(opalr)
-o <- opal.login("administrator", "password", "https://opal-demo.obiba.org", profile = "default")library(opalr)
+o <- opal.login("administrator", "password", "https://opal-demo.obiba.org", profile = "default")
Assign
@@ -127,42 +127,42 @@ Assign
Assign a Opal table to a data.frame (if user has permission to see values of the Opal table):
-opal.assign.table(o, symbol = "df", value = "CNSIM.CNSIM1")opal.assign.table(o, symbol = "df", value = "CNSIM.CNSIM1")
-opal.assign.table.tibble(o, symbol = "tbl", value = "CNSIM.CNSIM1")
-opal.assign.resource(o, symbol = "rsrc", value = "RSRC.CNSIM3")quote() to not interpret the expression in the client side
R session). As an example assign a function body:
-opal.assign.script(o, symbol = "hello", value = quote(function(x) { paste0("Hello ", x, "!") }))
-opal.symbols(o)Execute
R expressions can be executed on the server side:
-# column names
-opal.execute(o, script = "names(tbl)")
-# get variable description from column attributes
-opal.execute(o, script = "attributes(tbl$GENDER)")
-# coerce resource to a data.frame and plot histogram of one column
-plot(opal.execute(o, script = "hist(as.data.frame(rsrc)$LAB_HDL)"))
-# execute the custom function
-opal.execute(o, script = "hello('friends')")# column names
+opal.execute(o, script = "names(tbl)")
+# get variable description from column attributes
+opal.execute(o, script = "attributes(tbl$GENDER)")
+# coerce resource to a data.frame and plot histogram of one column
+plot(opal.execute(o, script = "hist(as.data.frame(rsrc)$LAB_HDL)"))
+# execute the custom function
+opal.execute(o, script = "hello('friends')")
-GENDER <- opal.execute(o, script = "tbl$GENDER")
-opal.execute.source(o, path = "/path/to/some_code.R")Files
@@ -170,11 +170,11 @@ Files
Files can be written from the Opal file system to the R server session folder:
-opal.file_write(o, source = "/projects/CNSIM/CNSIM3.zip", "test.zip")opal.file_write(o, source = "/projects/CNSIM/CNSIM3.zip", "test.zip")
-opal.file_read(o, source = "test.zip", destination = "/tmp")Teardown
@@ -191,7 +191,7 @@ TeardownGood practice is to free server resources by sending a logout
request:
-opal.logout(o)
+opal.logout(o)
-opal.logout(o)opal.logout(o)Site built with pkgdown 2.0.6.
+Site built with pkgdown 2.0.7.
diff --git a/docs/authors.html b/docs/authors.html index e777bdac..a50c4cbc 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -117,7 +117,7 @@Citation
diff --git a/docs/index.html b/docs/index.html index c90832dc..05f8608f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -95,27 +95,27 @@
-
+
@@ -190,7 +184,7 @@
Opal R Client for the Opal data warehouse. Most of the web services of Opal can be reached by an opalr function: import/export, data dictionaries, projects, tables, resources, permissions, users, DataSHIELD profiles etc.
See opalr documentation.
Installation:
-# install from CRAN
-install.packages("opalr")
-
-# or install latest development version
-remotes::install_github("obiba/opalr")# install from CRAN
+install.packages("opalr")
+
+# or install latest development version
+remotes::install_github("obiba/opalr")Basic usage:
-library(opalr)
-o <- opal.login('administrator', 'password', url = 'https://opal-demo.obiba.org')
-
-# assign a table (as a data.frame) to a R symbol
-opal.assign(o, 'D', 'CNSIM.CNSIM1')
-
-# perform R operations on the server side
-opal.execute(o, 'summary(D$GENDER)')
-opal.execute(o, 'summary(D$LAB_GLUC)')
-
-opal.logout(o)library(opalr)
+o <- opal.login('administrator', 'password', url = 'https://opal-demo.obiba.org')
+
+# assign a table (as a data.frame) to a R symbol
+opal.assign(o, 'D', 'CNSIM.CNSIM1')
+
+# perform R operations on the server side
+opal.execute(o, 'summary(D$GENDER)')
+opal.execute(o, 'summary(D$LAB_GLUC)')
+
+opal.logout(o)
-
+
Dev status
--
-
-
-
Dev status
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 384d3091..5adc2f4d 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,10 +1,10 @@ -pandoc: 2.19.2 -pkgdown: 2.0.6 +pandoc: 3.1.1 +pkgdown: 2.0.7 pkgdown_sha: ~ articles: datashield-admin: datashield-admin.html opal-files: opal-files.html opal-projects: opal-projects.html opal-rsession: opal-rsession.html -last_built: 2023-02-03T12:50Z +last_built: 2023-12-20T07:25Z diff --git a/docs/reference/dictionary.annotate.harmo_status.html b/docs/reference/dictionary.annotate.harmo_status.html index ff50a785..90a2c2bd 100644 --- a/docs/reference/dictionary.annotate.harmo_status.html +++ b/docs/reference/dictionary.annotate.harmo_status.html @@ -71,7 +71,7 @@Set variable annotation with Harmonization Status term
-
+
dictionary.annotate.harmo_status(tibble, variables = NULL, status)dictionary.annotate.harmo_status(tibble, variables = NULL, status)
@@ -98,14 +98,14 @@
@@ -120,7 +120,7 @@
diff --git a/docs/reference/dictionary.annotate.html b/docs/reference/dictionary.annotate.html
index 08eeae17..fa687aeb 100644
--- a/docs/reference/dictionary.annotate.html
+++ b/docs/reference/dictionary.annotate.html
@@ -69,13 +69,13 @@ Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-cqx <- dictionary.annotate.harmo_status(cqx,
- variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"),
- status = "complete")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+cqx <- dictionary.annotate.harmo_status(cqx,
+ variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"),
+ status = "complete")
+opal.logout(o)
+}
Examples
Set variable annotation with a taxonomy term
-
+
dictionary.annotate(
- tibble,
- variables = NULL,
- taxonomy = "Mlstr_area",
- vocabulary,
- term
-)dictionary.annotate(
+ tibble,
+ variables = NULL,
+ taxonomy = "Mlstr_area",
+ vocabulary,
+ term
+)
@@ -111,16 +111,16 @@
@@ -135,7 +135,7 @@
diff --git a/docs/reference/dictionary.annotations.html b/docs/reference/dictionary.annotations.html
index 122843f1..5f5227da 100644
--- a/docs/reference/dictionary.annotations.html
+++ b/docs/reference/dictionary.annotations.html
@@ -69,12 +69,12 @@ Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-cqx <- dictionary.annotate(cqx,
- variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"),
- taxonomy = "Mlstr_area",
- vocabulary = "Sociodemographic_economic_characteristics",
- term = "Education")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+cqx <- dictionary.annotate(cqx,
+ variables = c("A_SDC_EDU_LEVEL", "A_SDC_EDU_LEVEL_AGE"),
+ taxonomy = "Mlstr_area",
+ vocabulary = "Sociodemographic_economic_characteristics",
+ term = "Education")
+opal.logout(o)
+}
Examples
List the annotations
-
+
dictionary.annotations(
- tibble,
- variables = NULL,
- taxonomy = NULL,
- vocabulary = NULL
-)dictionary.annotations(
+ tibble,
+ variables = NULL,
+ taxonomy = NULL,
+ vocabulary = NULL
+)
@@ -105,12 +105,12 @@
@@ -125,7 +125,7 @@
diff --git a/docs/reference/dictionary.apply.html b/docs/reference/dictionary.apply.html
index 51b924fc..6440dfee 100644
--- a/docs/reference/dictionary.apply.html
+++ b/docs/reference/dictionary.apply.html
@@ -69,7 +69,7 @@ Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-annot <- dictionary.annotations(cqx, taxonomy = "Mlstr_harmo", vocabulary = "status")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+annot <- dictionary.annotations(cqx, taxonomy = "Mlstr_harmo", vocabulary = "status")
+opal.logout(o)
+}
Examples
Apply the dictionary to a tibble
-
+
dictionary.apply(tibble, variables, categories = NULL)dictionary.apply(tibble, variables, categories = NULL, merge = FALSE)
@@ -85,26 +85,30 @@ categories
merge
+
Arguments
A data frame with one row per category (columns variable and name) and then column per property/attribute.
Either append attributes to existing ones or replace them. Default is FALSE, for dictionary consistency.
Examples
-if (FALSE) {
-data <- tibble::as_tibble(mtcars)
-variables <- tibble::tribble(
- ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
- "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
- "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
- "disp", "decimal", "Disp label", NA, NA, 1, 3
-)
-categories <- tibble::tribble(
- ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
- "cyl", "4", 0, "Four", "Quatre",
- "cyl", "6", 0, "Six", "Six",
- "cyl", "8", 1, "Height", "Huit"
-)
-data <- dictionary.apply(data, variables, categories)
-}
+ if (FALSE) {
+data <- tibble::as_tibble(mtcars)
+variables <- tibble::tribble(
+ ~name, ~valueType, ~`label:en`, ~`label:fr`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
+ "mpg", "decimal", "Mpg label", "Mpg libellé", "Value1", "years", 0, 1,
+ "cyl", "decimal", "Cyl label", "Cyl libellé", "Value2", "kg/m2", 0, 2,
+ "disp", "decimal", "Disp label", "Disp libellé", NA, NA, 1, 3
+)
+categories <- tibble::tribble(
+ ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
+ "cyl", "4", 0, "Four", "Quatre",
+ "cyl", "6", 0, "Six", "Six",
+ "cyl", "8", 1, "Height", "Huit"
+)
+data <- dictionary.apply(data, variables, categories)
+}
Examples
diff --git a/docs/reference/dictionary.inspect.html b/docs/reference/dictionary.inspect.html index d0b9459d..7849106e 100644 --- a/docs/reference/dictionary.inspect.html +++ b/docs/reference/dictionary.inspect.html @@ -71,7 +71,7 @@Inspect the dictionary of a tibble
-
+
dictionary.inspect(tibble, id.name = "id", warn = TRUE)dictionary.inspect(tibble, id.name = "id", warn = TRUE)
@@ -97,34 +97,34 @@
@@ -139,7 +139,7 @@
diff --git a/docs/reference/dot-aclsToDataFrame.html b/docs/reference/dot-aclsToDataFrame.html
index 0381ab4d..2ae1faef 100644
--- a/docs/reference/dot-aclsToDataFrame.html
+++ b/docs/reference/dot-aclsToDataFrame.html
@@ -69,7 +69,7 @@ Value
Examples
-if (FALSE) {
-# prepare datasets of visits, several visits for one patient
-visits <- tibble::tribble(
-~id, ~patient_id, ~sex, ~visit_date,
-1, 1, "M", as.Date("2020-01-01"),
-2, 2, "F", as.Date("2020-01-02"),
-3, 3, "M", as.Date("2020-01-03"),
-4, 3, "M", as.Date("2020-01-04"))
-
-o <- opal.login("administrator", "password", url = "https://opal-demo.obiba.org")
-
-# save visits dataset
-opal.table_save(o, visits, "RSRC", "visits", type = "Visit", force = TRUE)
-
-# get visit and make it a dataset of patients
-patients <- opal.table_get(o, "RSRC", "visits", id.name = "id")
-# set dataset IDs
-patients$visit_id <- patients$id
-patients$id <- patients$patient_id
-patients$patient_id <- NULL
-patients
-
-# save patients dataset, there should be a warning that some variables are not repeatable
-# while there are patients with multiple data lines
-opal.table_save(o, patients, "RSRC", "patients", type = "Participant", force = TRUE)
-
-opal.logout(o)
-}
+ if (FALSE) {
+# prepare datasets of visits, several visits for one patient
+visits <- tibble::tribble(
+~id, ~patient_id, ~sex, ~visit_date,
+1, 1, "M", as.Date("2020-01-01"),
+2, 2, "F", as.Date("2020-01-02"),
+3, 3, "M", as.Date("2020-01-03"),
+4, 3, "M", as.Date("2020-01-04"))
+
+o <- opal.login("administrator", "password", url = "https://opal-demo.obiba.org")
+
+# save visits dataset
+opal.table_save(o, visits, "RSRC", "visits", type = "Visit", force = TRUE)
+
+# get visit and make it a dataset of patients
+patients <- opal.table_get(o, "RSRC", "visits", id.name = "id")
+# set dataset IDs
+patients$visit_id <- patients$id
+patients$id <- patients$patient_id
+patients$patient_id <- NULL
+patients
+
+# save patients dataset, there should be a warning that some variables are not repeatable
+# while there are patients with multiple data lines
+opal.table_save(o, patients, "RSRC", "patients", type = "Participant", force = TRUE)
+
+opal.logout(o)
+}
Examples
Permsissions (ACLs) into a data frame.
-
+
@@ -85,7 +85,7 @@ .aclsToDataFrame(perms, acls).aclsToDataFrame(perms, acls)Permsissions (ACLs) into a data frame.
diff --git a/docs/reference/dot-as.zeroOne.html b/docs/reference/dot-as.zeroOne.html index 9f8f9a3c..dabc54ad 100644 --- a/docs/reference/dot-as.zeroOne.html +++ b/docs/reference/dot-as.zeroOne.html @@ -69,7 +69,7 @@Turns a value into 0/1 numeric.
-
+
@@ -85,7 +85,7 @@ .as.zeroOne(value).as.zeroOne(value)Turns a value into 0/1 numeric.
diff --git a/docs/reference/dot-authorizationHeader.html b/docs/reference/dot-authorizationHeader.html index ede36fdb..e03112ce 100644 --- a/docs/reference/dot-authorizationHeader.html +++ b/docs/reference/dot-authorizationHeader.html @@ -69,7 +69,7 @@Constructs the value for the Authorization header
-
+
@@ -85,7 +85,7 @@ .authorizationHeader(username, password).authorizationHeader(username, password)Constructs the value for the Authorization header
diff --git a/docs/reference/dot-deparse.html b/docs/reference/dot-deparse.html index 55783b2a..e8d706e8 100644 --- a/docs/reference/dot-deparse.html +++ b/docs/reference/dot-deparse.html @@ -69,7 +69,7 @@Turn expression into character strings.
-
+
@@ -85,7 +85,7 @@ .deparse(expr).deparse(expr)Turn expression into character strings.
diff --git a/docs/reference/dot-extractJsonField.html b/docs/reference/dot-extractJsonField.html index d9a02ee7..413cef7a 100644 --- a/docs/reference/dot-extractJsonField.html +++ b/docs/reference/dot-extractJsonField.html @@ -69,7 +69,7 @@Extract JSON
-
+
@@ -85,7 +85,7 @@ .extractJsonField(json, fields = NULL, isArray = TRUE).extractJsonField(json, fields = NULL, isArray = TRUE)Extract JSON
diff --git a/docs/reference/dot-extractLabel.html b/docs/reference/dot-extractLabel.html index ccc51648..d43d866a 100644 --- a/docs/reference/dot-extractLabel.html +++ b/docs/reference/dot-extractLabel.html @@ -69,12 +69,12 @@Extract label for locale. If not found, fallback to undefined language label
- .extractLabel(
- locale = "en",
- labels = list(),
- localeKey = "locale",
- valueKey = "value"
-)
+ .extractLabel(
+ locale = "en",
+ labels = list(),
+ localeKey = "locale",
+ valueKey = "value"
+)
@@ -90,7 +90,7 @@ Extract label for locale. If not found, fallback to undefined language label
diff --git a/docs/reference/dot-extractOpalSessionId.html b/docs/reference/dot-extractOpalSessionId.html
index be99f00f..65cacd0d 100644
--- a/docs/reference/dot-extractOpalSessionId.html
+++ b/docs/reference/dot-extractOpalSessionId.html
@@ -69,7 +69,7 @@ Extract opalsid from cookie data frame.
- .extractOpalSessionId(cookies)
+ .extractOpalSessionId(cookies)
@@ -85,7 +85,7 @@ Extract opalsid from cookie data frame.
diff --git a/docs/reference/dot-getContent.html b/docs/reference/dot-getContent.html
index 26d95ecf..d81a8ab3 100644
--- a/docs/reference/dot-getContent.html
+++ b/docs/reference/dot-getContent.html
@@ -69,7 +69,7 @@ Wrapper of httr::content()
- .getContent(opal, response)
+ .getContent(opal, response)
@@ -85,7 +85,7 @@ Wrapper of httr::content()
diff --git a/docs/reference/dot-getPEMFilePath.html b/docs/reference/dot-getPEMFilePath.html
index 0601b98d..bac96b2d 100644
--- a/docs/reference/dot-getPEMFilePath.html
+++ b/docs/reference/dot-getPEMFilePath.html
@@ -69,7 +69,7 @@ Extract absolute path to the pem file
- .getPEMFilePath(pem, directory = "~/.ssh")
+ .getPEMFilePath(pem, directory = "~/.ssh")
@@ -85,7 +85,7 @@ Extract absolute path to the pem file
diff --git a/docs/reference/dot-getRSessionId.html b/docs/reference/dot-getRSessionId.html
index 2c8ffd1f..10b997f2 100644
--- a/docs/reference/dot-getRSessionId.html
+++ b/docs/reference/dot-getRSessionId.html
@@ -69,7 +69,7 @@ Extract R session Id from opal object, create a new R session if not found.<
- .getRSessionId(opal)
+ .getRSessionId(opal)
@@ -85,7 +85,7 @@ Extract R session Id from opal object, create a new R session if not found.<
diff --git a/docs/reference/dot-getSessions.html b/docs/reference/dot-getSessions.html
index 6a91fb4e..32bbbbbb 100644
--- a/docs/reference/dot-getSessions.html
+++ b/docs/reference/dot-getSessions.html
@@ -69,7 +69,7 @@ Get all R session in Opal.
- .getSessions(opal)
+ .getSessions(opal)
@@ -85,7 +85,7 @@ Get all R session in Opal.
diff --git a/docs/reference/dot-handleError.html b/docs/reference/dot-handleError.html
index 3f25f7b3..10a4a4d6 100644
--- a/docs/reference/dot-handleError.html
+++ b/docs/reference/dot-handleError.html
@@ -69,7 +69,7 @@ Handle error response
- .handleError(opal, response)
+ .handleError(opal, response)
@@ -85,7 +85,7 @@ Handle error response
diff --git a/docs/reference/dot-handleResponse.html b/docs/reference/dot-handleResponse.html
index 135a5f63..812aabe6 100644
--- a/docs/reference/dot-handleResponse.html
+++ b/docs/reference/dot-handleResponse.html
@@ -69,7 +69,7 @@ Default request response handler.
- .handleResponse(opal, response)
+ .handleResponse(opal, response)
@@ -85,7 +85,7 @@ Default request response handler.
diff --git a/docs/reference/dot-handleResponseLocation.html b/docs/reference/dot-handleResponseLocation.html
index 2aa7fa4a..1a9c550a 100644
--- a/docs/reference/dot-handleResponseLocation.html
+++ b/docs/reference/dot-handleResponseLocation.html
@@ -69,7 +69,7 @@ Default request response Location handler.
- .handleResponseLocation(opal, response)
+ .handleResponseLocation(opal, response)
@@ -85,7 +85,7 @@ Default request response Location handler.
diff --git a/docs/reference/dot-handleResponseOrCallback.html b/docs/reference/dot-handleResponseOrCallback.html
index 1c19cded..fd75863d 100644
--- a/docs/reference/dot-handleResponseOrCallback.html
+++ b/docs/reference/dot-handleResponseOrCallback.html
@@ -69,7 +69,7 @@ Process response with default handler or the provided one
- .handleResponseOrCallback(opal, response, callback = NULL)
+ .handleResponseOrCallback(opal, response, callback = NULL)
@@ -85,7 +85,7 @@ Process response with default handler or the provided one
diff --git a/docs/reference/dot-is.verbose.html b/docs/reference/dot-is.verbose.html
index f3462be7..ddaab2ed 100644
--- a/docs/reference/dot-is.verbose.html
+++ b/docs/reference/dot-is.verbose.html
@@ -69,7 +69,7 @@ Verbose option
- .is.verbose()
+ .is.verbose()
@@ -85,7 +85,7 @@ Verbose option
diff --git a/docs/reference/dot-isContentEmpty.html b/docs/reference/dot-isContentEmpty.html
index 2ca189f6..88320efd 100644
--- a/docs/reference/dot-isContentEmpty.html
+++ b/docs/reference/dot-isContentEmpty.html
@@ -69,7 +69,7 @@ Check if response content is empty.
- .isContentEmpty(content)
+ .isContentEmpty(content)
@@ -85,7 +85,7 @@ Check if response content is empty.
diff --git a/docs/reference/dot-listToJson.html b/docs/reference/dot-listToJson.html
index 9c4d2140..c0bd2195 100644
--- a/docs/reference/dot-listToJson.html
+++ b/docs/reference/dot-listToJson.html
@@ -69,7 +69,7 @@ Simple transformation function of a list into a JSON object/array.
- .listToJson(l)
+ .listToJson(l)
@@ -85,7 +85,7 @@ Simple transformation function of a list into a JSON object/array.
diff --git a/docs/reference/dot-newProgress.html b/docs/reference/dot-newProgress.html
index cdfa936f..c801ff16 100644
--- a/docs/reference/dot-newProgress.html
+++ b/docs/reference/dot-newProgress.html
@@ -69,12 +69,12 @@ Create a new progress instance with default settings.
- .newProgress(
- format = " :what [:bar] :percent /:elapsed",
- clear = getOption("opal.progress.clear", FALSE),
- total,
- width = 100
-)
+ .newProgress(
+ format = " :what [:bar] :percent /:elapsed",
+ clear = getOption("opal.progress.clear", FALSE),
+ total,
+ width = 100
+)
@@ -90,7 +90,7 @@ Create a new progress instance with default settings.
diff --git a/docs/reference/dot-newSession.html b/docs/reference/dot-newSession.html
index a3d04f33..b15cdaa4 100644
--- a/docs/reference/dot-newSession.html
+++ b/docs/reference/dot-newSession.html
@@ -69,7 +69,7 @@ Create a new R session in Opal.
- .newSession(opal, restore = NULL, profile = NULL)
+ .newSession(opal, restore = NULL, profile = NULL)
@@ -85,7 +85,7 @@ Create a new R session in Opal.
diff --git a/docs/reference/dot-opal.login.html b/docs/reference/dot-opal.login.html
index cf5be580..a2d29cf6 100644
--- a/docs/reference/dot-opal.login.html
+++ b/docs/reference/dot-opal.login.html
@@ -69,15 +69,15 @@ Create the opal object
- .opal.login(
- username,
- password,
- token,
- url,
- opts = list(),
- profile = profile,
- restore = NULL
-)
+ .opal.login(
+ username,
+ password,
+ token,
+ url,
+ opts = list(),
+ profile = profile,
+ restore = NULL
+)
@@ -93,7 +93,7 @@ Create the opal object
diff --git a/docs/reference/dot-rmOpalSession.html b/docs/reference/dot-rmOpalSession.html
index bfd20a01..a29f9e94 100644
--- a/docs/reference/dot-rmOpalSession.html
+++ b/docs/reference/dot-rmOpalSession.html
@@ -69,7 +69,7 @@ Remove a Opal session (logout)
- .rmOpalSession(opal)
+ .rmOpalSession(opal)
@@ -85,7 +85,7 @@ Remove a Opal session (logout)
diff --git a/docs/reference/dot-rmRSession.html b/docs/reference/dot-rmRSession.html
index b521882a..827d5ccb 100644
--- a/docs/reference/dot-rmRSession.html
+++ b/docs/reference/dot-rmRSession.html
@@ -69,7 +69,7 @@ Remove a R session from Opal.
- .rmRSession(opal, save = FALSE)
+ .rmRSession(opal, save = FALSE)
@@ -85,7 +85,7 @@ Remove a R session from Opal.
diff --git a/docs/reference/dot-select.html b/docs/reference/dot-select.html
index 43f6c002..13df65cb 100644
--- a/docs/reference/dot-select.html
+++ b/docs/reference/dot-select.html
@@ -69,7 +69,7 @@ Returns a list r such that r[[i]] == l[[i]][field] for all i:length(l)
- .select(l, field)
+ .select(l, field)
@@ -85,7 +85,7 @@ Returns a list r such that r[[i]] == l[[i]][field] for all i:length(l)
diff --git a/docs/reference/dot-tickProgress.html b/docs/reference/dot-tickProgress.html
index 46e06caa..0777056f 100644
--- a/docs/reference/dot-tickProgress.html
+++ b/docs/reference/dot-tickProgress.html
@@ -69,7 +69,7 @@ Output the progress status if option "datashield.progress" is allows to.
@@ -85,7 +85,7 @@ Output the progress status if option "datashield.progress" is allows to.
diff --git a/docs/reference/dot-tokenHeader.html b/docs/reference/dot-tokenHeader.html
index e6d91a46..a6265701 100644
--- a/docs/reference/dot-tokenHeader.html
+++ b/docs/reference/dot-tokenHeader.html
@@ -69,7 +69,7 @@ Constructs the value for the X-Opal-Auth header
- .tokenHeader(token)
+ .tokenHeader(token)
@@ -85,7 +85,7 @@ Constructs the value for the X-Opal-Auth header
diff --git a/docs/reference/dot-url.html b/docs/reference/dot-url.html
index 6f7da3b7..41bd1de4 100644
--- a/docs/reference/dot-url.html
+++ b/docs/reference/dot-url.html
@@ -69,7 +69,7 @@ Utility method to build urls. Concatenates all arguments and adds a '/' sepa
- .url(opal, ...)
+ .url(opal, ...)
@@ -85,7 +85,7 @@ Utility method to build urls. Concatenates all arguments and adds a '/' sepa
diff --git a/docs/reference/dot-verbose.html b/docs/reference/dot-verbose.html
index f47a65e5..3cf22c86 100644
--- a/docs/reference/dot-verbose.html
+++ b/docs/reference/dot-verbose.html
@@ -69,7 +69,7 @@ Verbose flag
- .verbose()
+ .verbose()
@@ -85,7 +85,7 @@ Verbose flag
diff --git a/docs/reference/dsadmin.activity.html b/docs/reference/dsadmin.activity.html
new file mode 100644
index 00000000..a0d1cc75
--- /dev/null
+++ b/docs/reference/dsadmin.activity.html
@@ -0,0 +1,146 @@
+
+Get DataSHIELD activity — dsadmin.activity • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded DataSHIELD session metrics.
+
+
+
+ dsadmin.activity(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+dsadmin.activity(o)
+# user and profile specific session metrics
+dsadmin.activity(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+dsadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.activity_summary.html b/docs/reference/dsadmin.activity_summary.html
new file mode 100644
index 00000000..c291b9fe
--- /dev/null
+++ b/docs/reference/dsadmin.activity_summary.html
@@ -0,0 +1,146 @@
+
+Get DataSHIELD activity summary — dsadmin.activity_summary • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded DataSHIELD session metrics, grouped by profile and user.
+
+
+
+ dsadmin.activity_summary(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+dsadmin.activity_summary(o)
+# user and profile specific session metrics
+dsadmin.activity_summary(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+dsadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.get_method.html b/docs/reference/dsadmin.get_method.html
index 35d8bada..7e0286ab 100644
--- a/docs/reference/dsadmin.get_method.html
+++ b/docs/reference/dsadmin.get_method.html
@@ -69,7 +69,7 @@ Get a DataSHIELD method
- dsadmin.get_method(opal, name, type = "aggregate", profile = NULL)
+ dsadmin.get_method(opal, name, type = "aggregate", profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_method(o, 'class')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_method(o, 'class')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.get_methods.html b/docs/reference/dsadmin.get_methods.html
index eb9d116f..332bd2e6 100644
--- a/docs/reference/dsadmin.get_methods.html
+++ b/docs/reference/dsadmin.get_methods.html
@@ -69,7 +69,7 @@ Get DataSHIELD methods
- dsadmin.get_methods(opal, type = "aggregate", profile = NULL)
+ dsadmin.get_methods(opal, type = "aggregate", profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_methods(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_methods(o)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.get_options.html b/docs/reference/dsadmin.get_options.html
index 41b6d38f..936afd9a 100644
--- a/docs/reference/dsadmin.get_options.html
+++ b/docs/reference/dsadmin.get_options.html
@@ -69,7 +69,7 @@ Get the DataSHIELD options
- dsadmin.get_options(opal, profile = NULL)
+ dsadmin.get_options(opal, profile = NULL)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_options(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_options(o)
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_github_package.html b/docs/reference/dsadmin.install_github_package.html
index 3cd61327..9cac06c4 100644
--- a/docs/reference/dsadmin.install_github_package.html
+++ b/docs/reference/dsadmin.install_github_package.html
@@ -69,13 +69,13 @@ Install a DataSHIELD package from GitHub
- dsadmin.install_github_package(
- opal,
- pkg,
- username = "datashield",
- ref = "master",
- profile = NULL
-)
+ dsadmin.install_github_package(
+ opal,
+ pkg,
+ username = "datashield",
+ ref = "master",
+ profile = NULL
+)
@@ -132,11 +132,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge')
+opal.logout(o)
+}
@@ -151,7 +151,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_local_package.html b/docs/reference/dsadmin.install_local_package.html
index a1a1c76d..d1a6d9a2 100644
--- a/docs/reference/dsadmin.install_local_package.html
+++ b/docs/reference/dsadmin.install_local_package.html
@@ -71,7 +71,7 @@ Install a DataSHIELD package from a local archive file
- dsadmin.install_local_package(opal, path, profile = NULL)
+ dsadmin.install_local_package(opal, path, profile = NULL)
@@ -114,14 +114,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# install a pre-built local archive file
-dsadmin.install_local_package(o, '~/dsExposome_1.0.0.tar.gz')
-# or build archive file from local package source (in current working folder)
-dsadmin.install_local_package(o, devtools::build())
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# install a pre-built local archive file
+dsadmin.install_local_package(o, '~/dsExposome_1.0.0.tar.gz')
+# or build archive file from local package source (in current working folder)
+dsadmin.install_local_package(o, devtools::build())
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_package.html b/docs/reference/dsadmin.install_package.html
index 5a0c9ad1..904d1231 100644
--- a/docs/reference/dsadmin.install_package.html
+++ b/docs/reference/dsadmin.install_package.html
@@ -69,13 +69,13 @@ Install a DataSHIELD package
- dsadmin.install_package(
- opal,
- pkg,
- githubusername = NULL,
- ref = NULL,
- profile = NULL
-)
+ dsadmin.install_package(
+ opal,
+ pkg,
+ githubusername = NULL,
+ ref = NULL,
+ profile = NULL
+)
@@ -132,11 +132,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.install_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.install_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -151,7 +151,7 @@ Examples
diff --git a/docs/reference/dsadmin.installed_package.html b/docs/reference/dsadmin.installed_package.html
index 65240b16..d4e1e5f8 100644
--- a/docs/reference/dsadmin.installed_package.html
+++ b/docs/reference/dsadmin.installed_package.html
@@ -69,7 +69,7 @@ Check DataSHIELD package
- dsadmin.installed_package(opal, pkg, profile = NULL)
+ dsadmin.installed_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.installed_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.installed_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/dsadmin.log.html b/docs/reference/dsadmin.log.html
new file mode 100644
index 00000000..76fcc36d
--- /dev/null
+++ b/docs/reference/dsadmin.log.html
@@ -0,0 +1,155 @@
+
+Get DataSHIELD logs — dsadmin.log • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ The DataSHIELD log is structured as follows:
+
+
+
+ dsadmin.log(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+ Details
+ Common fields
timestamp: when action is logged
version: not used
message: human readable message
logger_name: name of the log channel
thread_name: java thread name
level: log level (TRACE, DEBUG, INFO, WARN, ERROR)
level_value: log level numeric value
ip: ip origin of the request, when available
ds_id: unique DS session ID
ds_profile: DS profile name (available after the R server session is created, can be after authentication)
username: DS user name
r_duration: time spent by the remote R server action (all except PARSE)
r_size: R result serialized object size in bytes
ds_action: DS operation (OPEN, CLOSE, PARSE, ASSIGN, AGGREGATE, LS, RM, WS_SAVE, WS_RESTORE)
DS operations fields
OPEN: DS session opened (note: happens after successful authentication as R server session creation is deferred)
CLOSE: DS session closed
PARSE: R expression parsed
ds_map: DS function mappings used in the R parser, separated by semicolons when several functions are called
ds_script_in: R script as sent by DS user
ds_script_out: R script rewritten by opal, to be evaluated
ASSIGN:
ds_symbol: assigned symbol name
ds_table: table name that is assigned
ds_resource: resource name that is assigned
ds_eval: assign R expression that is evaluated
AGGREGATE:
ds_eval: aggregate R expression that is evaluated
LS: R symbols listed
RM: R symbol removed
ds_symbol: symbol name to remove
WS_SAVE:
ds_ws: workspace name
WS_RESTORE:
ds_ws: workspace name
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.log(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.package_description.html b/docs/reference/dsadmin.package_description.html
index 3351e46a..29694b5b 100644
--- a/docs/reference/dsadmin.package_description.html
+++ b/docs/reference/dsadmin.package_description.html
@@ -69,7 +69,7 @@ Get DataSHIELD package description
- dsadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
+ dsadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
@@ -117,11 +117,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_description(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_description(o, 'dsBase')
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/dsadmin.package_descriptions.html b/docs/reference/dsadmin.package_descriptions.html
index 5fb8ebc9..7707a023 100644
--- a/docs/reference/dsadmin.package_descriptions.html
+++ b/docs/reference/dsadmin.package_descriptions.html
@@ -69,7 +69,7 @@ Get DataSHIELD package descriptions
- dsadmin.package_descriptions(opal, fields = NULL, df = TRUE, profile = NULL)
+ dsadmin.package_descriptions(opal, fields = NULL, df = TRUE, profile = NULL)
@@ -123,11 +123,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_descriptions(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_descriptions(o)
+opal.logout(o)
+}
@@ -142,7 +142,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm.html b/docs/reference/dsadmin.perm.html
index c397d495..50f5957c 100644
--- a/docs/reference/dsadmin.perm.html
+++ b/docs/reference/dsadmin.perm.html
@@ -69,7 +69,7 @@ Get the DataSHIELD permissions
- dsadmin.perm(opal)
+ dsadmin.perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm_add.html b/docs/reference/dsadmin.perm_add.html
index 832ce0ce..e17b5796 100644
--- a/docs/reference/dsadmin.perm_add.html
+++ b/docs/reference/dsadmin.perm_add.html
@@ -69,7 +69,7 @@ Add or update a DataSHIELD permission
- dsadmin.perm_add(opal, subject, type = "user", permission)
+ dsadmin.perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm_delete.html b/docs/reference/dsadmin.perm_delete.html
index 91a12ac8..a5ce771c 100644
--- a/docs/reference/dsadmin.perm_delete.html
+++ b/docs/reference/dsadmin.perm_delete.html
@@ -69,7 +69,7 @@ Delete a DataSHIELD permission
- dsadmin.perm_delete(opal, subject, type = "user")
+ dsadmin.perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile.html b/docs/reference/dsadmin.profile.html
index d16b82ac..d8859752 100644
--- a/docs/reference/dsadmin.profile.html
+++ b/docs/reference/dsadmin.profile.html
@@ -73,7 +73,7 @@ Get a DataSHIELD profile
- dsadmin.profile(opal, name)
+ dsadmin.profile(opal, name)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile(o, name = 'default')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile(o, name = 'default')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_access.html b/docs/reference/dsadmin.profile_access.html
index b23f41c7..64ad8674 100644
--- a/docs/reference/dsadmin.profile_access.html
+++ b/docs/reference/dsadmin.profile_access.html
@@ -73,7 +73,7 @@ Restrict or open access to a DataSHIELD profile
- dsadmin.profile_access(opal, name, restricted = TRUE)
+ dsadmin.profile_access(opal, name, restricted = TRUE)
@@ -108,12 +108,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_access(o, name = 'survival', restricted = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_access(o, name = 'survival', restricted = TRUE)
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_create.html b/docs/reference/dsadmin.profile_create.html
index 5f5fb762..e377a2b7 100644
--- a/docs/reference/dsadmin.profile_create.html
+++ b/docs/reference/dsadmin.profile_create.html
@@ -69,7 +69,7 @@ Create a DataSHIELD profile
- dsadmin.profile_create(opal, name, cluster = "default", rParser = NULL)
+ dsadmin.profile_create(opal, name, cluster = "default", rParser = NULL)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_delete.html b/docs/reference/dsadmin.profile_delete.html
index 8bb60e74..de86336c 100644
--- a/docs/reference/dsadmin.profile_delete.html
+++ b/docs/reference/dsadmin.profile_delete.html
@@ -69,7 +69,7 @@ Delete a DataSHIELD profile
- dsadmin.profile_delete(opal, name)
+ dsadmin.profile_delete(opal, name)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_delete(o, name = 'survival')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_delete(o, name = 'survival')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_enable.html b/docs/reference/dsadmin.profile_enable.html
index 8901ed93..36ba9503 100644
--- a/docs/reference/dsadmin.profile_enable.html
+++ b/docs/reference/dsadmin.profile_enable.html
@@ -69,7 +69,7 @@ Enable or disable a DataSHIELD profile
- dsadmin.profile_enable(opal, name, enabled = TRUE)
+ dsadmin.profile_enable(opal, name, enabled = TRUE)
@@ -104,12 +104,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_enable(o, name = 'survival', enabled = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_enable(o, name = 'survival', enabled = TRUE)
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_exists.html b/docs/reference/dsadmin.profile_exists.html
index e5c19c97..5ea51e86 100644
--- a/docs/reference/dsadmin.profile_exists.html
+++ b/docs/reference/dsadmin.profile_exists.html
@@ -69,7 +69,7 @@ Check a DataSHIELD profile exists
- dsadmin.profile_exists(opal, name)
+ dsadmin.profile_exists(opal, name)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-if (!dsadmin.profile_exists(o, name = 'survival'))
- dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+if (!dsadmin.profile_exists(o, name = 'survival'))
+ dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_init.html b/docs/reference/dsadmin.profile_init.html
index 1d117fad..ad4fc311 100644
--- a/docs/reference/dsadmin.profile_init.html
+++ b/docs/reference/dsadmin.profile_init.html
@@ -73,7 +73,7 @@ Initialize a DataSHIELD profile
- dsadmin.profile_init(opal, name, packages = NULL)
+ dsadmin.profile_init(opal, name, packages = NULL)
@@ -108,12 +108,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_init(o, name = 'survival', packages = c('dsSurvival'))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_init(o, name = 'survival', packages = c('dsSurvival'))
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm.html b/docs/reference/dsadmin.profile_perm.html
index ea1913ac..3f90f5de 100644
--- a/docs/reference/dsadmin.profile_perm.html
+++ b/docs/reference/dsadmin.profile_perm.html
@@ -69,7 +69,7 @@ Get the permissions of a DataSHIELD profile
- dsadmin.profile_perm(opal, name)
+ dsadmin.profile_perm(opal, name)
@@ -106,13 +106,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm_add.html b/docs/reference/dsadmin.profile_perm_add.html
index 5aa4f324..e9b60807 100644
--- a/docs/reference/dsadmin.profile_perm_add.html
+++ b/docs/reference/dsadmin.profile_perm_add.html
@@ -71,13 +71,13 @@ Add or update a permission on a DataSHIELD profile
- dsadmin.profile_perm_add(
- opal,
- name,
- subject,
- type = "user",
- permission = "use"
-)
+ dsadmin.profile_perm_add(
+ opal,
+ name,
+ subject,
+ type = "user",
+ permission = "use"
+)
@@ -120,13 +120,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -141,7 +141,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm_delete.html b/docs/reference/dsadmin.profile_perm_delete.html
index 5b218b2b..8d2fa69a 100644
--- a/docs/reference/dsadmin.profile_perm_delete.html
+++ b/docs/reference/dsadmin.profile_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a DataSHIELD profile
- dsadmin.profile_perm_delete(opal, name, subject, type = "user")
+ dsadmin.profile_perm_delete(opal, name, subject, type = "user")
@@ -108,13 +108,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_rparser.html b/docs/reference/dsadmin.profile_rparser.html
index f24c5242..bf9617df 100644
--- a/docs/reference/dsadmin.profile_rparser.html
+++ b/docs/reference/dsadmin.profile_rparser.html
@@ -69,7 +69,7 @@ Set or remove the R parser version of a DataSHIELD profile
- dsadmin.profile_rparser(opal, name, rParser = NULL)
+ dsadmin.profile_rparser(opal, name, rParser = NULL)
@@ -105,15 +105,15 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-# apply R parser version v2
-dsadmin.profile_rparser(o, name = 'survival', rParser = 'v2')
-# apply system's default R parser version
-dsadmin.profile_rparser(o, name = 'survival')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+# apply R parser version v2
+dsadmin.profile_rparser(o, name = 'survival', rParser = 'v2')
+# apply system's default R parser version
+dsadmin.profile_rparser(o, name = 'survival')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profiles.html b/docs/reference/dsadmin.profiles.html
index 7f97e3ad..2ab7201f 100644
--- a/docs/reference/dsadmin.profiles.html
+++ b/docs/reference/dsadmin.profiles.html
@@ -69,7 +69,7 @@ Get DataSHIELD profiles
- dsadmin.profiles(opal, df = TRUE)
+ dsadmin.profiles(opal, df = TRUE)
@@ -106,11 +106,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_descriptions(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_descriptions(o)
+opal.logout(o)
+}
@@ -125,7 +125,7 @@ Examples
diff --git a/docs/reference/dsadmin.publish_package.html b/docs/reference/dsadmin.publish_package.html
index 1aed7d0b..db0a16e3 100644
--- a/docs/reference/dsadmin.publish_package.html
+++ b/docs/reference/dsadmin.publish_package.html
@@ -69,7 +69,7 @@ Publish DataSHIELD package settings
- dsadmin.publish_package(opal, pkg, profile = NULL)
+ dsadmin.publish_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.publish_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.publish_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/dsadmin.remove_package.html b/docs/reference/dsadmin.remove_package.html
index a696d968..11d7e1d3 100644
--- a/docs/reference/dsadmin.remove_package.html
+++ b/docs/reference/dsadmin.remove_package.html
@@ -69,7 +69,7 @@ Remove DataSHIELD package
- dsadmin.remove_package(opal, pkg, profile = NULL)
+ dsadmin.remove_package(opal, pkg, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.remove_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.remove_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_method.html b/docs/reference/dsadmin.rm_method.html
index cca7bb9e..b2d596b8 100644
--- a/docs/reference/dsadmin.rm_method.html
+++ b/docs/reference/dsadmin.rm_method.html
@@ -69,7 +69,7 @@ Remove DataSHIELD method
- dsadmin.rm_method(opal, name, type = "aggregate", profile = NULL)
+ dsadmin.rm_method(opal, name, type = "aggregate", profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_method(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_method(o, 'foo')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_methods.html b/docs/reference/dsadmin.rm_methods.html
index 2532751f..470d8498 100644
--- a/docs/reference/dsadmin.rm_methods.html
+++ b/docs/reference/dsadmin.rm_methods.html
@@ -69,7 +69,7 @@ Remove DataSHIELD methods.
- dsadmin.rm_methods(opal, type = NULL, profile = NULL)
+ dsadmin.rm_methods(opal, type = NULL, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_methods(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_methods(o)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_option.html b/docs/reference/dsadmin.rm_option.html
index 64995c5f..1b4ed85b 100644
--- a/docs/reference/dsadmin.rm_option.html
+++ b/docs/reference/dsadmin.rm_option.html
@@ -69,7 +69,7 @@ Remove a DataSHIELD option
- dsadmin.rm_option(opal, name, profile = NULL)
+ dsadmin.rm_option(opal, name, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_option(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_option(o, 'foo')
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_options.html b/docs/reference/dsadmin.rm_options.html
index 80414f34..2e4e1b38 100644
--- a/docs/reference/dsadmin.rm_options.html
+++ b/docs/reference/dsadmin.rm_options.html
@@ -69,7 +69,7 @@ Remove all DataSHIELD options
- dsadmin.rm_options(opal, profile = NULL)
+ dsadmin.rm_options(opal, profile = NULL)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_options(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_options(o, 'foo')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_package_methods.html b/docs/reference/dsadmin.rm_package_methods.html
index 26a699ef..f86188d4 100644
--- a/docs/reference/dsadmin.rm_package_methods.html
+++ b/docs/reference/dsadmin.rm_package_methods.html
@@ -69,7 +69,7 @@ Remove DataSHIELD package methods
- dsadmin.rm_package_methods(opal, pkg, type = NULL, profile = NULL)
+ dsadmin.rm_package_methods(opal, pkg, type = NULL, profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_package_methods(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_package_methods(o, 'dsBase')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_method.html b/docs/reference/dsadmin.set_method.html
index ab7bc9ff..a1287cc2 100644
--- a/docs/reference/dsadmin.set_method.html
+++ b/docs/reference/dsadmin.set_method.html
@@ -69,14 +69,14 @@ Set DataSHIELD method
- dsadmin.set_method(
- opal,
- name,
- func = NULL,
- path = NULL,
- type = "aggregate",
- profile = NULL
-)
+ dsadmin.set_method(
+ opal,
+ name,
+ func = NULL,
+ path = NULL,
+ type = "aggregate",
+ profile = NULL
+)
@@ -131,14 +131,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# as a package's function
-dsadmin.set_method(o, 'foo', func = 'base::mean')
-# as a custom function
-dsadmin.set_method(o, 'foo', func = function(x) { base::mean(x) })
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# as a package's function
+dsadmin.set_method(o, 'foo', func = 'base::mean')
+# as a custom function
+dsadmin.set_method(o, 'foo', func = function(x) { base::mean(x) })
+opal.logout(o)
+}
@@ -153,7 +153,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_option.html b/docs/reference/dsadmin.set_option.html
index fa661b5b..af2b415b 100644
--- a/docs/reference/dsadmin.set_option.html
+++ b/docs/reference/dsadmin.set_option.html
@@ -69,7 +69,7 @@ Set DataSHIELD option
- dsadmin.set_option(opal, name, value, profile = NULL)
+ dsadmin.set_option(opal, name, value, profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.set_option(o, 'foo', 'bar')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.set_option(o, 'foo', 'bar')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_package_methods.html b/docs/reference/dsadmin.set_package_methods.html
index 663ff9fd..91a0f0e5 100644
--- a/docs/reference/dsadmin.set_package_methods.html
+++ b/docs/reference/dsadmin.set_package_methods.html
@@ -69,7 +69,7 @@ Set DataSHIELD package methods
- dsadmin.set_package_methods(opal, pkg, type = NULL, profile = NULL)
+ dsadmin.set_package_methods(opal, pkg, type = NULL, profile = NULL)
@@ -122,11 +122,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.set_package_methods(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.set_package_methods(o, 'dsBase')
+opal.logout(o)
+}
@@ -141,7 +141,7 @@ Examples
diff --git a/docs/reference/dsadmin.unpublish_package.html b/docs/reference/dsadmin.unpublish_package.html
index 59177cb6..2f4cb561 100644
--- a/docs/reference/dsadmin.unpublish_package.html
+++ b/docs/reference/dsadmin.unpublish_package.html
@@ -69,7 +69,7 @@ Unpublish DataSHIELD package settings
- dsadmin.unpublish_package(opal, pkg, profile = NULL)
+ dsadmin.unpublish_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.unpublish_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.unpublish_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 7b8fa952..1410bfd7 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -86,6 +86,14 @@ All functions dictionary.inspect()
Inspect the dictionary of a tibble
+
+
+ Get DataSHIELD activity
+
+
+ Get DataSHIELD activity summary
@@ -114,6 +122,10 @@ All functions dsadmin.installed_package()
Check DataSHIELD package
+
+
+ Get DataSHIELD logs
@@ -226,6 +238,14 @@ All functions dsadmin.unpublish_package()
Unpublish DataSHIELD package settings
+
+
+ Get R activity
+
+
+ Get R activity summary
@@ -262,6 +282,18 @@ All functions oadmin.installed_packages()
List installed packages
+
+
+ Get Opal main logs
+
+
+ Get Opal REST API logs
+
+
+ Get Opal SQL API logs
@@ -486,6 +518,10 @@ All functions opal.logout()
Logout from Opal(s)
+
+
+ Get the permissions of a subject
@@ -847,7 +883,7 @@ All functions
diff --git a/docs/reference/oadmin.activity.html b/docs/reference/oadmin.activity.html
new file mode 100644
index 00000000..a11491b6
--- /dev/null
+++ b/docs/reference/oadmin.activity.html
@@ -0,0 +1,146 @@
+
+Get R activity — oadmin.activity • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics.
+
+
+
+ oadmin.activity(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity(o)
+# user and profile specific session metrics
+oadmin.activity(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.activity_summary.html b/docs/reference/oadmin.activity_summary.html
new file mode 100644
index 00000000..a8159421
--- /dev/null
+++ b/docs/reference/oadmin.activity_summary.html
@@ -0,0 +1,146 @@
+
+Get R activity summary — oadmin.activity_summary • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics, grouped by profile and user.
+
+
+
+ oadmin.activity_summary(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity_summary(o)
+# user and profile specific session metrics
+oadmin.activity_summary(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.install_bioconductor_package.html b/docs/reference/oadmin.install_bioconductor_package.html
index adde90ec..2c0551ed 100644
--- a/docs/reference/oadmin.install_bioconductor_package.html
+++ b/docs/reference/oadmin.install_bioconductor_package.html
@@ -69,7 +69,7 @@ Install a package from Bioconductor
- oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
+ oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_bioconductor_package(o, 'GWASTools')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_bioconductor_package(o, 'GWASTools')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.install_cran_package.html b/docs/reference/oadmin.install_cran_package.html
index 3e7e3a18..d229933e 100644
--- a/docs/reference/oadmin.install_cran_package.html
+++ b/docs/reference/oadmin.install_cran_package.html
@@ -69,7 +69,7 @@ Install a package from CRAN
- oadmin.install_cran_package(opal, pkg, profile = NULL)
+ oadmin.install_cran_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_cran_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_cran_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.install_devtools.html b/docs/reference/oadmin.install_devtools.html
index 3f2bc53c..79b175d3 100644
--- a/docs/reference/oadmin.install_devtools.html
+++ b/docs/reference/oadmin.install_devtools.html
@@ -69,7 +69,7 @@ Install devtools package
- oadmin.install_devtools(opal, profile = NULL)
+ oadmin.install_devtools(opal, profile = NULL)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_devtools(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.install_github_package.html b/docs/reference/oadmin.install_github_package.html
index 496f0075..ae130887 100644
--- a/docs/reference/oadmin.install_github_package.html
+++ b/docs/reference/oadmin.install_github_package.html
@@ -69,13 +69,13 @@ Install a package from GitHub
- oadmin.install_github_package(
- opal,
- pkg,
- username = getOption("github.user"),
- ref = "master",
- profile = NULL
-)
+ oadmin.install_github_package(
+ opal,
+ pkg,
+ username = getOption("github.user"),
+ ref = "master",
+ profile = NULL
+)
@@ -117,11 +117,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_github_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_github_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/oadmin.install_local_package.html b/docs/reference/oadmin.install_local_package.html
index 17ddc429..9ddb56c3 100644
--- a/docs/reference/oadmin.install_local_package.html
+++ b/docs/reference/oadmin.install_local_package.html
@@ -71,7 +71,7 @@ Install a package from a local archive file
- oadmin.install_local_package(opal, path, profile = NULL)
+ oadmin.install_local_package(opal, path, profile = NULL)
@@ -105,14 +105,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# install a pre-built local archive file
-oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
-# or build archive file from local package source (in current working folder)
-oadmin.install_local_package(o, devtools::build())
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# install a pre-built local archive file
+oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
+# or build archive file from local package source (in current working folder)
+oadmin.install_local_package(o, devtools::build())
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/oadmin.install_package.html b/docs/reference/oadmin.install_package.html
index 0b2c26c5..7539e7fc 100644
--- a/docs/reference/oadmin.install_package.html
+++ b/docs/reference/oadmin.install_package.html
@@ -69,7 +69,7 @@ Install CRAN package
- oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
+ oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
@@ -113,11 +113,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_package(o, 'xxx')
+opal.logout(o)
+}
@@ -132,7 +132,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_devtools.html b/docs/reference/oadmin.installed_devtools.html
index eaf1b900..a90063c1 100644
--- a/docs/reference/oadmin.installed_devtools.html
+++ b/docs/reference/oadmin.installed_devtools.html
@@ -69,7 +69,7 @@ Check devtools package
- oadmin.installed_devtools(opal, profile = NULL)
+ oadmin.installed_devtools(opal, profile = NULL)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_devtools(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_package.html b/docs/reference/oadmin.installed_package.html
index 604bd8ef..aa802b54 100644
--- a/docs/reference/oadmin.installed_package.html
+++ b/docs/reference/oadmin.installed_package.html
@@ -69,7 +69,7 @@ Check package is installed
- oadmin.installed_package(opal, pkg, profile = NULL)
+ oadmin.installed_package(opal, pkg, profile = NULL)
@@ -109,12 +109,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_package(o, 'xxx')
-oadmin.installed_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_package(o, 'xxx')
+oadmin.installed_package(o, 'stats')
+opal.logout(o)
+}
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_packages.html b/docs/reference/oadmin.installed_packages.html
index 2bc6bfc8..2034f299 100644
--- a/docs/reference/oadmin.installed_packages.html
+++ b/docs/reference/oadmin.installed_packages.html
@@ -69,7 +69,7 @@ List installed packages
- oadmin.installed_packages(opal, profile = NULL)
+ oadmin.installed_packages(opal, profile = NULL)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_packages(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_packages(o)
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/oadmin.log.html b/docs/reference/oadmin.log.html
new file mode 100644
index 00000000..2204fa48
--- /dev/null
+++ b/docs/reference/oadmin.log.html
@@ -0,0 +1,118 @@
+
+Get Opal main logs — oadmin.log • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal main logs
+
+
+
+ oadmin.log(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.log_rest.html b/docs/reference/oadmin.log_rest.html
new file mode 100644
index 00000000..fd2f9ef2
--- /dev/null
+++ b/docs/reference/oadmin.log_rest.html
@@ -0,0 +1,118 @@
+
+Get Opal REST API logs — oadmin.log_rest • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal REST API logs
+
+
+
+ oadmin.log_rest(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_rest(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.log_sql.html b/docs/reference/oadmin.log_sql.html
new file mode 100644
index 00000000..0dc4fae5
--- /dev/null
+++ b/docs/reference/oadmin.log_sql.html
@@ -0,0 +1,118 @@
+
+Get Opal SQL API logs — oadmin.log_sql • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal SQL API logs
+
+
+
+ oadmin.log_sql(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_sql(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.package_description.html b/docs/reference/oadmin.package_description.html
index d07d871e..d402b336 100644
--- a/docs/reference/oadmin.package_description.html
+++ b/docs/reference/oadmin.package_description.html
@@ -69,7 +69,7 @@ Get package description
- oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
+ oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.package_description(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.package_description(o, 'stats')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/oadmin.perm.html b/docs/reference/oadmin.perm.html
index b61d3e13..20a30ecc 100644
--- a/docs/reference/oadmin.perm.html
+++ b/docs/reference/oadmin.perm.html
@@ -69,7 +69,7 @@ Get the R permissions (deprecated)
- oadmin.perm(opal)
+ oadmin.perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.perm_add.html b/docs/reference/oadmin.perm_add.html
index b3a39610..df43a7c7 100644
--- a/docs/reference/oadmin.perm_add.html
+++ b/docs/reference/oadmin.perm_add.html
@@ -69,7 +69,7 @@ Add or update a R permission (deprecated)
- oadmin.perm_add(opal, subject, type = "user", permission)
+ oadmin.perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.perm_delete.html b/docs/reference/oadmin.perm_delete.html
index f629e6fc..fa8fa4de 100644
--- a/docs/reference/oadmin.perm_delete.html
+++ b/docs/reference/oadmin.perm_delete.html
@@ -69,7 +69,7 @@ Delete a R permission (deprecated)
- oadmin.perm_delete(opal, subject, type = "user")
+ oadmin.perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm.html b/docs/reference/oadmin.r_perm.html
index 4bae064d..12b32d20 100644
--- a/docs/reference/oadmin.r_perm.html
+++ b/docs/reference/oadmin.r_perm.html
@@ -69,7 +69,7 @@ Get the R permissions
- oadmin.r_perm(opal)
+ oadmin.r_perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm_add.html b/docs/reference/oadmin.r_perm_add.html
index 06ec844e..fc74abf1 100644
--- a/docs/reference/oadmin.r_perm_add.html
+++ b/docs/reference/oadmin.r_perm_add.html
@@ -69,7 +69,7 @@ Add or update a R permission
- oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
+ oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm_delete.html b/docs/reference/oadmin.r_perm_delete.html
index c68d1ff5..01177602 100644
--- a/docs/reference/oadmin.r_perm_delete.html
+++ b/docs/reference/oadmin.r_perm_delete.html
@@ -69,7 +69,7 @@ Delete a R permission
- oadmin.r_perm_delete(opal, subject, type = "user")
+ oadmin.r_perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.remove_package.html b/docs/reference/oadmin.remove_package.html
index 7d9fd447..0953b827 100644
--- a/docs/reference/oadmin.remove_package.html
+++ b/docs/reference/oadmin.remove_package.html
@@ -69,7 +69,7 @@ Remove package
- oadmin.remove_package(opal, pkg, profile = NULL)
+ oadmin.remove_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.remove_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.remove_package(o, 'xxx')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.system_metrics.html b/docs/reference/oadmin.system_metrics.html
index 4e5ba20e..9eb7d54a 100644
--- a/docs/reference/oadmin.system_metrics.html
+++ b/docs/reference/oadmin.system_metrics.html
@@ -81,7 +81,7 @@ Get system metrics
- oadmin.system_metrics(opal)
+ oadmin.system_metrics(opal)
@@ -93,11 +93,11 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_metrics(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_metrics(o)
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm.html b/docs/reference/oadmin.system_perm.html
index a858025b..5cc5a542 100644
--- a/docs/reference/oadmin.system_perm.html
+++ b/docs/reference/oadmin.system_perm.html
@@ -69,7 +69,7 @@ Get the System permissions
- oadmin.system_perm(opal)
+ oadmin.system_perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm_add.html b/docs/reference/oadmin.system_perm_add.html
index 8b06fd5e..ecc56a90 100644
--- a/docs/reference/oadmin.system_perm_add.html
+++ b/docs/reference/oadmin.system_perm_add.html
@@ -69,7 +69,7 @@ Add or update a System permission
- oadmin.system_perm_add(opal, subject, type = "user", permission)
+ oadmin.system_perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm_delete.html b/docs/reference/oadmin.system_perm_delete.html
index c78fc7d4..5268feec 100644
--- a/docs/reference/oadmin.system_perm_delete.html
+++ b/docs/reference/oadmin.system_perm_delete.html
@@ -69,7 +69,7 @@ Delete a System permission
- oadmin.system_perm_delete(opal, subject, type = "user")
+ oadmin.system_perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.user_add.html b/docs/reference/oadmin.user_add.html
index e5a58e5b..1b82c9b6 100644
--- a/docs/reference/oadmin.user_add.html
+++ b/docs/reference/oadmin.user_add.html
@@ -69,7 +69,7 @@ Add a user
- oadmin.user_add(opal, name, groups = NULL, password = NULL)
+ oadmin.user_add(opal, name, groups = NULL, password = NULL)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/oadmin.user_delete.html b/docs/reference/oadmin.user_delete.html
index 123be6e5..1ae1cb20 100644
--- a/docs/reference/oadmin.user_delete.html
+++ b/docs/reference/oadmin.user_delete.html
@@ -69,7 +69,7 @@ Delete a user
- oadmin.user_delete(opal, name)
+ oadmin.user_delete(opal, name)
@@ -96,12 +96,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_delete(o, "foo")
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/oadmin.user_enable.html b/docs/reference/oadmin.user_enable.html
index 1b531f3a..5b480d04 100644
--- a/docs/reference/oadmin.user_enable.html
+++ b/docs/reference/oadmin.user_enable.html
@@ -69,7 +69,7 @@ Enable a user
- oadmin.user_enable(opal, name, enabled = TRUE)
+ oadmin.user_enable(opal, name, enabled = TRUE)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_enable(o, "foo", enabled = FALSE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_enable(o, "foo", enabled = FALSE)
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/oadmin.user_exists.html b/docs/reference/oadmin.user_exists.html
index e05a1f79..fad76e33 100644
--- a/docs/reference/oadmin.user_exists.html
+++ b/docs/reference/oadmin.user_exists.html
@@ -71,7 +71,7 @@ Check user exists
- oadmin.user_exists(opal, name)
+ oadmin.user_exists(opal, name)
@@ -98,12 +98,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-if (!oadmin.user_exists(o, "foo"))
- oadmin.user_add(o, "foo", password = "bar123")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+if (!oadmin.user_exists(o, "foo"))
+ oadmin.user_add(o, "foo", password = "bar123")
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.user_profile_delete.html b/docs/reference/oadmin.user_profile_delete.html
index e1aab115..2e585266 100644
--- a/docs/reference/oadmin.user_profile_delete.html
+++ b/docs/reference/oadmin.user_profile_delete.html
@@ -75,7 +75,7 @@ Delete a user profile
- oadmin.user_profile_delete(opal, name)
+ oadmin.user_profile_delete(opal, name)
@@ -102,12 +102,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_profile_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_profile_delete(o, "foo")
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.user_profiles.html b/docs/reference/oadmin.user_profiles.html
index 2c1e5a94..f23f1669 100644
--- a/docs/reference/oadmin.user_profiles.html
+++ b/docs/reference/oadmin.user_profiles.html
@@ -71,7 +71,7 @@ Get user profiles
- oadmin.user_profiles(opal, df = TRUE)
+ oadmin.user_profiles(opal, df = TRUE)
@@ -98,11 +98,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.user_profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.user_profiles(o)
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/oadmin.user_reset_password.html b/docs/reference/oadmin.user_reset_password.html
index 7bc446ae..75e27675 100644
--- a/docs/reference/oadmin.user_reset_password.html
+++ b/docs/reference/oadmin.user_reset_password.html
@@ -69,7 +69,7 @@ Reset user password
- oadmin.user_reset_password(opal, name, password = NULL)
+ oadmin.user_reset_password(opal, name, password = NULL)
@@ -100,13 +100,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_reset_password(o, "foo", password = "password1234")
-oadmin.user_rm(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_reset_password(o, "foo", password = "password1234")
+oadmin.user_rm(o, "foo")
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/oadmin.users.html b/docs/reference/oadmin.users.html
index e16383d7..f7a3388e 100644
--- a/docs/reference/oadmin.users.html
+++ b/docs/reference/oadmin.users.html
@@ -69,7 +69,7 @@ Get the users
- oadmin.users(opal, df = TRUE)
+ oadmin.users(opal, df = TRUE)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.users(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.users(o)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.annotate.html b/docs/reference/opal.annotate.html
index f8b0529c..d0970046 100644
--- a/docs/reference/opal.annotate.html
+++ b/docs/reference/opal.annotate.html
@@ -71,7 +71,7 @@ Apply the annotations to a Opal table
- opal.annotate(opal, datasource, table, annotations)
+ opal.annotate(opal, datasource, table, annotations)
@@ -111,12 +111,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/opal.annotations.html b/docs/reference/opal.annotations.html
index 54727239..9f6b17eb 100644
--- a/docs/reference/opal.annotations.html
+++ b/docs/reference/opal.annotations.html
@@ -69,7 +69,7 @@ Get the annotations of a Opal table
- opal.annotations(opal, datasource, table)
+ opal.annotations(opal, datasource, table)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.as_md_table.html b/docs/reference/opal.as_md_table.html
index e37dd66e..b6b4c121 100644
--- a/docs/reference/opal.as_md_table.html
+++ b/docs/reference/opal.as_md_table.html
@@ -69,14 +69,14 @@ Array to Markdown
-
+
@@ -108,11 +108,11 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/opal.assign.data.html b/docs/reference/opal.assign.data.html
index e7b39e90..2be27522 100644
--- a/docs/reference/opal.assign.data.html
+++ b/docs/reference/opal.assign.data.html
@@ -69,7 +69,7 @@ Data assignment
- opal.assign.data(opal, symbol, value, async = FALSE)
+ opal.assign.data(opal, symbol, value, async = FALSE)
@@ -102,16 +102,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# push an arbitrary data frame to the R server
-opal.assign.data(o, "D", mtcars)
-# push an arbitrary vector to the R server
-opal.assign.data(o, "C", mtcars$cyl)
-# push a string
-opal.assign.data(o, "S", "Hello!")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# push an arbitrary data frame to the R server
+opal.assign.data(o, "D", mtcars)
+# push an arbitrary vector to the R server
+opal.assign.data(o, "C", mtcars$cyl)
+# push a string
+opal.assign.data(o, "S", "Hello!")
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.assign.html b/docs/reference/opal.assign.html
index c0c14727..83bab276 100644
--- a/docs/reference/opal.assign.html
+++ b/docs/reference/opal.assign.html
@@ -69,17 +69,17 @@ Data or expression assignment
- opal.assign(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- async = FALSE
-)
+ opal.assign(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ async = FALSE
+)
@@ -132,21 +132,21 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-# push an arbitrary data frame to the R server
-#opal.assign(o, "D", mtcars)
-# push an arbitrary vector to the R server
-#opal.assign(o, "C", mtcars$cyl)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+# push an arbitrary data frame to the R server
+#opal.assign(o, "D", mtcars)
+# push an arbitrary vector to the R server
+#opal.assign(o, "C", mtcars$cyl)
+opal.logout(o)
+}
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/opal.assign.resource.html b/docs/reference/opal.assign.resource.html
index 649d475e..b06c3fee 100644
--- a/docs/reference/opal.assign.resource.html
+++ b/docs/reference/opal.assign.resource.html
@@ -69,7 +69,7 @@ Resource assignment
- opal.assign.resource(opal, symbol, value, async = FALSE)
+ opal.assign.resource(opal, symbol, value, async = FALSE)
@@ -102,13 +102,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a resource and make some operation on it
-opal.assign.resource(o, "D", "datashield.cram1")
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a resource and make some operation on it
+opal.assign.resource(o, "D", "datashield.cram1")
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.assign.script.html b/docs/reference/opal.assign.script.html
index ce2ee8a8..4826146e 100644
--- a/docs/reference/opal.assign.script.html
+++ b/docs/reference/opal.assign.script.html
@@ -69,7 +69,7 @@ R script assignment
- opal.assign.script(opal, symbol, value, async = FALSE)
+ opal.assign.script(opal, symbol, value, async = FALSE)
@@ -102,13 +102,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.assign.table.html b/docs/reference/opal.assign.table.html
index f23b63b9..b853219b 100644
--- a/docs/reference/opal.assign.table.html
+++ b/docs/reference/opal.assign.table.html
@@ -69,18 +69,18 @@ Data assignment to a data.frame
- opal.assign.table(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- class = "data.frame",
- async = FALSE
-)
+ opal.assign.table(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ class = "data.frame",
+ async = FALSE
+)
@@ -137,19 +137,19 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-opal.execute(o, "colnames(D)")
-# assign a table CNSIM1 with a identifiers column
-opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
-opal.execute(o, "colnames(H)")
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-opal.execute(o, "colnames(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+opal.execute(o, "colnames(D)")
+# assign a table CNSIM1 with a identifiers column
+opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
+opal.execute(o, "colnames(H)")
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+opal.execute(o, "colnames(D)")
+opal.logout(o)
+}
@@ -164,7 +164,7 @@ Examples
diff --git a/docs/reference/opal.assign.table.tibble.html b/docs/reference/opal.assign.table.tibble.html
index 95dc04a3..e508e729 100644
--- a/docs/reference/opal.assign.table.tibble.html
+++ b/docs/reference/opal.assign.table.tibble.html
@@ -69,18 +69,18 @@ Data assignment to a tibble
- opal.assign.table.tibble(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = "id",
- with.factors = FALSE,
- updated.name = NULL,
- async = FALSE
-)
+ opal.assign.table.tibble(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = "id",
+ with.factors = FALSE,
+ updated.name = NULL,
+ async = FALSE
+)
@@ -137,13 +137,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a table and make some operation on it
-opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a table and make some operation on it
+opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
@@ -158,7 +158,7 @@ Examples
diff --git a/docs/reference/opal.attribute_values.html b/docs/reference/opal.attribute_values.html
index dd1b1537..98a94106 100644
--- a/docs/reference/opal.attribute_values.html
+++ b/docs/reference/opal.attribute_values.html
@@ -69,7 +69,7 @@ Get a vector of attribute values
- opal.attribute_values(attributes, namespace = NULL, name = "label")
+ opal.attribute_values(attributes, namespace = NULL, name = "label")
@@ -103,12 +103,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.attribute_values(var$attributes)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.attribute_values(var$attributes)
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.command.html b/docs/reference/opal.command.html
index 0f88509d..4f419a6e 100644
--- a/docs/reference/opal.command.html
+++ b/docs/reference/opal.command.html
@@ -69,7 +69,7 @@ Get an asynchronous command
- opal.command(opal, id, wait = FALSE)
+ opal.command(opal, id, wait = FALSE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command(o, '1234')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.command_result.html b/docs/reference/opal.command_result.html
index 5289b55a..35bc7964 100644
--- a/docs/reference/opal.command_result.html
+++ b/docs/reference/opal.command_result.html
@@ -71,7 +71,7 @@ Get result of an asynchronous command
- opal.command_result(opal, id, wait = FALSE)
+ opal.command_result(opal, id, wait = FALSE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_result(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_result(o, '1234')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.command_rm.html b/docs/reference/opal.command_rm.html
index c43351fa..e7fea6bb 100644
--- a/docs/reference/opal.command_rm.html
+++ b/docs/reference/opal.command_rm.html
@@ -69,7 +69,7 @@ Remove an asynchronous command
- opal.command_rm(opal, id)
+ opal.command_rm(opal, id)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_rm(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_rm(o, '1234')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.commands.html b/docs/reference/opal.commands.html
index f184c2a2..e5067c0f 100644
--- a/docs/reference/opal.commands.html
+++ b/docs/reference/opal.commands.html
@@ -69,7 +69,7 @@ List the asynchronous commands
- opal.commands(opal, df = TRUE)
+ opal.commands(opal, df = TRUE)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands(o)
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.commands_rm.html b/docs/reference/opal.commands_rm.html
index a79be20b..dad19270 100644
--- a/docs/reference/opal.commands_rm.html
+++ b/docs/reference/opal.commands_rm.html
@@ -69,7 +69,7 @@ Remove all asynchronous commands
- opal.commands_rm(opal)
+ opal.commands_rm(opal)
@@ -89,11 +89,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands_rm(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands_rm(o)
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/opal.datasource.html b/docs/reference/opal.datasource.html
index db4e3140..18ec94fc 100644
--- a/docs/reference/opal.datasource.html
+++ b/docs/reference/opal.datasource.html
@@ -69,7 +69,7 @@ Get a datasource
- opal.datasource(opal, datasource)
+ opal.datasource(opal, datasource)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasource(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasource(o, 'CNSIM')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.datasources.html b/docs/reference/opal.datasources.html
index 2c0c3136..b541b556 100644
--- a/docs/reference/opal.datasources.html
+++ b/docs/reference/opal.datasources.html
@@ -69,7 +69,7 @@ Get datasources
- opal.datasources(opal, df = TRUE)
+ opal.datasources(opal, df = TRUE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasources(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasources(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.delete.html b/docs/reference/opal.delete.html
index 9acf1da1..97b75ae3 100644
--- a/docs/reference/opal.delete.html
+++ b/docs/reference/opal.delete.html
@@ -69,7 +69,7 @@ Generic REST resource deletion.
- opal.delete(opal, ..., query = list(), callback = NULL)
+ opal.delete(opal, ..., query = list(), callback = NULL)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.delete(o, 'some', 'resource')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.delete(o, 'some', 'resource')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.execute.html b/docs/reference/opal.execute.html
index 244ade02..f91dcca6 100644
--- a/docs/reference/opal.execute.html
+++ b/docs/reference/opal.execute.html
@@ -69,7 +69,7 @@ Execute a R script
- opal.execute(opal, script, async = FALSE)
+ opal.execute(opal, script, async = FALSE)
@@ -97,12 +97,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute(o, "x <- 'foo'")
-opal.execute(o, "ls()")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute(o, "x <- 'foo'")
+opal.execute(o, "ls()")
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/opal.execute.source.html b/docs/reference/opal.execute.source.html
index 9ad4eef0..f512ffb2 100644
--- a/docs/reference/opal.execute.source.html
+++ b/docs/reference/opal.execute.source.html
@@ -69,7 +69,7 @@ Execute a R file script
- opal.execute.source(opal, path, async = FALSE)
+ opal.execute.source(opal, path, async = FALSE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute.source(o, "myscript.R")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute.source(o, "myscript.R")
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.file.html b/docs/reference/opal.file.html
index 074023d1..72a13d97 100644
--- a/docs/reference/opal.file.html
+++ b/docs/reference/opal.file.html
@@ -69,7 +69,7 @@ Get file content
- opal.file(opal, path, key = NULL)
+ opal.file(opal, path, key = NULL)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.file(o, '/home/administrator/joins/join-src-3.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.file(o, '/home/administrator/joins/join-src-3.csv')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.file_cp.html b/docs/reference/opal.file_cp.html
index c895e41c..33bb18fd 100644
--- a/docs/reference/opal.file_cp.html
+++ b/docs/reference/opal.file_cp.html
@@ -69,7 +69,7 @@ Copy a file
- opal.file_cp(opal, source, destination)
+ opal.file_cp(opal, source, destination)
@@ -104,14 +104,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# copy a file to another folder
-opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# copy recursively a folder to another folder
-opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# copy a file to another folder
+opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# copy recursively a folder to another folder
+opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.file_download.html b/docs/reference/opal.file_download.html
index dde0cba7..e6770678 100644
--- a/docs/reference/opal.file_download.html
+++ b/docs/reference/opal.file_download.html
@@ -69,7 +69,7 @@ Download a file
- opal.file_download(opal, source, destination = NULL, key = NULL)
+ opal.file_download(opal, source, destination = NULL, key = NULL)
@@ -108,19 +108,19 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# download a file
-opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
-# download a file encrypted by a key: resulting file is a zip with an encrypted content
-opal.file_download(o, '/home/administrator/export/some-data.csv',
- destination='some-data.zip', key='AZF57893FBDE')
-# download, create destination folder and rename file
-opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
-# download a folder
-opal.file_download(o, '/home/administrator/export', 'export.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# download a file
+opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
+# download a file encrypted by a key: resulting file is a zip with an encrypted content
+opal.file_download(o, '/home/administrator/export/some-data.csv',
+ destination='some-data.zip', key='AZF57893FBDE')
+# download, create destination folder and rename file
+opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
+# download a folder
+opal.file_download(o, '/home/administrator/export', 'export.zip')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.file_ls.html b/docs/reference/opal.file_ls.html
index c57e02da..8664df11 100644
--- a/docs/reference/opal.file_ls.html
+++ b/docs/reference/opal.file_ls.html
@@ -69,7 +69,7 @@ List content of a folder
- opal.file_ls(opal, path)
+ opal.file_ls(opal, path)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# list content of a folder
-opal.file_ls(o, '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# list content of a folder
+opal.file_ls(o, '/home/administrator')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.file_mkdir.html b/docs/reference/opal.file_mkdir.html
index 0ed72ad7..d15743df 100644
--- a/docs/reference/opal.file_mkdir.html
+++ b/docs/reference/opal.file_mkdir.html
@@ -71,7 +71,7 @@ Make a folder
- opal.file_mkdir(opal, path, parents = FALSE)
+ opal.file_mkdir(opal, path, parents = FALSE)
@@ -106,12 +106,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.file_mkdir_tmp.html b/docs/reference/opal.file_mkdir_tmp.html
index 396c04ff..8e187fcb 100644
--- a/docs/reference/opal.file_mkdir_tmp.html
+++ b/docs/reference/opal.file_mkdir_tmp.html
@@ -69,7 +69,7 @@ Make a temporary folder
- opal.file_mkdir_tmp(opal)
+ opal.file_mkdir_tmp(opal)
@@ -102,12 +102,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-path <- opal.file_mkdir_tmp(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+path <- opal.file_mkdir_tmp(o)
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/opal.file_mv.html b/docs/reference/opal.file_mv.html
index fc322297..1d6874df 100644
--- a/docs/reference/opal.file_mv.html
+++ b/docs/reference/opal.file_mv.html
@@ -69,7 +69,7 @@ Move and/or rename a file
- opal.file_mv(opal, source, destination)
+ opal.file_mv(opal, source, destination)
@@ -104,18 +104,18 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# move a file to another folder
-opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/administrator/export/some-data.csv')
-# move and rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/userx/deliverables/some-data.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# move a file to another folder
+opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/administrator/export/some-data.csv')
+# move and rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/userx/deliverables/some-data.csv')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.file_read.html b/docs/reference/opal.file_read.html
index 64f4982d..1807b28c 100644
--- a/docs/reference/opal.file_read.html
+++ b/docs/reference/opal.file_read.html
@@ -69,7 +69,7 @@ Read a file
- opal.file_read(opal, source, destination)
+ opal.file_read(opal, source, destination)
@@ -104,16 +104,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# read into folder
-opal.file_read(o,"DatabaseTest.sav", "/tmp")
-# read and rename
-opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
-# user home expansion
-opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# read into folder
+opal.file_read(o,"DatabaseTest.sav", "/tmp")
+# read and rename
+opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
+# user home expansion
+opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.file_rm.html b/docs/reference/opal.file_rm.html
index a23dee2e..5d79795c 100644
--- a/docs/reference/opal.file_rm.html
+++ b/docs/reference/opal.file_rm.html
@@ -69,7 +69,7 @@ Remove a file
- opal.file_rm(opal, path)
+ opal.file_rm(opal, path)
@@ -100,14 +100,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# remove a file
-opal.file_rm(o, '/home/administrator/export/some-data.csv')
-# remove recursively a folder
-opal.file_rm(o, '/home/administrator/export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# remove a file
+opal.file_rm(o, '/home/administrator/export/some-data.csv')
+# remove recursively a folder
+opal.file_rm(o, '/home/administrator/export')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/opal.file_unzip.html b/docs/reference/opal.file_unzip.html
index 66eaea32..a695dfec 100644
--- a/docs/reference/opal.file_unzip.html
+++ b/docs/reference/opal.file_unzip.html
@@ -69,7 +69,7 @@ Unzip a zip archive file
- opal.file_unzip(opal, source, destination, key = NULL)
+ opal.file_unzip(opal, source, destination, key = NULL)
@@ -114,12 +114,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# unzip
-path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# unzip
+path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.file_upload.html b/docs/reference/opal.file_upload.html
index 83a6426c..70c2faea 100644
--- a/docs/reference/opal.file_upload.html
+++ b/docs/reference/opal.file_upload.html
@@ -71,7 +71,7 @@ Upload a file or a folder
- opal.file_upload(opal, source, destination, all.files = TRUE)
+ opal.file_upload(opal, source, destination, all.files = TRUE)
@@ -111,14 +111,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# upload a file
-opal.file_upload(o, 'some_data.csv', '/home/administrator')
-# upload a folder
-opal.file_upload(o, 'some_data', '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# upload a file
+opal.file_upload(o, 'some_data.csv', '/home/administrator')
+# upload a folder
+opal.file_upload(o, 'some_data', '/home/administrator')
+opal.logout(o)
+}
@@ -133,7 +133,7 @@ Examples
diff --git a/docs/reference/opal.file_write.html b/docs/reference/opal.file_write.html
index a1bfb19d..f0835d11 100644
--- a/docs/reference/opal.file_write.html
+++ b/docs/reference/opal.file_write.html
@@ -69,7 +69,7 @@ Write a file
- opal.file_write(opal, source, destination = NULL)
+ opal.file_write(opal, source, destination = NULL)
@@ -104,16 +104,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# user home expansion
-opal.file_write(o, "~/spss/DatabaseTest.sav")
-# rename file
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
-# create sub-folder
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# user home expansion
+opal.file_write(o, "~/spss/DatabaseTest.sav")
+# rename file
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
+# create sub-folder
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.get.html b/docs/reference/opal.get.html
index 19e0f260..f83d5cb9 100644
--- a/docs/reference/opal.get.html
+++ b/docs/reference/opal.get.html
@@ -69,14 +69,14 @@ Generic REST resource getter.
- opal.get(
- opal,
- ...,
- query = list(),
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)
+ opal.get(
+ opal,
+ ...,
+ query = list(),
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)
@@ -115,11 +115,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.get(o, 'project', 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.get(o, 'project', 'CNSIM')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.load_package.html b/docs/reference/opal.load_package.html
index 15e9967f..cba05243 100644
--- a/docs/reference/opal.load_package.html
+++ b/docs/reference/opal.load_package.html
@@ -69,7 +69,7 @@ Load package
- opal.load_package(opal, pkg)
+ opal.load_package(opal, pkg)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.load_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.load_package(o, 'stats')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.login.html b/docs/reference/opal.login.html
index f9523698..549cdc71 100644
--- a/docs/reference/opal.login.html
+++ b/docs/reference/opal.login.html
@@ -73,15 +73,15 @@ Opal login
-
+
@@ -132,44 +132,44 @@ See also
Examples
- if (FALSE) {
-#### The below examples illustrate the different ways to login in opal ####
-
-# explicite username/password login
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
- # explicite personal access token login
-o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login using options and user credentials
-options(opal.username = 'administrator',
- opal.password = 'password',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using options and personal access token
-options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using ssl key pair
-options(opal.opts = list(
- sslcert = 'my-publickey.pem',
- sslkey = 'my-privatekey.pem'))
-o <- opal.login(url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login with a R server profile
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org', profile = 'default')
-opal.logout(o)
-}
+ if (FALSE) {
+#### The below examples illustrate the different ways to login in opal ####
+
+# explicite username/password login
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+ # explicite personal access token login
+o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login using options and user credentials
+options(opal.username = 'administrator',
+ opal.password = 'password',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using options and personal access token
+options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using ssl key pair
+options(opal.opts = list(
+ sslcert = 'my-publickey.pem',
+ sslkey = 'my-privatekey.pem'))
+o <- opal.login(url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login with a R server profile
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org', profile = 'default')
+opal.logout(o)
+}
@@ -184,7 +184,7 @@ Examples
diff --git a/docs/reference/opal.logout.html b/docs/reference/opal.logout.html
index e64f3e86..b91868aa 100644
--- a/docs/reference/opal.logout.html
+++ b/docs/reference/opal.logout.html
@@ -69,7 +69,7 @@ Logout from Opal(s)
- opal.logout(opal, save = FALSE)
+ opal.logout(opal, save = FALSE)
@@ -91,10 +91,10 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+}
@@ -109,7 +109,7 @@ Examples
diff --git a/docs/reference/opal.perms.html b/docs/reference/opal.perms.html
new file mode 100644
index 00000000..aab233ff
--- /dev/null
+++ b/docs/reference/opal.perms.html
@@ -0,0 +1,154 @@
+
+Get the permissions of a subject — opal.perms • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the permissions of a subject. If the subject is a user, the permissions of
+the groups to which the user belongs are also added to the result.
+
+
+
+ opal.perms(opal, subject, type = "user")
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- subject
+A subject identifier: user or group name.
- type
+The type of subject: user (default) or group.
+
+ Value
+
+
+A data.frame with columns: subject, type, target (path to the opal object to which
+the permission applies), target_type and perm (the permission name)
+
+
+ See also
+ Other table functions:
+opal.resource_view_create(),
+opal.resource_view_reconnect(),
+opal.table_create(),
+opal.table_delete(),
+opal.table_dictionary_get(),
+opal.table_dictionary_update(),
+opal.table_exists(),
+opal.table_export(),
+opal.table_get(),
+opal.table_import(),
+opal.table_perm_add(),
+opal.table_perm_delete(),
+opal.table_perm(),
+opal.table_save(),
+opal.table_truncate(),
+opal.table_view_create(),
+opal.table_view_update()
+
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.perms(o, 'andrei')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/opal.post.html b/docs/reference/opal.post.html
index d93bb6bf..f7d80068 100644
--- a/docs/reference/opal.post.html
+++ b/docs/reference/opal.post.html
@@ -69,16 +69,16 @@ Generic REST resource creation.
- opal.post(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)
+ opal.post(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)
@@ -125,11 +125,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.post(o, 'some', 'resources', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.post(o, 'some', 'resources', body = '{"some":"value"}')
+opal.logout(o)
+}
@@ -144,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.profiles.html b/docs/reference/opal.profiles.html
index 067273c2..1e96f85c 100644
--- a/docs/reference/opal.profiles.html
+++ b/docs/reference/opal.profiles.html
@@ -71,7 +71,7 @@ List R profiles
- opal.profiles(opal, df = TRUE)
+ opal.profiles(opal, df = TRUE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.profiles(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.project.html b/docs/reference/opal.project.html
index cd3a4f68..3e6b4a16 100644
--- a/docs/reference/opal.project.html
+++ b/docs/reference/opal.project.html
@@ -69,7 +69,7 @@ Get a project
- opal.project(opal, project)
+ opal.project(opal, project)
@@ -94,11 +94,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project(o, 'datashield')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project(o, 'datashield')
+opal.logout(o)
+}
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/opal.project_backup.html b/docs/reference/opal.project_backup.html
index 9fe7543f..58bf4b6e 100644
--- a/docs/reference/opal.project_backup.html
+++ b/docs/reference/opal.project_backup.html
@@ -75,14 +75,14 @@ Backup a project
- opal.project_backup(
- opal,
- project,
- archive,
- viewsAsTables = FALSE,
- override = TRUE,
- wait = TRUE
-)
+ opal.project_backup(
+ opal,
+ project,
+ archive,
+ viewsAsTables = FALSE,
+ override = TRUE,
+ wait = TRUE
+)
@@ -120,12 +120,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
-opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
+opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
+opal.logout(o)
+}
@@ -140,7 +140,7 @@ Examples
diff --git a/docs/reference/opal.project_command.html b/docs/reference/opal.project_command.html
index 13740837..9e6c5e62 100644
--- a/docs/reference/opal.project_command.html
+++ b/docs/reference/opal.project_command.html
@@ -69,7 +69,7 @@ Get project task
- opal.project_command(opal, project, id)
+ opal.project_command(opal, project, id)
@@ -95,12 +95,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
-opal.project_command(opal, 'GREENSPACE', id)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
+opal.project_command(opal, 'GREENSPACE', id)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.project_create.html b/docs/reference/opal.project_create.html
index 2524037d..d1eb8488 100644
--- a/docs/reference/opal.project_create.html
+++ b/docs/reference/opal.project_create.html
@@ -69,15 +69,15 @@ Create a project
- opal.project_create(
- opal,
- project,
- database = NULL,
- title = NULL,
- description = NULL,
- tags = NULL,
- exportFolder = NULL
-)
+ opal.project_create(
+ opal,
+ project,
+ database = NULL,
+ title = NULL,
+ description = NULL,
+ tags = NULL,
+ exportFolder = NULL
+)
@@ -124,16 +124,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with named database
-opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
-# with default database
-opal.project_create(o, 'test_default_db', database = TRUE)
-# no database, for views and resources only
-opal.project_create(o, 'test_no_db')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with named database
+opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
+# with default database
+opal.project_create(o, 'test_default_db', database = TRUE)
+# no database, for views and resources only
+opal.project_create(o, 'test_no_db')
+opal.logout(o)
+}
@@ -148,7 +148,7 @@ Examples
diff --git a/docs/reference/opal.project_delete.html b/docs/reference/opal.project_delete.html
index 0975b5d4..249dfdd3 100644
--- a/docs/reference/opal.project_delete.html
+++ b/docs/reference/opal.project_delete.html
@@ -69,7 +69,7 @@ Delete a project
- opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
+ opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
@@ -102,11 +102,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_delete(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_delete(o, 'test')
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/opal.project_exists.html b/docs/reference/opal.project_exists.html
index 2d217cab..10266208 100644
--- a/docs/reference/opal.project_exists.html
+++ b/docs/reference/opal.project_exists.html
@@ -69,7 +69,7 @@ Check a project exists
- opal.project_exists(opal, project)
+ opal.project_exists(opal, project)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_exists(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_exists(o, 'test')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.project_perm.html b/docs/reference/opal.project_perm.html
index 07a974c3..abba6946 100644
--- a/docs/reference/opal.project_perm.html
+++ b/docs/reference/opal.project_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a project
- opal.project_perm(opal, project)
+ opal.project_perm(opal, project)
@@ -91,13 +91,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.project_perm_add.html b/docs/reference/opal.project_perm_add.html
index 1fd19072..e134d7b0 100644
--- a/docs/reference/opal.project_perm_add.html
+++ b/docs/reference/opal.project_perm_add.html
@@ -69,13 +69,13 @@ Add or update a permission on a project
- opal.project_perm_add(
- opal,
- project,
- subject,
- type = "user",
- permission = "administrate"
-)
+ opal.project_perm_add(
+ opal,
+ project,
+ subject,
+ type = "user",
+ permission = "administrate"
+)
@@ -103,13 +103,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.project_perm_delete.html b/docs/reference/opal.project_perm_delete.html
index 8a290c35..885e9c53 100644
--- a/docs/reference/opal.project_perm_delete.html
+++ b/docs/reference/opal.project_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a project
- opal.project_perm_delete(opal, project, subject, type = "user")
+ opal.project_perm_delete(opal, project, subject, type = "user")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/opal.project_restore.html b/docs/reference/opal.project_restore.html
index 76c5f138..8f4c0d05 100644
--- a/docs/reference/opal.project_restore.html
+++ b/docs/reference/opal.project_restore.html
@@ -75,14 +75,14 @@ Restore a project
- opal.project_restore(
- opal,
- project,
- archive,
- key = NULL,
- override = TRUE,
- wait = TRUE
-)
+ opal.project_restore(
+ opal,
+ project,
+ archive,
+ key = NULL,
+ override = TRUE,
+ wait = TRUE
+)
@@ -120,15 +120,15 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# create the project to restore, with the default database (to store tables)
-opal.project_create(o, 'GREENSPACE2', database = TRUE)
-# upload backup zip and launch restore task
-opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
-opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# create the project to restore, with the default database (to store tables)
+opal.project_create(o, 'GREENSPACE2', database = TRUE)
+# upload backup zip and launch restore task
+opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
+opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
+opal.logout(o)
+}
@@ -143,7 +143,7 @@ Examples
diff --git a/docs/reference/opal.projects.html b/docs/reference/opal.projects.html
index e8d51a41..73e9e973 100644
--- a/docs/reference/opal.projects.html
+++ b/docs/reference/opal.projects.html
@@ -69,7 +69,7 @@ Get projects
- opal.projects(opal, df = TRUE)
+ opal.projects(opal, df = TRUE)
@@ -94,11 +94,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects(o)
+opal.logout(o)
+}
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/opal.projects_databases.html b/docs/reference/opal.projects_databases.html
index 45f818b3..2a9dc9f0 100644
--- a/docs/reference/opal.projects_databases.html
+++ b/docs/reference/opal.projects_databases.html
@@ -69,7 +69,7 @@ Get projects databases
- opal.projects_databases(opal)
+ opal.projects_databases(opal)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects_databases(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects_databases(o)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.put.html b/docs/reference/opal.put.html
index de59ef78..1622010c 100644
--- a/docs/reference/opal.put.html
+++ b/docs/reference/opal.put.html
@@ -69,14 +69,14 @@ Generic REST resource update.
- opal.put(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- callback = NULL
-)
+ opal.put(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ callback = NULL
+)
@@ -115,11 +115,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.report.html b/docs/reference/opal.report.html
index eaf6c399..efc8d7c1 100644
--- a/docs/reference/opal.report.html
+++ b/docs/reference/opal.report.html
@@ -69,13 +69,13 @@ Opal report
- opal.report(
- input,
- output = NULL,
- progress = FALSE,
- verbose = FALSE,
- boot_style = NULL
-)
+ opal.report(
+ input,
+ output = NULL,
+ progress = FALSE,
+ verbose = FALSE,
+ boot_style = NULL
+)
@@ -103,9 +103,9 @@ Arguments
Examples
- if (FALSE) {
-opal.report('input.Rmd', 'report', progress=TRUE)
-}
+ if (FALSE) {
+opal.report('input.Rmd', 'report', progress=TRUE)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.report_md.html b/docs/reference/opal.report_md.html
index ad0cadd5..50a44df1 100644
--- a/docs/reference/opal.report_md.html
+++ b/docs/reference/opal.report_md.html
@@ -69,7 +69,7 @@ Turn a R markdown file to html.
- opal.report_md(inputFile, progress, verbose)
+ opal.report_md(inputFile, progress, verbose)
@@ -85,7 +85,7 @@ Turn a R markdown file to html.
diff --git a/docs/reference/opal.resource.html b/docs/reference/opal.resource.html
index 8040add0..128ece62 100644
--- a/docs/reference/opal.resource.html
+++ b/docs/reference/opal.resource.html
@@ -69,7 +69,7 @@ Get a resource reference of a project
- opal.resource(opal, project, resource)
+ opal.resource(opal, project, resource)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.resource_create.html b/docs/reference/opal.resource_create.html
index a7f47634..9ed343f2 100644
--- a/docs/reference/opal.resource_create.html
+++ b/docs/reference/opal.resource_create.html
@@ -69,17 +69,17 @@ Create a resource reference in a project
- opal.resource_create(
- opal,
- project,
- name,
- url,
- description = NULL,
- format = NULL,
- package = NULL,
- identity = NULL,
- secret = NULL
-)
+ opal.resource_create(
+ opal,
+ project,
+ name,
+ url,
+ description = NULL,
+ format = NULL,
+ package = NULL,
+ identity = NULL,
+ secret = NULL
+)
@@ -139,13 +139,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_create(o, 'RSRC', 'CNSIM4',
- url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
- format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_create(o, 'RSRC', 'CNSIM4',
+ url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
+ format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
+opal.logout(o)
+}
@@ -160,7 +160,7 @@ Examples
diff --git a/docs/reference/opal.resource_delete.html b/docs/reference/opal.resource_delete.html
index 41eee541..a3e48fb8 100644
--- a/docs/reference/opal.resource_delete.html
+++ b/docs/reference/opal.resource_delete.html
@@ -69,7 +69,7 @@ Delete a resource reference
- opal.resource_delete(opal, project, resource, silent = TRUE)
+ opal.resource_delete(opal, project, resource, silent = TRUE)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_delete(o, "RSRC", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_delete(o, "RSRC", "CNSIM4")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.resource_exists.html b/docs/reference/opal.resource_exists.html
index 7a5852e1..700fd693 100644
--- a/docs/reference/opal.resource_exists.html
+++ b/docs/reference/opal.resource_exists.html
@@ -69,7 +69,7 @@ Check a resource reference exists
- opal.resource_exists(opal, project, resource)
+ opal.resource_exists(opal, project, resource)
@@ -111,11 +111,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_exists(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_exists(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.resource_extension_create.html b/docs/reference/opal.resource_extension_create.html
index c0a045fe..1c8013c4 100644
--- a/docs/reference/opal.resource_extension_create.html
+++ b/docs/reference/opal.resource_extension_create.html
@@ -69,16 +69,16 @@ Create an extended resource reference in a project
- opal.resource_extension_create(
- opal,
- project,
- name,
- provider,
- factory,
- parameters,
- description = NULL,
- credentials = NULL
-)
+ opal.resource_extension_create(
+ opal,
+ project,
+ name,
+ provider,
+ factory,
+ parameters,
+ description = NULL,
+ credentials = NULL
+)
@@ -134,21 +134,21 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
- provider = 'dsOmics', factory = 'ga4gh-htsget',
- parameters = list(
- host = 'https://htsget.ga4gh.org',
- sample = '1000genomes.phase1.chr1',
- reference = '1',
- start = '1',
- end = '100000',
- format = 'GA4GHVCF'
- )
-)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
+ provider = 'dsOmics', factory = 'ga4gh-htsget',
+ parameters = list(
+ host = 'https://htsget.ga4gh.org',
+ sample = '1000genomes.phase1.chr1',
+ reference = '1',
+ start = '1',
+ end = '100000',
+ format = 'GA4GHVCF'
+ )
+)
+opal.logout(o)
+}
@@ -163,7 +163,7 @@ Examples
diff --git a/docs/reference/opal.resource_get.html b/docs/reference/opal.resource_get.html
index ae00707a..80a02871 100644
--- a/docs/reference/opal.resource_get.html
+++ b/docs/reference/opal.resource_get.html
@@ -69,7 +69,7 @@ Get the resource object of a project
- opal.resource_get(opal, project, resource)
+ opal.resource_get(opal, project, resource)
@@ -105,17 +105,17 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
-# then interpret locally the resource object (load the appropriate R packages)
-library(resourcer)
-# coerce to a data.frame
-as.data.frame(res)
-# or get the resource client object for low-level interactions
-rescli <- resourcer::newResourceClient(res)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
+# then interpret locally the resource object (load the appropriate R packages)
+library(resourcer)
+# coerce to a data.frame
+as.data.frame(res)
+# or get the resource client object for low-level interactions
+rescli <- resourcer::newResourceClient(res)
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm.html b/docs/reference/opal.resource_perm.html
index e6856cab..d97e7fef 100644
--- a/docs/reference/opal.resource_perm.html
+++ b/docs/reference/opal.resource_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a resource
- opal.resource_perm(opal, project, resource)
+ opal.resource_perm(opal, project, resource)
@@ -111,13 +111,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -132,7 +132,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm_add.html b/docs/reference/opal.resource_perm_add.html
index 9c3d1438..6ad84919 100644
--- a/docs/reference/opal.resource_perm_add.html
+++ b/docs/reference/opal.resource_perm_add.html
@@ -69,14 +69,14 @@ Add or update a permission on a resource
- opal.resource_perm_add(
- opal,
- project,
- resource,
- subject,
- type = "user",
- permission
-)
+ opal.resource_perm_add(
+ opal,
+ project,
+ resource,
+ subject,
+ type = "user",
+ permission
+)
@@ -125,13 +125,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -146,7 +146,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm_delete.html b/docs/reference/opal.resource_perm_delete.html
index df299ed2..541396ce 100644
--- a/docs/reference/opal.resource_perm_delete.html
+++ b/docs/reference/opal.resource_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a resource
- opal.resource_perm_delete(opal, project, resource, subject, type = "user")
+ opal.resource_perm_delete(opal, project, resource, subject, type = "user")
@@ -113,13 +113,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.resource_view_create.html b/docs/reference/opal.resource_view_create.html
index d653a1cf..f3a7a1f2 100644
--- a/docs/reference/opal.resource_view_create.html
+++ b/docs/reference/opal.resource_view_create.html
@@ -73,15 +73,15 @@ Create an Opal view over a resource reference
- opal.resource_view_create(
- opal,
- project,
- table,
- resource,
- type = "Participant",
- idColumn = NULL,
- profile = NULL
-)
+ opal.resource_view_create(
+ opal,
+ project,
+ table,
+ resource,
+ type = "Participant",
+ idColumn = NULL,
+ profile = NULL
+)
@@ -119,6 +119,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
@@ -139,14 +140,14 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
- resource = "RSRC.FEMALE_2439", idColumn = "Name")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
+ resource = "RSRC.FEMALE_2439", idColumn = "Name")
+opal.logout(o)
+}
@@ -161,7 +162,7 @@ Examples
diff --git a/docs/reference/opal.resource_view_reconnect.html b/docs/reference/opal.resource_view_reconnect.html
index e8650b92..06f03a44 100644
--- a/docs/reference/opal.resource_view_reconnect.html
+++ b/docs/reference/opal.resource_view_reconnect.html
@@ -73,7 +73,7 @@ Reconnect an Opal view to its underlying resource
- opal.resource_view_reconnect(opal, project, table)
+ opal.resource_view_reconnect(opal, project, table)
@@ -93,6 +93,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.table_create(),
opal.table_delete(),
@@ -113,14 +114,14 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-# re-initialize the view's connection to the resource
-opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+# re-initialize the view's connection to the resource
+opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
+opal.logout(o)
+}
@@ -135,7 +136,7 @@ Examples
diff --git a/docs/reference/opal.resources.html b/docs/reference/opal.resources.html
index 305236d9..1219e1b9 100644
--- a/docs/reference/opal.resources.html
+++ b/docs/reference/opal.resources.html
@@ -69,7 +69,7 @@ Get the resource references of a project
- opal.resources(opal, project, df = TRUE)
+ opal.resources(opal, project, df = TRUE)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources(o, 'RSRC')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources(o, 'RSRC')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm.html b/docs/reference/opal.resources_perm.html
index ba3302b2..c53289ba 100644
--- a/docs/reference/opal.resources_perm.html
+++ b/docs/reference/opal.resources_perm.html
@@ -69,7 +69,7 @@ Get the permissions on any resource
- opal.resources_perm(opal, project)
+ opal.resources_perm(opal, project)
@@ -107,13 +107,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm_add.html b/docs/reference/opal.resources_perm_add.html
index 1a4a38e2..f1c870b4 100644
--- a/docs/reference/opal.resources_perm_add.html
+++ b/docs/reference/opal.resources_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on any resource
- opal.resources_perm_add(opal, project, subject, type = "user", permission)
+ opal.resources_perm_add(opal, project, subject, type = "user", permission)
@@ -114,13 +114,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm_delete.html b/docs/reference/opal.resources_perm_delete.html
index e7c09535..5c093566 100644
--- a/docs/reference/opal.resources_perm_delete.html
+++ b/docs/reference/opal.resources_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from any resource
- opal.resources_perm_delete(opal, project, subject, type = "user")
+ opal.resources_perm_delete(opal, project, subject, type = "user")
@@ -109,13 +109,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM', 'CNSIM1')
-opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM', 'CNSIM1')
+opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.rm.html b/docs/reference/opal.rm.html
index f444e41c..728ec6d4 100644
--- a/docs/reference/opal.rm.html
+++ b/docs/reference/opal.rm.html
@@ -69,7 +69,7 @@ Remove a R symbol (deprecated)
- opal.rm(opal, symbol)
+ opal.rm(opal, symbol)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.rm(o, 'D')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.sql.html b/docs/reference/opal.sql.html
index 41f13417..5fa1f9b8 100644
--- a/docs/reference/opal.sql.html
+++ b/docs/reference/opal.sql.html
@@ -75,7 +75,7 @@ Execute a SQL query on tables
- opal.sql(opal, query, project = NULL, id.name = "_id")
+ opal.sql(opal, query, project = NULL, id.name = "_id")
@@ -106,23 +106,23 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from CNSIM1
- where LAB_HDL is not null
- group by GENDER',
- 'CNSIM')
-# without project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from `CNSIM.CNSIM1`
- where LAB_HDL is not null
- group by GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from CNSIM1
+ where LAB_HDL is not null
+ group by GENDER',
+ 'CNSIM')
+# without project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from `CNSIM.CNSIM1`
+ where LAB_HDL is not null
+ group by GENDER')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/opal.sql_history.html b/docs/reference/opal.sql_history.html
index ff53d0db..1bd338f2 100644
--- a/docs/reference/opal.sql_history.html
+++ b/docs/reference/opal.sql_history.html
@@ -71,14 +71,14 @@ SQL query execution history
- opal.sql_history(
- opal,
- project = NULL,
- offset = 0,
- limit = 100,
- user = NULL,
- df = TRUE
-)
+ opal.sql_history(
+ opal,
+ project = NULL,
+ offset = 0,
+ limit = 100,
+ user = NULL,
+ df = TRUE
+)
@@ -118,16 +118,16 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql_history(o, 'CNSIM')
-# without project context
-opal.sql_history(o, NA)
-# with or without project context
-opal.sql_history(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql_history(o, 'CNSIM')
+# without project context
+opal.sql_history(o, NA)
+# with or without project context
+opal.sql_history(o)
+opal.logout(o)
+}
@@ -142,7 +142,7 @@ Examples
diff --git a/docs/reference/opal.symbol_import.html b/docs/reference/opal.symbol_import.html
index ae50bd82..5ee219a5 100644
--- a/docs/reference/opal.symbol_import.html
+++ b/docs/reference/opal.symbol_import.html
@@ -71,16 +71,16 @@ Import a tibble
- opal.symbol_import(
- opal,
- symbol,
- project,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)
+ opal.symbol_import(
+ opal,
+ symbol,
+ project,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)
@@ -128,11 +128,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_import(o, 'D', 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_import(o, 'D', 'test')
+opal.logout(o)
+}
@@ -147,7 +147,7 @@ Examples
diff --git a/docs/reference/opal.symbol_rm.html b/docs/reference/opal.symbol_rm.html
index d0cfd696..6d16a689 100644
--- a/docs/reference/opal.symbol_rm.html
+++ b/docs/reference/opal.symbol_rm.html
@@ -69,7 +69,7 @@ Remove a R symbol
- opal.symbol_rm(opal, symbol)
+ opal.symbol_rm(opal, symbol)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_rm(o, 'D')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.symbol_save.html b/docs/reference/opal.symbol_save.html
index f2a900f1..79035aa9 100644
--- a/docs/reference/opal.symbol_save.html
+++ b/docs/reference/opal.symbol_save.html
@@ -69,7 +69,7 @@ Save a tibble
- opal.symbol_save(opal, symbol, destination)
+ opal.symbol_save(opal, symbol, destination)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_save(o, 'D', 'test.sav')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_save(o, 'D', 'test.sav')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.symbols.html b/docs/reference/opal.symbols.html
index bb88de70..1b7894c4 100644
--- a/docs/reference/opal.symbols.html
+++ b/docs/reference/opal.symbols.html
@@ -69,7 +69,7 @@ List R symbols
- opal.symbols(opal)
+ opal.symbols(opal)
@@ -89,11 +89,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbols(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbols(o)
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/opal.table.html b/docs/reference/opal.table.html
index b4d05790..be03e321 100644
--- a/docs/reference/opal.table.html
+++ b/docs/reference/opal.table.html
@@ -69,7 +69,7 @@ Get a table of a datasource
- opal.table(opal, datasource, table, counts = FALSE)
+ opal.table(opal, datasource, table, counts = FALSE)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.table_create.html b/docs/reference/opal.table_create.html
index 44e433ba..46cf045b 100644
--- a/docs/reference/opal.table_create.html
+++ b/docs/reference/opal.table_create.html
@@ -73,7 +73,7 @@ Create an Opal table or view
- opal.table_create(opal, project, table, type = "Participant", tables = NULL)
+ opal.table_create(opal, project, table, type = "Participant", tables = NULL)
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_delete(),
@@ -122,15 +123,15 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a raw table
-opal.table_create(o, "CNSIM", "CNSIM4")
-# make a view
-opal.table_create(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a raw table
+opal.table_create(o, "CNSIM", "CNSIM4")
+# make a view
+opal.table_create(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
@@ -145,7 +146,7 @@ Examples
diff --git a/docs/reference/opal.table_delete.html b/docs/reference/opal.table_delete.html
index 778f2343..cba12a39 100644
--- a/docs/reference/opal.table_delete.html
+++ b/docs/reference/opal.table_delete.html
@@ -71,7 +71,7 @@ Delete a Opal table
- opal.table_delete(opal, project, table, silent = TRUE)
+ opal.table_delete(opal, project, table, silent = TRUE)
@@ -95,6 +95,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,11 +116,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_delete(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_delete(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -134,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.table_dictionary_get.html b/docs/reference/opal.table_dictionary_get.html
index 95a5c21a..59126cc2 100644
--- a/docs/reference/opal.table_dictionary_get.html
+++ b/docs/reference/opal.table_dictionary_get.html
@@ -69,7 +69,7 @@ Get the dictionary of a Opal table
- opal.table_dictionary_get(opal, project, table)
+ opal.table_dictionary_get(opal, project, table)
@@ -89,6 +89,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -109,11 +110,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -128,7 +129,7 @@ Examples
diff --git a/docs/reference/opal.table_dictionary_update.html b/docs/reference/opal.table_dictionary_update.html
index c2e5bfc5..090a7d91 100644
--- a/docs/reference/opal.table_dictionary_update.html
+++ b/docs/reference/opal.table_dictionary_update.html
@@ -69,13 +69,13 @@ Update the dictionary of a Opal table
- opal.table_dictionary_update(
- opal,
- project,
- table,
- variables,
- categories = NULL
-)
+ opal.table_dictionary_update(
+ opal,
+ project,
+ table,
+ variables,
+ categories = NULL
+)
@@ -104,6 +104,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -124,23 +125,23 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-variables <- tibble::tribble(
- ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
- "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
- "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
- "disp", "decimal", "Disp label", NA, NA, 1, 3
-)
-categories <- tibble::tribble(
- ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
- "cyl", "4", 0, "Four", "Quatre",
- "cyl", "6", 0, "Six", "Six",
- "cyl", "8", 1, "Height", "Huit"
-)
-opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+variables <- tibble::tribble(
+ ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
+ "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
+ "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
+ "disp", "decimal", "Disp label", NA, NA, 1, 3
+)
+categories <- tibble::tribble(
+ ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
+ "cyl", "4", 0, "Four", "Quatre",
+ "cyl", "6", 0, "Six", "Six",
+ "cyl", "8", 1, "Height", "Huit"
+)
+opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
+opal.logout(o)
+}
@@ -155,7 +156,7 @@ Examples
diff --git a/docs/reference/opal.table_exists.html b/docs/reference/opal.table_exists.html
index 10649da8..e4ac20bb 100644
--- a/docs/reference/opal.table_exists.html
+++ b/docs/reference/opal.table_exists.html
@@ -71,7 +71,7 @@ Check a Opal table exists
- opal.table_exists(opal, project, table, view = NA)
+ opal.table_exists(opal, project, table, view = NA)
@@ -96,6 +96,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -116,16 +117,16 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# check table exists
-opal.table_exists(o, "CNSIM", "CNSIM1")
-# check table exists AND is a NOT a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
-# check table exists AND is a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# check table exists
+opal.table_exists(o, "CNSIM", "CNSIM1")
+# check table exists AND is a NOT a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
+# check table exists AND is a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
+opal.logout(o)
+}
@@ -140,7 +141,7 @@ Examples
diff --git a/docs/reference/opal.table_export.html b/docs/reference/opal.table_export.html
index f5eb8c76..5110bb07 100644
--- a/docs/reference/opal.table_export.html
+++ b/docs/reference/opal.table_export.html
@@ -73,15 +73,15 @@ Export a table as a file
- opal.table_export(
- opal,
- project,
- table,
- file,
- identifiers = NULL,
- id.name = "id",
- wait = TRUE
-)
+ opal.table_export(
+ opal,
+ project,
+ table,
+ file,
+ identifiers = NULL,
+ id.name = "id",
+ wait = TRUE
+)
@@ -120,6 +120,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -140,12 +141,12 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
- file = "/home/administrator/cnsim1.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
+ file = "/home/administrator/cnsim1.sav")
+opal.logout(o)
+}
@@ -160,7 +161,7 @@ Examples
diff --git a/docs/reference/opal.table_get.html b/docs/reference/opal.table_get.html
index 8a695e18..50b31621 100644
--- a/docs/reference/opal.table_get.html
+++ b/docs/reference/opal.table_get.html
@@ -73,14 +73,14 @@ Get a Opal table as a tibble
- opal.table_get(
- opal,
- project,
- table,
- id.name = "id",
- variables = NULL,
- missings = TRUE
-)
+ opal.table_get(
+ opal,
+ project,
+ table,
+ id.name = "id",
+ variables = NULL,
+ missings = TRUE
+)
@@ -112,6 +112,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -132,11 +133,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+opal.logout(o)
+}
@@ -151,7 +152,7 @@ Examples
diff --git a/docs/reference/opal.table_import.html b/docs/reference/opal.table_import.html
index e7a050a5..587ba457 100644
--- a/docs/reference/opal.table_import.html
+++ b/docs/reference/opal.table_import.html
@@ -77,17 +77,17 @@ Import a file as table
- opal.table_import(
- opal,
- file,
- project,
- table,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)
+ opal.table_import(
+ opal,
+ file,
+ project,
+ table,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)
@@ -131,6 +131,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -151,11 +152,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
+opal.logout(o)
+}
@@ -170,7 +171,7 @@ Examples
diff --git a/docs/reference/opal.table_perm.html b/docs/reference/opal.table_perm.html
index d6ebf2a3..b007ebba 100644
--- a/docs/reference/opal.table_perm.html
+++ b/docs/reference/opal.table_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a table
- opal.table_perm(opal, project, table)
+ opal.table_perm(opal, project, table)
@@ -95,6 +95,7 @@ Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,13 +116,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -136,7 +137,7 @@ Examples
diff --git a/docs/reference/opal.table_perm_add.html b/docs/reference/opal.table_perm_add.html
index dcd7c7bc..0a6d3975 100644
--- a/docs/reference/opal.table_perm_add.html
+++ b/docs/reference/opal.table_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on a table
- opal.table_perm_add(opal, project, table, subject, type = "user", permission)
+ opal.table_perm_add(opal, project, table, subject, type = "user", permission)
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -143,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.table_perm_delete.html b/docs/reference/opal.table_perm_delete.html
index 8b9b72de..940dd6c6 100644
--- a/docs/reference/opal.table_perm_delete.html
+++ b/docs/reference/opal.table_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a table
- opal.table_perm_delete(opal, project, table, subject, type = "user")
+ opal.table_perm_delete(opal, project, table, subject, type = "user")
@@ -97,6 +97,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -117,13 +118,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -138,7 +139,7 @@ Examples
diff --git a/docs/reference/opal.table_save.html b/docs/reference/opal.table_save.html
index 99d85274..b60ae4ab 100644
--- a/docs/reference/opal.table_save.html
+++ b/docs/reference/opal.table_save.html
@@ -71,18 +71,18 @@ Save a local tibble as a Opal table
- opal.table_save(
- opal,
- tibble,
- project,
- table,
- overwrite = TRUE,
- force = FALSE,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant"
-)
+ opal.table_save(
+ opal,
+ tibble,
+ project,
+ table,
+ overwrite = TRUE,
+ force = FALSE,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant"
+)
@@ -142,6 +142,7 @@ Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -162,15 +163,15 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-# do some (meta)data transformations, then save in opal's database
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
-# or overwrite data only (keep original data dictionary)
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+# do some (meta)data transformations, then save in opal's database
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
+# or overwrite data only (keep original data dictionary)
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
+opal.logout(o)
+}
@@ -185,7 +186,7 @@ Examples
diff --git a/docs/reference/opal.table_truncate.html b/docs/reference/opal.table_truncate.html
index 13487c0d..41394336 100644
--- a/docs/reference/opal.table_truncate.html
+++ b/docs/reference/opal.table_truncate.html
@@ -71,7 +71,7 @@ Truncate a Opal table
- opal.table_truncate(opal, project, table)
+ opal.table_truncate(opal, project, table)
@@ -91,6 +91,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -111,11 +112,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_truncate(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_truncate(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -130,7 +131,7 @@ Examples
diff --git a/docs/reference/opal.table_view_create.html b/docs/reference/opal.table_view_create.html
index 9b40db41..704d8e1c 100644
--- a/docs/reference/opal.table_view_create.html
+++ b/docs/reference/opal.table_view_create.html
@@ -73,7 +73,7 @@ Create an Opal view over tables
- opal.table_view_create(opal, project, table, tables, type = "Participant")
+ opal.table_view_create(opal, project, table, tables, type = "Participant")
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
@@ -143,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.table_view_update.html b/docs/reference/opal.table_view_update.html
index c4892e57..edf8750f 100644
--- a/docs/reference/opal.table_view_update.html
+++ b/docs/reference/opal.table_view_update.html
@@ -73,7 +73,7 @@ Update the table references and the entity filter of an Opal view
- opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
+ opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
@@ -101,6 +101,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -121,28 +122,28 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1"))
-
-# update the table references
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-
-# update the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
-
-# remove the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
-
-# update both the table references and the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
- where = "$('LAB_TSC').ge(5)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1"))
+
+# update the table references
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+
+# update the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
+
+# remove the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
+
+# update both the table references and the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
+ where = "$('LAB_TSC').ge(5)")
+opal.logout(o)
+}
@@ -157,7 +158,7 @@ Examples
diff --git a/docs/reference/opal.tables.html b/docs/reference/opal.tables.html
index da771ccc..3523f1ce 100644
--- a/docs/reference/opal.tables.html
+++ b/docs/reference/opal.tables.html
@@ -69,7 +69,7 @@ Get tables of a datasource
- opal.tables(opal, datasource, counts = FALSE, df = TRUE)
+ opal.tables(opal, datasource, counts = FALSE, df = TRUE)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables(o, 'CNSIM')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm.html b/docs/reference/opal.tables_perm.html
index e401969e..eaf76e27 100644
--- a/docs/reference/opal.tables_perm.html
+++ b/docs/reference/opal.tables_perm.html
@@ -69,7 +69,7 @@ Get the permissions on any table of a project
- opal.tables_perm(opal, project)
+ opal.tables_perm(opal, project)
@@ -91,13 +91,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm_add.html b/docs/reference/opal.tables_perm_add.html
index f9f318fe..34f1092b 100644
--- a/docs/reference/opal.tables_perm_add.html
+++ b/docs/reference/opal.tables_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on any table of a project
- opal.tables_perm_add(opal, project, subject, type = "user", permission)
+ opal.tables_perm_add(opal, project, subject, type = "user", permission)
@@ -97,13 +97,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm_delete.html b/docs/reference/opal.tables_perm_delete.html
index 58317fa1..c6c2bbb4 100644
--- a/docs/reference/opal.tables_perm_delete.html
+++ b/docs/reference/opal.tables_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from any table of a project
- opal.tables_perm_delete(opal, project, subject, type = "user")
+ opal.tables_perm_delete(opal, project, subject, type = "user")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/opal.task.html b/docs/reference/opal.task.html
index 5f63c0bb..9f2abe58 100644
--- a/docs/reference/opal.task.html
+++ b/docs/reference/opal.task.html
@@ -69,7 +69,7 @@ Get a task
- opal.task(opal, id)
+ opal.task(opal, id)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task(o, '1')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.task_cancel.html b/docs/reference/opal.task_cancel.html
index 4d2f68ff..a6d3af66 100644
--- a/docs/reference/opal.task_cancel.html
+++ b/docs/reference/opal.task_cancel.html
@@ -69,7 +69,7 @@ Cancel a task
- opal.task_cancel(opal, id)
+ opal.task_cancel(opal, id)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_cancel(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_cancel(o, '1')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.task_wait.html b/docs/reference/opal.task_wait.html
index e46c9ad1..c75baf8d 100644
--- a/docs/reference/opal.task_wait.html
+++ b/docs/reference/opal.task_wait.html
@@ -69,7 +69,7 @@ Wait for a task to complete.
- opal.task_wait(opal, id, max = NULL)
+ opal.task_wait(opal, id, max = NULL)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_wait(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_wait(o, '1')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.tasks.html b/docs/reference/opal.tasks.html
index b03cca25..bbc1909c 100644
--- a/docs/reference/opal.tasks.html
+++ b/docs/reference/opal.tasks.html
@@ -69,7 +69,7 @@ Get the tasks
- opal.tasks(opal, df = TRUE)
+ opal.tasks(opal, df = TRUE)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tasks(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tasks(o)
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.taxonomies.html b/docs/reference/opal.taxonomies.html
index 6eb7c9fc..7fdeb65c 100644
--- a/docs/reference/opal.taxonomies.html
+++ b/docs/reference/opal.taxonomies.html
@@ -71,7 +71,7 @@ Get taxonomies
- opal.taxonomies(opal, locale = "en", df = TRUE)
+ opal.taxonomies(opal, locale = "en", df = TRUE)
@@ -102,11 +102,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomies(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomies(o)
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy.html b/docs/reference/opal.taxonomy.html
index 588356cb..830f2f20 100644
--- a/docs/reference/opal.taxonomy.html
+++ b/docs/reference/opal.taxonomy.html
@@ -69,7 +69,7 @@ Get a taxonomy
- opal.taxonomy(opal, taxonomy)
+ opal.taxonomy(opal, taxonomy)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_delete.html b/docs/reference/opal.taxonomy_delete.html
index 56a28d51..16c5fe75 100644
--- a/docs/reference/opal.taxonomy_delete.html
+++ b/docs/reference/opal.taxonomy_delete.html
@@ -69,7 +69,7 @@ Delete a taxonomy
- opal.taxonomy_delete(opal, taxonomy)
+ opal.taxonomy_delete(opal, taxonomy)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_delete(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_delete(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_download.html b/docs/reference/opal.taxonomy_download.html
index bde9b7cc..72ddba73 100644
--- a/docs/reference/opal.taxonomy_download.html
+++ b/docs/reference/opal.taxonomy_download.html
@@ -69,7 +69,7 @@ Download a taxonomy file
- opal.taxonomy_download(opal, taxonomy, destination = NULL)
+ opal.taxonomy_download(opal, taxonomy, destination = NULL)
@@ -101,11 +101,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_upload.html b/docs/reference/opal.taxonomy_upload.html
index f64a1c9c..33aa2918 100644
--- a/docs/reference/opal.taxonomy_upload.html
+++ b/docs/reference/opal.taxonomy_upload.html
@@ -71,7 +71,7 @@ Upload a taxonomy file
- opal.taxonomy_upload(opal, path)
+ opal.taxonomy_upload(opal, path)
@@ -98,11 +98,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/opal.terms.html b/docs/reference/opal.terms.html
index 42d3ba1c..4514444d 100644
--- a/docs/reference/opal.terms.html
+++ b/docs/reference/opal.terms.html
@@ -69,7 +69,7 @@ Get the terms of a vocabulary
- opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
+ opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/opal.token.html b/docs/reference/opal.token.html
index 139cfb7f..2b23254c 100644
--- a/docs/reference/opal.token.html
+++ b/docs/reference/opal.token.html
@@ -71,7 +71,7 @@ Get a personal access token
- opal.token(opal, name)
+ opal.token(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_datashield_create.html b/docs/reference/opal.token_datashield_create.html
index 3eb7cd13..2f127a6b 100644
--- a/docs/reference/opal.token_datashield_create.html
+++ b/docs/reference/opal.token_datashield_create.html
@@ -71,7 +71,7 @@ Create a personal access token for Datashield usage
- opal.token_datashield_create(opal, name, projects = NULL)
+ opal.token_datashield_create(opal, name, projects = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_datashield_create(o, 'ds-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_datashield_create(o, 'ds-1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.token_delete.html b/docs/reference/opal.token_delete.html
index 780eb5ed..402a3d26 100644
--- a/docs/reference/opal.token_delete.html
+++ b/docs/reference/opal.token_delete.html
@@ -71,7 +71,7 @@ Delete a personal access token
- opal.token_delete(opal, name)
+ opal.token_delete(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_delete(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_delete(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_r_create.html b/docs/reference/opal.token_r_create.html
index b0b36787..c8222189 100644
--- a/docs/reference/opal.token_r_create.html
+++ b/docs/reference/opal.token_r_create.html
@@ -71,13 +71,13 @@ Create a personal access token for R usage
- opal.token_r_create(
- opal,
- name,
- projects = NULL,
- access = NULL,
- commands = c("export")
-)
+ opal.token_r_create(
+ opal,
+ name,
+ projects = NULL,
+ access = NULL,
+ commands = c("export")
+)
@@ -121,11 +121,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
+opal.logout(o)
+}
@@ -140,7 +140,7 @@ Examples
diff --git a/docs/reference/opal.token_renew.html b/docs/reference/opal.token_renew.html
index 72208339..e11a4f33 100644
--- a/docs/reference/opal.token_renew.html
+++ b/docs/reference/opal.token_renew.html
@@ -71,7 +71,7 @@ Renew an inactive personal access token
- opal.token_renew(opal, name)
+ opal.token_renew(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_renew(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_renew(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_sql_create.html b/docs/reference/opal.token_sql_create.html
index b618980e..d65e177c 100644
--- a/docs/reference/opal.token_sql_create.html
+++ b/docs/reference/opal.token_sql_create.html
@@ -71,7 +71,7 @@ Create a personal access token for SQL usage
- opal.token_sql_create(opal, name, projects = NULL)
+ opal.token_sql_create(opal, name, projects = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_sql_create(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_sql_create(o, 'sql-1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.tokens.html b/docs/reference/opal.tokens.html
index 59d4edfa..703771e5 100644
--- a/docs/reference/opal.tokens.html
+++ b/docs/reference/opal.tokens.html
@@ -71,7 +71,7 @@ Get the personal access tokens
- opal.tokens(opal, df = TRUE)
+ opal.tokens(opal, df = TRUE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tokens(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tokens(o)
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.unload_package.html b/docs/reference/opal.unload_package.html
index cb7ded42..6b5ebac0 100644
--- a/docs/reference/opal.unload_package.html
+++ b/docs/reference/opal.unload_package.html
@@ -69,7 +69,7 @@ Unload package
- opal.unload_package(opal, pkg)
+ opal.unload_package(opal, pkg)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.unload_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.unload_package(o, 'stats')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.valueset.html b/docs/reference/opal.valueset.html
index 7bbd50a4..d0c5c00a 100644
--- a/docs/reference/opal.valueset.html
+++ b/docs/reference/opal.valueset.html
@@ -69,7 +69,7 @@ Get the values of an entity
- opal.valueset(opal, datasource, table, identifier)
+ opal.valueset(opal, datasource, table, identifier)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.variable.html b/docs/reference/opal.variable.html
index 3e2e9155..2269ea5d 100644
--- a/docs/reference/opal.variable.html
+++ b/docs/reference/opal.variable.html
@@ -69,7 +69,7 @@ Get a variable of a table
- opal.variable(opal, datasource, table, variable)
+ opal.variable(opal, datasource, table, variable)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.variable_summary.html b/docs/reference/opal.variable_summary.html
index 75fda252..5686692d 100644
--- a/docs/reference/opal.variable_summary.html
+++ b/docs/reference/opal.variable_summary.html
@@ -69,14 +69,14 @@ Get summary statistics of a variable of a table
- opal.variable_summary(
- opal,
- datasource,
- table,
- variable,
- cached = TRUE,
- nature = NULL
-)
+ opal.variable_summary(
+ opal,
+ datasource,
+ table,
+ variable,
+ cached = TRUE,
+ nature = NULL
+)
@@ -124,11 +124,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
@@ -143,7 +143,7 @@ Examples
diff --git a/docs/reference/opal.variables.html b/docs/reference/opal.variables.html
index e1072df8..3ea90c87 100644
--- a/docs/reference/opal.variables.html
+++ b/docs/reference/opal.variables.html
@@ -69,7 +69,7 @@ Get variables of a table
- opal.variables(opal, datasource, table, locale = "en", df = TRUE)
+ opal.variables(opal, datasource, table, locale = "en", df = TRUE)
@@ -111,11 +111,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variables(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variables(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.version_compare.html b/docs/reference/opal.version_compare.html
index f9a8bc44..b8a11b96 100644
--- a/docs/reference/opal.version_compare.html
+++ b/docs/reference/opal.version_compare.html
@@ -71,7 +71,7 @@ Compare
- opal.version_compare(opal, version)
+ opal.version_compare(opal, version)
@@ -93,11 +93,11 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.version_compare(o, "2.6.0")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.version_compare(o, "2.6.0")
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.vocabularies.html b/docs/reference/opal.vocabularies.html
index 2a4ae4ac..edaf165e 100644
--- a/docs/reference/opal.vocabularies.html
+++ b/docs/reference/opal.vocabularies.html
@@ -69,7 +69,7 @@ Get the vocabularies of a taxonomy
- opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
+ opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabularies(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabularies(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.vocabulary.html b/docs/reference/opal.vocabulary.html
index 8dd847d4..18c471f7 100644
--- a/docs/reference/opal.vocabulary.html
+++ b/docs/reference/opal.vocabulary.html
@@ -69,7 +69,7 @@ Get a taxonomy vocabulary
- opal.vocabulary(opal, taxonomy, vocabulary)
+ opal.vocabulary(opal, taxonomy, vocabulary)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.workspace_restore.html b/docs/reference/opal.workspace_restore.html
index 192c945b..705b823a 100644
--- a/docs/reference/opal.workspace_restore.html
+++ b/docs/reference/opal.workspace_restore.html
@@ -69,7 +69,7 @@ Restore a R workspace from a opal.
- opal.workspace_restore(opal, ws)
+ opal.workspace_restore(opal, ws)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_restore(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_restore(o, 'test')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.workspace_rm.html b/docs/reference/opal.workspace_rm.html
index e33cf1d2..4bce81f9 100644
--- a/docs/reference/opal.workspace_rm.html
+++ b/docs/reference/opal.workspace_rm.html
@@ -69,7 +69,7 @@ Remove a R workspace from a opal.
- opal.workspace_rm(opal, ws, user = NULL)
+ opal.workspace_rm(opal, ws, user = NULL)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_rm(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_rm(o, 'test')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.workspace_save.html b/docs/reference/opal.workspace_save.html
index 074274e0..aa974933 100644
--- a/docs/reference/opal.workspace_save.html
+++ b/docs/reference/opal.workspace_save.html
@@ -69,7 +69,7 @@ Save the current session in a opal R workspace.
- opal.workspace_save(opal, save = TRUE)
+ opal.workspace_save(opal, save = TRUE)
@@ -98,14 +98,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# provide a workspace ID
-opal.workspace_save(o, 'test')
-# or use default one
-id <- opal.workspace_save(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# provide a workspace ID
+opal.workspace_save(o, 'test')
+# or use default one
+id <- opal.workspace_save(o)
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.workspaces.html b/docs/reference/opal.workspaces.html
index 83f92fdc..f4b0c155 100644
--- a/docs/reference/opal.workspaces.html
+++ b/docs/reference/opal.workspaces.html
@@ -69,7 +69,7 @@ Get the R workspaces from a opal.
- opal.workspaces(opal)
+ opal.workspaces(opal)
@@ -88,11 +88,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspaces(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspaces(o)
+opal.logout(o)
+}
@@ -107,7 +107,7 @@ Examples
diff --git a/docs/reference/opalr-package.html b/docs/reference/opalr-package.html
index acf0539c..7a3957ef 100644
--- a/docs/reference/opalr-package.html
+++ b/docs/reference/opalr-package.html
@@ -99,7 +99,7 @@ Author
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index db0185af..5d5b6ce2 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -123,6 +123,12 @@
/reference/dot-verbose.html
+
+ /reference/dsadmin.activity.html
+
+
+ /reference/dsadmin.activity_summary.html
+
/reference/dsadmin.get_method.html
@@ -144,6 +150,9 @@
/reference/dsadmin.installed_package.html
+
+ /reference/dsadmin.log.html
+
/reference/dsadmin.package_description.html
@@ -231,6 +240,12 @@
/reference/index.html
+
+ /reference/oadmin.activity.html
+
+
+ /reference/oadmin.activity_summary.html
+
/reference/oadmin.install_bioconductor_package.html
@@ -258,6 +273,15 @@
/reference/oadmin.installed_packages.html
+
+ /reference/oadmin.log.html
+
+
+ /reference/oadmin.log_rest.html
+
+
+ /reference/oadmin.log_sql.html
+
/reference/oadmin.package_description.html
@@ -426,6 +450,9 @@
/reference/opal.logout.html
+
+ /reference/opal.perms.html
+
/reference/opal.post.html
.extractLabel(
- locale = "en",
- labels = list(),
- localeKey = "locale",
- valueKey = "value"
-).extractLabel(
+ locale = "en",
+ labels = list(),
+ localeKey = "locale",
+ valueKey = "value"
+)Extract opalsid from cookie data frame.
-
+
@@ -85,7 +85,7 @@ .extractOpalSessionId(cookies).extractOpalSessionId(cookies)Extract opalsid from cookie data frame.
diff --git a/docs/reference/dot-getContent.html b/docs/reference/dot-getContent.html index 26d95ecf..d81a8ab3 100644 --- a/docs/reference/dot-getContent.html +++ b/docs/reference/dot-getContent.html @@ -69,7 +69,7 @@Wrapper of httr::content()
-
+
@@ -85,7 +85,7 @@ .getContent(opal, response).getContent(opal, response)Wrapper of httr::content()
diff --git a/docs/reference/dot-getPEMFilePath.html b/docs/reference/dot-getPEMFilePath.html index 0601b98d..bac96b2d 100644 --- a/docs/reference/dot-getPEMFilePath.html +++ b/docs/reference/dot-getPEMFilePath.html @@ -69,7 +69,7 @@Extract absolute path to the pem file
-
+
@@ -85,7 +85,7 @@ .getPEMFilePath(pem, directory = "~/.ssh").getPEMFilePath(pem, directory = "~/.ssh")Extract absolute path to the pem file
diff --git a/docs/reference/dot-getRSessionId.html b/docs/reference/dot-getRSessionId.html index 2c8ffd1f..10b997f2 100644 --- a/docs/reference/dot-getRSessionId.html +++ b/docs/reference/dot-getRSessionId.html @@ -69,7 +69,7 @@Extract R session Id from opal object, create a new R session if not found.<
- .getRSessionId(opal)
+ .getRSessionId(opal)
@@ -85,7 +85,7 @@ Extract R session Id from opal object, create a new R session if not found.<
diff --git a/docs/reference/dot-getSessions.html b/docs/reference/dot-getSessions.html
index 6a91fb4e..32bbbbbb 100644
--- a/docs/reference/dot-getSessions.html
+++ b/docs/reference/dot-getSessions.html
@@ -69,7 +69,7 @@ Get all R session in Opal.
- .getSessions(opal)
+ .getSessions(opal)
@@ -85,7 +85,7 @@ Get all R session in Opal.
diff --git a/docs/reference/dot-handleError.html b/docs/reference/dot-handleError.html
index 3f25f7b3..10a4a4d6 100644
--- a/docs/reference/dot-handleError.html
+++ b/docs/reference/dot-handleError.html
@@ -69,7 +69,7 @@ Handle error response
- .handleError(opal, response)
+ .handleError(opal, response)
@@ -85,7 +85,7 @@ Handle error response
diff --git a/docs/reference/dot-handleResponse.html b/docs/reference/dot-handleResponse.html
index 135a5f63..812aabe6 100644
--- a/docs/reference/dot-handleResponse.html
+++ b/docs/reference/dot-handleResponse.html
@@ -69,7 +69,7 @@ Default request response handler.
- .handleResponse(opal, response)
+ .handleResponse(opal, response)
@@ -85,7 +85,7 @@ Default request response handler.
diff --git a/docs/reference/dot-handleResponseLocation.html b/docs/reference/dot-handleResponseLocation.html
index 2aa7fa4a..1a9c550a 100644
--- a/docs/reference/dot-handleResponseLocation.html
+++ b/docs/reference/dot-handleResponseLocation.html
@@ -69,7 +69,7 @@ Default request response Location handler.
- .handleResponseLocation(opal, response)
+ .handleResponseLocation(opal, response)
@@ -85,7 +85,7 @@ Default request response Location handler.
diff --git a/docs/reference/dot-handleResponseOrCallback.html b/docs/reference/dot-handleResponseOrCallback.html
index 1c19cded..fd75863d 100644
--- a/docs/reference/dot-handleResponseOrCallback.html
+++ b/docs/reference/dot-handleResponseOrCallback.html
@@ -69,7 +69,7 @@ Process response with default handler or the provided one
- .handleResponseOrCallback(opal, response, callback = NULL)
+ .handleResponseOrCallback(opal, response, callback = NULL)
@@ -85,7 +85,7 @@ Process response with default handler or the provided one
diff --git a/docs/reference/dot-is.verbose.html b/docs/reference/dot-is.verbose.html
index f3462be7..ddaab2ed 100644
--- a/docs/reference/dot-is.verbose.html
+++ b/docs/reference/dot-is.verbose.html
@@ -69,7 +69,7 @@ Verbose option
- .is.verbose()
+ .is.verbose()
@@ -85,7 +85,7 @@ Verbose option
diff --git a/docs/reference/dot-isContentEmpty.html b/docs/reference/dot-isContentEmpty.html
index 2ca189f6..88320efd 100644
--- a/docs/reference/dot-isContentEmpty.html
+++ b/docs/reference/dot-isContentEmpty.html
@@ -69,7 +69,7 @@ Check if response content is empty.
- .isContentEmpty(content)
+ .isContentEmpty(content)
@@ -85,7 +85,7 @@ Check if response content is empty.
diff --git a/docs/reference/dot-listToJson.html b/docs/reference/dot-listToJson.html
index 9c4d2140..c0bd2195 100644
--- a/docs/reference/dot-listToJson.html
+++ b/docs/reference/dot-listToJson.html
@@ -69,7 +69,7 @@ Simple transformation function of a list into a JSON object/array.
- .listToJson(l)
+ .listToJson(l)
@@ -85,7 +85,7 @@ Simple transformation function of a list into a JSON object/array.
diff --git a/docs/reference/dot-newProgress.html b/docs/reference/dot-newProgress.html
index cdfa936f..c801ff16 100644
--- a/docs/reference/dot-newProgress.html
+++ b/docs/reference/dot-newProgress.html
@@ -69,12 +69,12 @@ Create a new progress instance with default settings.
- .newProgress(
- format = " :what [:bar] :percent /:elapsed",
- clear = getOption("opal.progress.clear", FALSE),
- total,
- width = 100
-)
+ .newProgress(
+ format = " :what [:bar] :percent /:elapsed",
+ clear = getOption("opal.progress.clear", FALSE),
+ total,
+ width = 100
+)
@@ -90,7 +90,7 @@ Create a new progress instance with default settings.
diff --git a/docs/reference/dot-newSession.html b/docs/reference/dot-newSession.html
index a3d04f33..b15cdaa4 100644
--- a/docs/reference/dot-newSession.html
+++ b/docs/reference/dot-newSession.html
@@ -69,7 +69,7 @@ Create a new R session in Opal.
- .newSession(opal, restore = NULL, profile = NULL)
+ .newSession(opal, restore = NULL, profile = NULL)
@@ -85,7 +85,7 @@ Create a new R session in Opal.
diff --git a/docs/reference/dot-opal.login.html b/docs/reference/dot-opal.login.html
index cf5be580..a2d29cf6 100644
--- a/docs/reference/dot-opal.login.html
+++ b/docs/reference/dot-opal.login.html
@@ -69,15 +69,15 @@ Create the opal object
- .opal.login(
- username,
- password,
- token,
- url,
- opts = list(),
- profile = profile,
- restore = NULL
-)
+ .opal.login(
+ username,
+ password,
+ token,
+ url,
+ opts = list(),
+ profile = profile,
+ restore = NULL
+)
@@ -93,7 +93,7 @@ Create the opal object
diff --git a/docs/reference/dot-rmOpalSession.html b/docs/reference/dot-rmOpalSession.html
index bfd20a01..a29f9e94 100644
--- a/docs/reference/dot-rmOpalSession.html
+++ b/docs/reference/dot-rmOpalSession.html
@@ -69,7 +69,7 @@ Remove a Opal session (logout)
- .rmOpalSession(opal)
+ .rmOpalSession(opal)
@@ -85,7 +85,7 @@ Remove a Opal session (logout)
diff --git a/docs/reference/dot-rmRSession.html b/docs/reference/dot-rmRSession.html
index b521882a..827d5ccb 100644
--- a/docs/reference/dot-rmRSession.html
+++ b/docs/reference/dot-rmRSession.html
@@ -69,7 +69,7 @@ Remove a R session from Opal.
- .rmRSession(opal, save = FALSE)
+ .rmRSession(opal, save = FALSE)
@@ -85,7 +85,7 @@ Remove a R session from Opal.
diff --git a/docs/reference/dot-select.html b/docs/reference/dot-select.html
index 43f6c002..13df65cb 100644
--- a/docs/reference/dot-select.html
+++ b/docs/reference/dot-select.html
@@ -69,7 +69,7 @@ Returns a list r such that r[[i]] == l[[i]][field] for all i:length(l)
- .select(l, field)
+ .select(l, field)
@@ -85,7 +85,7 @@ Returns a list r such that r[[i]] == l[[i]][field] for all i:length(l)
diff --git a/docs/reference/dot-tickProgress.html b/docs/reference/dot-tickProgress.html
index 46e06caa..0777056f 100644
--- a/docs/reference/dot-tickProgress.html
+++ b/docs/reference/dot-tickProgress.html
@@ -69,7 +69,7 @@ Output the progress status if option "datashield.progress" is allows to.
@@ -85,7 +85,7 @@ Output the progress status if option "datashield.progress" is allows to.
diff --git a/docs/reference/dot-tokenHeader.html b/docs/reference/dot-tokenHeader.html
index e6d91a46..a6265701 100644
--- a/docs/reference/dot-tokenHeader.html
+++ b/docs/reference/dot-tokenHeader.html
@@ -69,7 +69,7 @@ Constructs the value for the X-Opal-Auth header
- .tokenHeader(token)
+ .tokenHeader(token)
@@ -85,7 +85,7 @@ Constructs the value for the X-Opal-Auth header
diff --git a/docs/reference/dot-url.html b/docs/reference/dot-url.html
index 6f7da3b7..41bd1de4 100644
--- a/docs/reference/dot-url.html
+++ b/docs/reference/dot-url.html
@@ -69,7 +69,7 @@ Utility method to build urls. Concatenates all arguments and adds a '/' sepa
- .url(opal, ...)
+ .url(opal, ...)
@@ -85,7 +85,7 @@ Utility method to build urls. Concatenates all arguments and adds a '/' sepa
diff --git a/docs/reference/dot-verbose.html b/docs/reference/dot-verbose.html
index f47a65e5..3cf22c86 100644
--- a/docs/reference/dot-verbose.html
+++ b/docs/reference/dot-verbose.html
@@ -69,7 +69,7 @@ Verbose flag
- .verbose()
+ .verbose()
@@ -85,7 +85,7 @@ Verbose flag
diff --git a/docs/reference/dsadmin.activity.html b/docs/reference/dsadmin.activity.html
new file mode 100644
index 00000000..a0d1cc75
--- /dev/null
+++ b/docs/reference/dsadmin.activity.html
@@ -0,0 +1,146 @@
+
+Get DataSHIELD activity — dsadmin.activity • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded DataSHIELD session metrics.
+
+
+
+ dsadmin.activity(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+dsadmin.activity(o)
+# user and profile specific session metrics
+dsadmin.activity(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+dsadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.activity_summary.html b/docs/reference/dsadmin.activity_summary.html
new file mode 100644
index 00000000..c291b9fe
--- /dev/null
+++ b/docs/reference/dsadmin.activity_summary.html
@@ -0,0 +1,146 @@
+
+Get DataSHIELD activity summary — dsadmin.activity_summary • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded DataSHIELD session metrics, grouped by profile and user.
+
+
+
+ dsadmin.activity_summary(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+dsadmin.activity_summary(o)
+# user and profile specific session metrics
+dsadmin.activity_summary(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+dsadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.get_method.html b/docs/reference/dsadmin.get_method.html
index 35d8bada..7e0286ab 100644
--- a/docs/reference/dsadmin.get_method.html
+++ b/docs/reference/dsadmin.get_method.html
@@ -69,7 +69,7 @@ Get a DataSHIELD method
- dsadmin.get_method(opal, name, type = "aggregate", profile = NULL)
+ dsadmin.get_method(opal, name, type = "aggregate", profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_method(o, 'class')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_method(o, 'class')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.get_methods.html b/docs/reference/dsadmin.get_methods.html
index eb9d116f..332bd2e6 100644
--- a/docs/reference/dsadmin.get_methods.html
+++ b/docs/reference/dsadmin.get_methods.html
@@ -69,7 +69,7 @@ Get DataSHIELD methods
- dsadmin.get_methods(opal, type = "aggregate", profile = NULL)
+ dsadmin.get_methods(opal, type = "aggregate", profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_methods(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_methods(o)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.get_options.html b/docs/reference/dsadmin.get_options.html
index 41b6d38f..936afd9a 100644
--- a/docs/reference/dsadmin.get_options.html
+++ b/docs/reference/dsadmin.get_options.html
@@ -69,7 +69,7 @@ Get the DataSHIELD options
- dsadmin.get_options(opal, profile = NULL)
+ dsadmin.get_options(opal, profile = NULL)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_options(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_options(o)
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_github_package.html b/docs/reference/dsadmin.install_github_package.html
index 3cd61327..9cac06c4 100644
--- a/docs/reference/dsadmin.install_github_package.html
+++ b/docs/reference/dsadmin.install_github_package.html
@@ -69,13 +69,13 @@ Install a DataSHIELD package from GitHub
- dsadmin.install_github_package(
- opal,
- pkg,
- username = "datashield",
- ref = "master",
- profile = NULL
-)
+ dsadmin.install_github_package(
+ opal,
+ pkg,
+ username = "datashield",
+ ref = "master",
+ profile = NULL
+)
@@ -132,11 +132,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge')
+opal.logout(o)
+}
@@ -151,7 +151,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_local_package.html b/docs/reference/dsadmin.install_local_package.html
index a1a1c76d..d1a6d9a2 100644
--- a/docs/reference/dsadmin.install_local_package.html
+++ b/docs/reference/dsadmin.install_local_package.html
@@ -71,7 +71,7 @@ Install a DataSHIELD package from a local archive file
- dsadmin.install_local_package(opal, path, profile = NULL)
+ dsadmin.install_local_package(opal, path, profile = NULL)
@@ -114,14 +114,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# install a pre-built local archive file
-dsadmin.install_local_package(o, '~/dsExposome_1.0.0.tar.gz')
-# or build archive file from local package source (in current working folder)
-dsadmin.install_local_package(o, devtools::build())
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# install a pre-built local archive file
+dsadmin.install_local_package(o, '~/dsExposome_1.0.0.tar.gz')
+# or build archive file from local package source (in current working folder)
+dsadmin.install_local_package(o, devtools::build())
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_package.html b/docs/reference/dsadmin.install_package.html
index 5a0c9ad1..904d1231 100644
--- a/docs/reference/dsadmin.install_package.html
+++ b/docs/reference/dsadmin.install_package.html
@@ -69,13 +69,13 @@ Install a DataSHIELD package
- dsadmin.install_package(
- opal,
- pkg,
- githubusername = NULL,
- ref = NULL,
- profile = NULL
-)
+ dsadmin.install_package(
+ opal,
+ pkg,
+ githubusername = NULL,
+ ref = NULL,
+ profile = NULL
+)
@@ -132,11 +132,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.install_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.install_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -151,7 +151,7 @@ Examples
diff --git a/docs/reference/dsadmin.installed_package.html b/docs/reference/dsadmin.installed_package.html
index 65240b16..d4e1e5f8 100644
--- a/docs/reference/dsadmin.installed_package.html
+++ b/docs/reference/dsadmin.installed_package.html
@@ -69,7 +69,7 @@ Check DataSHIELD package
- dsadmin.installed_package(opal, pkg, profile = NULL)
+ dsadmin.installed_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.installed_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.installed_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/dsadmin.log.html b/docs/reference/dsadmin.log.html
new file mode 100644
index 00000000..76fcc36d
--- /dev/null
+++ b/docs/reference/dsadmin.log.html
@@ -0,0 +1,155 @@
+
+Get DataSHIELD logs — dsadmin.log • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ The DataSHIELD log is structured as follows:
+
+
+
+ dsadmin.log(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+ Details
+ Common fields
timestamp: when action is logged
version: not used
message: human readable message
logger_name: name of the log channel
thread_name: java thread name
level: log level (TRACE, DEBUG, INFO, WARN, ERROR)
level_value: log level numeric value
ip: ip origin of the request, when available
ds_id: unique DS session ID
ds_profile: DS profile name (available after the R server session is created, can be after authentication)
username: DS user name
r_duration: time spent by the remote R server action (all except PARSE)
r_size: R result serialized object size in bytes
ds_action: DS operation (OPEN, CLOSE, PARSE, ASSIGN, AGGREGATE, LS, RM, WS_SAVE, WS_RESTORE)
DS operations fields
OPEN: DS session opened (note: happens after successful authentication as R server session creation is deferred)
CLOSE: DS session closed
PARSE: R expression parsed
ds_map: DS function mappings used in the R parser, separated by semicolons when several functions are called
ds_script_in: R script as sent by DS user
ds_script_out: R script rewritten by opal, to be evaluated
ASSIGN:
ds_symbol: assigned symbol name
ds_table: table name that is assigned
ds_resource: resource name that is assigned
ds_eval: assign R expression that is evaluated
AGGREGATE:
ds_eval: aggregate R expression that is evaluated
LS: R symbols listed
RM: R symbol removed
ds_symbol: symbol name to remove
WS_SAVE:
ds_ws: workspace name
WS_RESTORE:
ds_ws: workspace name
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.log(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.package_description.html b/docs/reference/dsadmin.package_description.html
index 3351e46a..29694b5b 100644
--- a/docs/reference/dsadmin.package_description.html
+++ b/docs/reference/dsadmin.package_description.html
@@ -69,7 +69,7 @@ Get DataSHIELD package description
- dsadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
+ dsadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
@@ -117,11 +117,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_description(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_description(o, 'dsBase')
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/dsadmin.package_descriptions.html b/docs/reference/dsadmin.package_descriptions.html
index 5fb8ebc9..7707a023 100644
--- a/docs/reference/dsadmin.package_descriptions.html
+++ b/docs/reference/dsadmin.package_descriptions.html
@@ -69,7 +69,7 @@ Get DataSHIELD package descriptions
- dsadmin.package_descriptions(opal, fields = NULL, df = TRUE, profile = NULL)
+ dsadmin.package_descriptions(opal, fields = NULL, df = TRUE, profile = NULL)
@@ -123,11 +123,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_descriptions(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_descriptions(o)
+opal.logout(o)
+}
@@ -142,7 +142,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm.html b/docs/reference/dsadmin.perm.html
index c397d495..50f5957c 100644
--- a/docs/reference/dsadmin.perm.html
+++ b/docs/reference/dsadmin.perm.html
@@ -69,7 +69,7 @@ Get the DataSHIELD permissions
- dsadmin.perm(opal)
+ dsadmin.perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm_add.html b/docs/reference/dsadmin.perm_add.html
index 832ce0ce..e17b5796 100644
--- a/docs/reference/dsadmin.perm_add.html
+++ b/docs/reference/dsadmin.perm_add.html
@@ -69,7 +69,7 @@ Add or update a DataSHIELD permission
- dsadmin.perm_add(opal, subject, type = "user", permission)
+ dsadmin.perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm_delete.html b/docs/reference/dsadmin.perm_delete.html
index 91a12ac8..a5ce771c 100644
--- a/docs/reference/dsadmin.perm_delete.html
+++ b/docs/reference/dsadmin.perm_delete.html
@@ -69,7 +69,7 @@ Delete a DataSHIELD permission
- dsadmin.perm_delete(opal, subject, type = "user")
+ dsadmin.perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile.html b/docs/reference/dsadmin.profile.html
index d16b82ac..d8859752 100644
--- a/docs/reference/dsadmin.profile.html
+++ b/docs/reference/dsadmin.profile.html
@@ -73,7 +73,7 @@ Get a DataSHIELD profile
- dsadmin.profile(opal, name)
+ dsadmin.profile(opal, name)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile(o, name = 'default')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile(o, name = 'default')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_access.html b/docs/reference/dsadmin.profile_access.html
index b23f41c7..64ad8674 100644
--- a/docs/reference/dsadmin.profile_access.html
+++ b/docs/reference/dsadmin.profile_access.html
@@ -73,7 +73,7 @@ Restrict or open access to a DataSHIELD profile
- dsadmin.profile_access(opal, name, restricted = TRUE)
+ dsadmin.profile_access(opal, name, restricted = TRUE)
@@ -108,12 +108,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_access(o, name = 'survival', restricted = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_access(o, name = 'survival', restricted = TRUE)
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_create.html b/docs/reference/dsadmin.profile_create.html
index 5f5fb762..e377a2b7 100644
--- a/docs/reference/dsadmin.profile_create.html
+++ b/docs/reference/dsadmin.profile_create.html
@@ -69,7 +69,7 @@ Create a DataSHIELD profile
- dsadmin.profile_create(opal, name, cluster = "default", rParser = NULL)
+ dsadmin.profile_create(opal, name, cluster = "default", rParser = NULL)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_delete.html b/docs/reference/dsadmin.profile_delete.html
index 8bb60e74..de86336c 100644
--- a/docs/reference/dsadmin.profile_delete.html
+++ b/docs/reference/dsadmin.profile_delete.html
@@ -69,7 +69,7 @@ Delete a DataSHIELD profile
- dsadmin.profile_delete(opal, name)
+ dsadmin.profile_delete(opal, name)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_delete(o, name = 'survival')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_delete(o, name = 'survival')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_enable.html b/docs/reference/dsadmin.profile_enable.html
index 8901ed93..36ba9503 100644
--- a/docs/reference/dsadmin.profile_enable.html
+++ b/docs/reference/dsadmin.profile_enable.html
@@ -69,7 +69,7 @@ Enable or disable a DataSHIELD profile
- dsadmin.profile_enable(opal, name, enabled = TRUE)
+ dsadmin.profile_enable(opal, name, enabled = TRUE)
@@ -104,12 +104,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_enable(o, name = 'survival', enabled = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_enable(o, name = 'survival', enabled = TRUE)
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_exists.html b/docs/reference/dsadmin.profile_exists.html
index e5c19c97..5ea51e86 100644
--- a/docs/reference/dsadmin.profile_exists.html
+++ b/docs/reference/dsadmin.profile_exists.html
@@ -69,7 +69,7 @@ Check a DataSHIELD profile exists
- dsadmin.profile_exists(opal, name)
+ dsadmin.profile_exists(opal, name)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-if (!dsadmin.profile_exists(o, name = 'survival'))
- dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+if (!dsadmin.profile_exists(o, name = 'survival'))
+ dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_init.html b/docs/reference/dsadmin.profile_init.html
index 1d117fad..ad4fc311 100644
--- a/docs/reference/dsadmin.profile_init.html
+++ b/docs/reference/dsadmin.profile_init.html
@@ -73,7 +73,7 @@ Initialize a DataSHIELD profile
- dsadmin.profile_init(opal, name, packages = NULL)
+ dsadmin.profile_init(opal, name, packages = NULL)
@@ -108,12 +108,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_init(o, name = 'survival', packages = c('dsSurvival'))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_init(o, name = 'survival', packages = c('dsSurvival'))
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm.html b/docs/reference/dsadmin.profile_perm.html
index ea1913ac..3f90f5de 100644
--- a/docs/reference/dsadmin.profile_perm.html
+++ b/docs/reference/dsadmin.profile_perm.html
@@ -69,7 +69,7 @@ Get the permissions of a DataSHIELD profile
- dsadmin.profile_perm(opal, name)
+ dsadmin.profile_perm(opal, name)
@@ -106,13 +106,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm_add.html b/docs/reference/dsadmin.profile_perm_add.html
index 5aa4f324..e9b60807 100644
--- a/docs/reference/dsadmin.profile_perm_add.html
+++ b/docs/reference/dsadmin.profile_perm_add.html
@@ -71,13 +71,13 @@ Add or update a permission on a DataSHIELD profile
- dsadmin.profile_perm_add(
- opal,
- name,
- subject,
- type = "user",
- permission = "use"
-)
+ dsadmin.profile_perm_add(
+ opal,
+ name,
+ subject,
+ type = "user",
+ permission = "use"
+)
@@ -120,13 +120,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -141,7 +141,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm_delete.html b/docs/reference/dsadmin.profile_perm_delete.html
index 5b218b2b..8d2fa69a 100644
--- a/docs/reference/dsadmin.profile_perm_delete.html
+++ b/docs/reference/dsadmin.profile_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a DataSHIELD profile
- dsadmin.profile_perm_delete(opal, name, subject, type = "user")
+ dsadmin.profile_perm_delete(opal, name, subject, type = "user")
@@ -108,13 +108,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_rparser.html b/docs/reference/dsadmin.profile_rparser.html
index f24c5242..bf9617df 100644
--- a/docs/reference/dsadmin.profile_rparser.html
+++ b/docs/reference/dsadmin.profile_rparser.html
@@ -69,7 +69,7 @@ Set or remove the R parser version of a DataSHIELD profile
- dsadmin.profile_rparser(opal, name, rParser = NULL)
+ dsadmin.profile_rparser(opal, name, rParser = NULL)
@@ -105,15 +105,15 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-# apply R parser version v2
-dsadmin.profile_rparser(o, name = 'survival', rParser = 'v2')
-# apply system's default R parser version
-dsadmin.profile_rparser(o, name = 'survival')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+# apply R parser version v2
+dsadmin.profile_rparser(o, name = 'survival', rParser = 'v2')
+# apply system's default R parser version
+dsadmin.profile_rparser(o, name = 'survival')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profiles.html b/docs/reference/dsadmin.profiles.html
index 7f97e3ad..2ab7201f 100644
--- a/docs/reference/dsadmin.profiles.html
+++ b/docs/reference/dsadmin.profiles.html
@@ -69,7 +69,7 @@ Get DataSHIELD profiles
- dsadmin.profiles(opal, df = TRUE)
+ dsadmin.profiles(opal, df = TRUE)
@@ -106,11 +106,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_descriptions(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_descriptions(o)
+opal.logout(o)
+}
@@ -125,7 +125,7 @@ Examples
diff --git a/docs/reference/dsadmin.publish_package.html b/docs/reference/dsadmin.publish_package.html
index 1aed7d0b..db0a16e3 100644
--- a/docs/reference/dsadmin.publish_package.html
+++ b/docs/reference/dsadmin.publish_package.html
@@ -69,7 +69,7 @@ Publish DataSHIELD package settings
- dsadmin.publish_package(opal, pkg, profile = NULL)
+ dsadmin.publish_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.publish_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.publish_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/dsadmin.remove_package.html b/docs/reference/dsadmin.remove_package.html
index a696d968..11d7e1d3 100644
--- a/docs/reference/dsadmin.remove_package.html
+++ b/docs/reference/dsadmin.remove_package.html
@@ -69,7 +69,7 @@ Remove DataSHIELD package
- dsadmin.remove_package(opal, pkg, profile = NULL)
+ dsadmin.remove_package(opal, pkg, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.remove_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.remove_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_method.html b/docs/reference/dsadmin.rm_method.html
index cca7bb9e..b2d596b8 100644
--- a/docs/reference/dsadmin.rm_method.html
+++ b/docs/reference/dsadmin.rm_method.html
@@ -69,7 +69,7 @@ Remove DataSHIELD method
- dsadmin.rm_method(opal, name, type = "aggregate", profile = NULL)
+ dsadmin.rm_method(opal, name, type = "aggregate", profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_method(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_method(o, 'foo')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_methods.html b/docs/reference/dsadmin.rm_methods.html
index 2532751f..470d8498 100644
--- a/docs/reference/dsadmin.rm_methods.html
+++ b/docs/reference/dsadmin.rm_methods.html
@@ -69,7 +69,7 @@ Remove DataSHIELD methods.
- dsadmin.rm_methods(opal, type = NULL, profile = NULL)
+ dsadmin.rm_methods(opal, type = NULL, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_methods(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_methods(o)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_option.html b/docs/reference/dsadmin.rm_option.html
index 64995c5f..1b4ed85b 100644
--- a/docs/reference/dsadmin.rm_option.html
+++ b/docs/reference/dsadmin.rm_option.html
@@ -69,7 +69,7 @@ Remove a DataSHIELD option
- dsadmin.rm_option(opal, name, profile = NULL)
+ dsadmin.rm_option(opal, name, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_option(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_option(o, 'foo')
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_options.html b/docs/reference/dsadmin.rm_options.html
index 80414f34..2e4e1b38 100644
--- a/docs/reference/dsadmin.rm_options.html
+++ b/docs/reference/dsadmin.rm_options.html
@@ -69,7 +69,7 @@ Remove all DataSHIELD options
- dsadmin.rm_options(opal, profile = NULL)
+ dsadmin.rm_options(opal, profile = NULL)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_options(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_options(o, 'foo')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_package_methods.html b/docs/reference/dsadmin.rm_package_methods.html
index 26a699ef..f86188d4 100644
--- a/docs/reference/dsadmin.rm_package_methods.html
+++ b/docs/reference/dsadmin.rm_package_methods.html
@@ -69,7 +69,7 @@ Remove DataSHIELD package methods
- dsadmin.rm_package_methods(opal, pkg, type = NULL, profile = NULL)
+ dsadmin.rm_package_methods(opal, pkg, type = NULL, profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_package_methods(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_package_methods(o, 'dsBase')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_method.html b/docs/reference/dsadmin.set_method.html
index ab7bc9ff..a1287cc2 100644
--- a/docs/reference/dsadmin.set_method.html
+++ b/docs/reference/dsadmin.set_method.html
@@ -69,14 +69,14 @@ Set DataSHIELD method
- dsadmin.set_method(
- opal,
- name,
- func = NULL,
- path = NULL,
- type = "aggregate",
- profile = NULL
-)
+ dsadmin.set_method(
+ opal,
+ name,
+ func = NULL,
+ path = NULL,
+ type = "aggregate",
+ profile = NULL
+)
@@ -131,14 +131,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# as a package's function
-dsadmin.set_method(o, 'foo', func = 'base::mean')
-# as a custom function
-dsadmin.set_method(o, 'foo', func = function(x) { base::mean(x) })
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# as a package's function
+dsadmin.set_method(o, 'foo', func = 'base::mean')
+# as a custom function
+dsadmin.set_method(o, 'foo', func = function(x) { base::mean(x) })
+opal.logout(o)
+}
@@ -153,7 +153,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_option.html b/docs/reference/dsadmin.set_option.html
index fa661b5b..af2b415b 100644
--- a/docs/reference/dsadmin.set_option.html
+++ b/docs/reference/dsadmin.set_option.html
@@ -69,7 +69,7 @@ Set DataSHIELD option
- dsadmin.set_option(opal, name, value, profile = NULL)
+ dsadmin.set_option(opal, name, value, profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.set_option(o, 'foo', 'bar')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.set_option(o, 'foo', 'bar')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_package_methods.html b/docs/reference/dsadmin.set_package_methods.html
index 663ff9fd..91a0f0e5 100644
--- a/docs/reference/dsadmin.set_package_methods.html
+++ b/docs/reference/dsadmin.set_package_methods.html
@@ -69,7 +69,7 @@ Set DataSHIELD package methods
- dsadmin.set_package_methods(opal, pkg, type = NULL, profile = NULL)
+ dsadmin.set_package_methods(opal, pkg, type = NULL, profile = NULL)
@@ -122,11 +122,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.set_package_methods(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.set_package_methods(o, 'dsBase')
+opal.logout(o)
+}
@@ -141,7 +141,7 @@ Examples
diff --git a/docs/reference/dsadmin.unpublish_package.html b/docs/reference/dsadmin.unpublish_package.html
index 59177cb6..2f4cb561 100644
--- a/docs/reference/dsadmin.unpublish_package.html
+++ b/docs/reference/dsadmin.unpublish_package.html
@@ -69,7 +69,7 @@ Unpublish DataSHIELD package settings
- dsadmin.unpublish_package(opal, pkg, profile = NULL)
+ dsadmin.unpublish_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.unpublish_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.unpublish_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 7b8fa952..1410bfd7 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -86,6 +86,14 @@ All functions dictionary.inspect()
Inspect the dictionary of a tibble
+
+
+ Get DataSHIELD activity
+
+
+ Get DataSHIELD activity summary
@@ -114,6 +122,10 @@ All functions dsadmin.installed_package()
Check DataSHIELD package
+
+
+ Get DataSHIELD logs
@@ -226,6 +238,14 @@ All functions dsadmin.unpublish_package()
Unpublish DataSHIELD package settings
+
+
+ Get R activity
+
+
+ Get R activity summary
@@ -262,6 +282,18 @@ All functions oadmin.installed_packages()
List installed packages
+
+
+ Get Opal main logs
+
+
+ Get Opal REST API logs
+
+
+ Get Opal SQL API logs
@@ -486,6 +518,10 @@ All functions opal.logout()
Logout from Opal(s)
+
+
+ Get the permissions of a subject
@@ -847,7 +883,7 @@ All functions
diff --git a/docs/reference/oadmin.activity.html b/docs/reference/oadmin.activity.html
new file mode 100644
index 00000000..a11491b6
--- /dev/null
+++ b/docs/reference/oadmin.activity.html
@@ -0,0 +1,146 @@
+
+Get R activity — oadmin.activity • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics.
+
+
+
+ oadmin.activity(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity(o)
+# user and profile specific session metrics
+oadmin.activity(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.activity_summary.html b/docs/reference/oadmin.activity_summary.html
new file mode 100644
index 00000000..a8159421
--- /dev/null
+++ b/docs/reference/oadmin.activity_summary.html
@@ -0,0 +1,146 @@
+
+Get R activity summary — oadmin.activity_summary • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics, grouped by profile and user.
+
+
+
+ oadmin.activity_summary(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity_summary(o)
+# user and profile specific session metrics
+oadmin.activity_summary(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.install_bioconductor_package.html b/docs/reference/oadmin.install_bioconductor_package.html
index adde90ec..2c0551ed 100644
--- a/docs/reference/oadmin.install_bioconductor_package.html
+++ b/docs/reference/oadmin.install_bioconductor_package.html
@@ -69,7 +69,7 @@ Install a package from Bioconductor
- oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
+ oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_bioconductor_package(o, 'GWASTools')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_bioconductor_package(o, 'GWASTools')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.install_cran_package.html b/docs/reference/oadmin.install_cran_package.html
index 3e7e3a18..d229933e 100644
--- a/docs/reference/oadmin.install_cran_package.html
+++ b/docs/reference/oadmin.install_cran_package.html
@@ -69,7 +69,7 @@ Install a package from CRAN
- oadmin.install_cran_package(opal, pkg, profile = NULL)
+ oadmin.install_cran_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_cran_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_cran_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.install_devtools.html b/docs/reference/oadmin.install_devtools.html
index 3f2bc53c..79b175d3 100644
--- a/docs/reference/oadmin.install_devtools.html
+++ b/docs/reference/oadmin.install_devtools.html
@@ -69,7 +69,7 @@ Install devtools package
- oadmin.install_devtools(opal, profile = NULL)
+ oadmin.install_devtools(opal, profile = NULL)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_devtools(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.install_github_package.html b/docs/reference/oadmin.install_github_package.html
index 496f0075..ae130887 100644
--- a/docs/reference/oadmin.install_github_package.html
+++ b/docs/reference/oadmin.install_github_package.html
@@ -69,13 +69,13 @@ Install a package from GitHub
- oadmin.install_github_package(
- opal,
- pkg,
- username = getOption("github.user"),
- ref = "master",
- profile = NULL
-)
+ oadmin.install_github_package(
+ opal,
+ pkg,
+ username = getOption("github.user"),
+ ref = "master",
+ profile = NULL
+)
@@ -117,11 +117,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_github_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_github_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/oadmin.install_local_package.html b/docs/reference/oadmin.install_local_package.html
index 17ddc429..9ddb56c3 100644
--- a/docs/reference/oadmin.install_local_package.html
+++ b/docs/reference/oadmin.install_local_package.html
@@ -71,7 +71,7 @@ Install a package from a local archive file
- oadmin.install_local_package(opal, path, profile = NULL)
+ oadmin.install_local_package(opal, path, profile = NULL)
@@ -105,14 +105,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# install a pre-built local archive file
-oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
-# or build archive file from local package source (in current working folder)
-oadmin.install_local_package(o, devtools::build())
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# install a pre-built local archive file
+oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
+# or build archive file from local package source (in current working folder)
+oadmin.install_local_package(o, devtools::build())
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/oadmin.install_package.html b/docs/reference/oadmin.install_package.html
index 0b2c26c5..7539e7fc 100644
--- a/docs/reference/oadmin.install_package.html
+++ b/docs/reference/oadmin.install_package.html
@@ -69,7 +69,7 @@ Install CRAN package
- oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
+ oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
@@ -113,11 +113,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_package(o, 'xxx')
+opal.logout(o)
+}
@@ -132,7 +132,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_devtools.html b/docs/reference/oadmin.installed_devtools.html
index eaf1b900..a90063c1 100644
--- a/docs/reference/oadmin.installed_devtools.html
+++ b/docs/reference/oadmin.installed_devtools.html
@@ -69,7 +69,7 @@ Check devtools package
- oadmin.installed_devtools(opal, profile = NULL)
+ oadmin.installed_devtools(opal, profile = NULL)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_devtools(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_package.html b/docs/reference/oadmin.installed_package.html
index 604bd8ef..aa802b54 100644
--- a/docs/reference/oadmin.installed_package.html
+++ b/docs/reference/oadmin.installed_package.html
@@ -69,7 +69,7 @@ Check package is installed
- oadmin.installed_package(opal, pkg, profile = NULL)
+ oadmin.installed_package(opal, pkg, profile = NULL)
@@ -109,12 +109,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_package(o, 'xxx')
-oadmin.installed_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_package(o, 'xxx')
+oadmin.installed_package(o, 'stats')
+opal.logout(o)
+}
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_packages.html b/docs/reference/oadmin.installed_packages.html
index 2bc6bfc8..2034f299 100644
--- a/docs/reference/oadmin.installed_packages.html
+++ b/docs/reference/oadmin.installed_packages.html
@@ -69,7 +69,7 @@ List installed packages
- oadmin.installed_packages(opal, profile = NULL)
+ oadmin.installed_packages(opal, profile = NULL)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_packages(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_packages(o)
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/oadmin.log.html b/docs/reference/oadmin.log.html
new file mode 100644
index 00000000..2204fa48
--- /dev/null
+++ b/docs/reference/oadmin.log.html
@@ -0,0 +1,118 @@
+
+Get Opal main logs — oadmin.log • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal main logs
+
+
+
+ oadmin.log(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.log_rest.html b/docs/reference/oadmin.log_rest.html
new file mode 100644
index 00000000..fd2f9ef2
--- /dev/null
+++ b/docs/reference/oadmin.log_rest.html
@@ -0,0 +1,118 @@
+
+Get Opal REST API logs — oadmin.log_rest • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal REST API logs
+
+
+
+ oadmin.log_rest(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_rest(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.log_sql.html b/docs/reference/oadmin.log_sql.html
new file mode 100644
index 00000000..0dc4fae5
--- /dev/null
+++ b/docs/reference/oadmin.log_sql.html
@@ -0,0 +1,118 @@
+
+Get Opal SQL API logs — oadmin.log_sql • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal SQL API logs
+
+
+
+ oadmin.log_sql(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_sql(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.package_description.html b/docs/reference/oadmin.package_description.html
index d07d871e..d402b336 100644
--- a/docs/reference/oadmin.package_description.html
+++ b/docs/reference/oadmin.package_description.html
@@ -69,7 +69,7 @@ Get package description
- oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
+ oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.package_description(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.package_description(o, 'stats')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/oadmin.perm.html b/docs/reference/oadmin.perm.html
index b61d3e13..20a30ecc 100644
--- a/docs/reference/oadmin.perm.html
+++ b/docs/reference/oadmin.perm.html
@@ -69,7 +69,7 @@ Get the R permissions (deprecated)
- oadmin.perm(opal)
+ oadmin.perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.perm_add.html b/docs/reference/oadmin.perm_add.html
index b3a39610..df43a7c7 100644
--- a/docs/reference/oadmin.perm_add.html
+++ b/docs/reference/oadmin.perm_add.html
@@ -69,7 +69,7 @@ Add or update a R permission (deprecated)
- oadmin.perm_add(opal, subject, type = "user", permission)
+ oadmin.perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.perm_delete.html b/docs/reference/oadmin.perm_delete.html
index f629e6fc..fa8fa4de 100644
--- a/docs/reference/oadmin.perm_delete.html
+++ b/docs/reference/oadmin.perm_delete.html
@@ -69,7 +69,7 @@ Delete a R permission (deprecated)
- oadmin.perm_delete(opal, subject, type = "user")
+ oadmin.perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm.html b/docs/reference/oadmin.r_perm.html
index 4bae064d..12b32d20 100644
--- a/docs/reference/oadmin.r_perm.html
+++ b/docs/reference/oadmin.r_perm.html
@@ -69,7 +69,7 @@ Get the R permissions
- oadmin.r_perm(opal)
+ oadmin.r_perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm_add.html b/docs/reference/oadmin.r_perm_add.html
index 06ec844e..fc74abf1 100644
--- a/docs/reference/oadmin.r_perm_add.html
+++ b/docs/reference/oadmin.r_perm_add.html
@@ -69,7 +69,7 @@ Add or update a R permission
- oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
+ oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm_delete.html b/docs/reference/oadmin.r_perm_delete.html
index c68d1ff5..01177602 100644
--- a/docs/reference/oadmin.r_perm_delete.html
+++ b/docs/reference/oadmin.r_perm_delete.html
@@ -69,7 +69,7 @@ Delete a R permission
- oadmin.r_perm_delete(opal, subject, type = "user")
+ oadmin.r_perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.remove_package.html b/docs/reference/oadmin.remove_package.html
index 7d9fd447..0953b827 100644
--- a/docs/reference/oadmin.remove_package.html
+++ b/docs/reference/oadmin.remove_package.html
@@ -69,7 +69,7 @@ Remove package
- oadmin.remove_package(opal, pkg, profile = NULL)
+ oadmin.remove_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.remove_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.remove_package(o, 'xxx')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.system_metrics.html b/docs/reference/oadmin.system_metrics.html
index 4e5ba20e..9eb7d54a 100644
--- a/docs/reference/oadmin.system_metrics.html
+++ b/docs/reference/oadmin.system_metrics.html
@@ -81,7 +81,7 @@ Get system metrics
- oadmin.system_metrics(opal)
+ oadmin.system_metrics(opal)
@@ -93,11 +93,11 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_metrics(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_metrics(o)
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm.html b/docs/reference/oadmin.system_perm.html
index a858025b..5cc5a542 100644
--- a/docs/reference/oadmin.system_perm.html
+++ b/docs/reference/oadmin.system_perm.html
@@ -69,7 +69,7 @@ Get the System permissions
- oadmin.system_perm(opal)
+ oadmin.system_perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm_add.html b/docs/reference/oadmin.system_perm_add.html
index 8b06fd5e..ecc56a90 100644
--- a/docs/reference/oadmin.system_perm_add.html
+++ b/docs/reference/oadmin.system_perm_add.html
@@ -69,7 +69,7 @@ Add or update a System permission
- oadmin.system_perm_add(opal, subject, type = "user", permission)
+ oadmin.system_perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm_delete.html b/docs/reference/oadmin.system_perm_delete.html
index c78fc7d4..5268feec 100644
--- a/docs/reference/oadmin.system_perm_delete.html
+++ b/docs/reference/oadmin.system_perm_delete.html
@@ -69,7 +69,7 @@ Delete a System permission
- oadmin.system_perm_delete(opal, subject, type = "user")
+ oadmin.system_perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.user_add.html b/docs/reference/oadmin.user_add.html
index e5a58e5b..1b82c9b6 100644
--- a/docs/reference/oadmin.user_add.html
+++ b/docs/reference/oadmin.user_add.html
@@ -69,7 +69,7 @@ Add a user
- oadmin.user_add(opal, name, groups = NULL, password = NULL)
+ oadmin.user_add(opal, name, groups = NULL, password = NULL)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/oadmin.user_delete.html b/docs/reference/oadmin.user_delete.html
index 123be6e5..1ae1cb20 100644
--- a/docs/reference/oadmin.user_delete.html
+++ b/docs/reference/oadmin.user_delete.html
@@ -69,7 +69,7 @@ Delete a user
- oadmin.user_delete(opal, name)
+ oadmin.user_delete(opal, name)
@@ -96,12 +96,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_delete(o, "foo")
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/oadmin.user_enable.html b/docs/reference/oadmin.user_enable.html
index 1b531f3a..5b480d04 100644
--- a/docs/reference/oadmin.user_enable.html
+++ b/docs/reference/oadmin.user_enable.html
@@ -69,7 +69,7 @@ Enable a user
- oadmin.user_enable(opal, name, enabled = TRUE)
+ oadmin.user_enable(opal, name, enabled = TRUE)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_enable(o, "foo", enabled = FALSE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_enable(o, "foo", enabled = FALSE)
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/oadmin.user_exists.html b/docs/reference/oadmin.user_exists.html
index e05a1f79..fad76e33 100644
--- a/docs/reference/oadmin.user_exists.html
+++ b/docs/reference/oadmin.user_exists.html
@@ -71,7 +71,7 @@ Check user exists
- oadmin.user_exists(opal, name)
+ oadmin.user_exists(opal, name)
@@ -98,12 +98,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-if (!oadmin.user_exists(o, "foo"))
- oadmin.user_add(o, "foo", password = "bar123")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+if (!oadmin.user_exists(o, "foo"))
+ oadmin.user_add(o, "foo", password = "bar123")
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.user_profile_delete.html b/docs/reference/oadmin.user_profile_delete.html
index e1aab115..2e585266 100644
--- a/docs/reference/oadmin.user_profile_delete.html
+++ b/docs/reference/oadmin.user_profile_delete.html
@@ -75,7 +75,7 @@ Delete a user profile
- oadmin.user_profile_delete(opal, name)
+ oadmin.user_profile_delete(opal, name)
@@ -102,12 +102,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_profile_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_profile_delete(o, "foo")
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.user_profiles.html b/docs/reference/oadmin.user_profiles.html
index 2c1e5a94..f23f1669 100644
--- a/docs/reference/oadmin.user_profiles.html
+++ b/docs/reference/oadmin.user_profiles.html
@@ -71,7 +71,7 @@ Get user profiles
- oadmin.user_profiles(opal, df = TRUE)
+ oadmin.user_profiles(opal, df = TRUE)
@@ -98,11 +98,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.user_profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.user_profiles(o)
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/oadmin.user_reset_password.html b/docs/reference/oadmin.user_reset_password.html
index 7bc446ae..75e27675 100644
--- a/docs/reference/oadmin.user_reset_password.html
+++ b/docs/reference/oadmin.user_reset_password.html
@@ -69,7 +69,7 @@ Reset user password
- oadmin.user_reset_password(opal, name, password = NULL)
+ oadmin.user_reset_password(opal, name, password = NULL)
@@ -100,13 +100,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_reset_password(o, "foo", password = "password1234")
-oadmin.user_rm(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_reset_password(o, "foo", password = "password1234")
+oadmin.user_rm(o, "foo")
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/oadmin.users.html b/docs/reference/oadmin.users.html
index e16383d7..f7a3388e 100644
--- a/docs/reference/oadmin.users.html
+++ b/docs/reference/oadmin.users.html
@@ -69,7 +69,7 @@ Get the users
- oadmin.users(opal, df = TRUE)
+ oadmin.users(opal, df = TRUE)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.users(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.users(o)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.annotate.html b/docs/reference/opal.annotate.html
index f8b0529c..d0970046 100644
--- a/docs/reference/opal.annotate.html
+++ b/docs/reference/opal.annotate.html
@@ -71,7 +71,7 @@ Apply the annotations to a Opal table
- opal.annotate(opal, datasource, table, annotations)
+ opal.annotate(opal, datasource, table, annotations)
@@ -111,12 +111,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/opal.annotations.html b/docs/reference/opal.annotations.html
index 54727239..9f6b17eb 100644
--- a/docs/reference/opal.annotations.html
+++ b/docs/reference/opal.annotations.html
@@ -69,7 +69,7 @@ Get the annotations of a Opal table
- opal.annotations(opal, datasource, table)
+ opal.annotations(opal, datasource, table)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.as_md_table.html b/docs/reference/opal.as_md_table.html
index e37dd66e..b6b4c121 100644
--- a/docs/reference/opal.as_md_table.html
+++ b/docs/reference/opal.as_md_table.html
@@ -69,14 +69,14 @@ Array to Markdown
-
+
@@ -108,11 +108,11 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/opal.assign.data.html b/docs/reference/opal.assign.data.html
index e7b39e90..2be27522 100644
--- a/docs/reference/opal.assign.data.html
+++ b/docs/reference/opal.assign.data.html
@@ -69,7 +69,7 @@ Data assignment
- opal.assign.data(opal, symbol, value, async = FALSE)
+ opal.assign.data(opal, symbol, value, async = FALSE)
@@ -102,16 +102,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# push an arbitrary data frame to the R server
-opal.assign.data(o, "D", mtcars)
-# push an arbitrary vector to the R server
-opal.assign.data(o, "C", mtcars$cyl)
-# push a string
-opal.assign.data(o, "S", "Hello!")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# push an arbitrary data frame to the R server
+opal.assign.data(o, "D", mtcars)
+# push an arbitrary vector to the R server
+opal.assign.data(o, "C", mtcars$cyl)
+# push a string
+opal.assign.data(o, "S", "Hello!")
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.assign.html b/docs/reference/opal.assign.html
index c0c14727..83bab276 100644
--- a/docs/reference/opal.assign.html
+++ b/docs/reference/opal.assign.html
@@ -69,17 +69,17 @@ Data or expression assignment
- opal.assign(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- async = FALSE
-)
+ opal.assign(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ async = FALSE
+)
@@ -132,21 +132,21 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-# push an arbitrary data frame to the R server
-#opal.assign(o, "D", mtcars)
-# push an arbitrary vector to the R server
-#opal.assign(o, "C", mtcars$cyl)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+# push an arbitrary data frame to the R server
+#opal.assign(o, "D", mtcars)
+# push an arbitrary vector to the R server
+#opal.assign(o, "C", mtcars$cyl)
+opal.logout(o)
+}
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/opal.assign.resource.html b/docs/reference/opal.assign.resource.html
index 649d475e..b06c3fee 100644
--- a/docs/reference/opal.assign.resource.html
+++ b/docs/reference/opal.assign.resource.html
@@ -69,7 +69,7 @@ Resource assignment
- opal.assign.resource(opal, symbol, value, async = FALSE)
+ opal.assign.resource(opal, symbol, value, async = FALSE)
@@ -102,13 +102,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a resource and make some operation on it
-opal.assign.resource(o, "D", "datashield.cram1")
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a resource and make some operation on it
+opal.assign.resource(o, "D", "datashield.cram1")
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.assign.script.html b/docs/reference/opal.assign.script.html
index ce2ee8a8..4826146e 100644
--- a/docs/reference/opal.assign.script.html
+++ b/docs/reference/opal.assign.script.html
@@ -69,7 +69,7 @@ R script assignment
- opal.assign.script(opal, symbol, value, async = FALSE)
+ opal.assign.script(opal, symbol, value, async = FALSE)
@@ -102,13 +102,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.assign.table.html b/docs/reference/opal.assign.table.html
index f23b63b9..b853219b 100644
--- a/docs/reference/opal.assign.table.html
+++ b/docs/reference/opal.assign.table.html
@@ -69,18 +69,18 @@ Data assignment to a data.frame
- opal.assign.table(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- class = "data.frame",
- async = FALSE
-)
+ opal.assign.table(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ class = "data.frame",
+ async = FALSE
+)
@@ -137,19 +137,19 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-opal.execute(o, "colnames(D)")
-# assign a table CNSIM1 with a identifiers column
-opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
-opal.execute(o, "colnames(H)")
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-opal.execute(o, "colnames(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+opal.execute(o, "colnames(D)")
+# assign a table CNSIM1 with a identifiers column
+opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
+opal.execute(o, "colnames(H)")
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+opal.execute(o, "colnames(D)")
+opal.logout(o)
+}
@@ -164,7 +164,7 @@ Examples
diff --git a/docs/reference/opal.assign.table.tibble.html b/docs/reference/opal.assign.table.tibble.html
index 95dc04a3..e508e729 100644
--- a/docs/reference/opal.assign.table.tibble.html
+++ b/docs/reference/opal.assign.table.tibble.html
@@ -69,18 +69,18 @@ Data assignment to a tibble
- opal.assign.table.tibble(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = "id",
- with.factors = FALSE,
- updated.name = NULL,
- async = FALSE
-)
+ opal.assign.table.tibble(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = "id",
+ with.factors = FALSE,
+ updated.name = NULL,
+ async = FALSE
+)
@@ -137,13 +137,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a table and make some operation on it
-opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a table and make some operation on it
+opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
@@ -158,7 +158,7 @@ Examples
diff --git a/docs/reference/opal.attribute_values.html b/docs/reference/opal.attribute_values.html
index dd1b1537..98a94106 100644
--- a/docs/reference/opal.attribute_values.html
+++ b/docs/reference/opal.attribute_values.html
@@ -69,7 +69,7 @@ Get a vector of attribute values
- opal.attribute_values(attributes, namespace = NULL, name = "label")
+ opal.attribute_values(attributes, namespace = NULL, name = "label")
@@ -103,12 +103,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.attribute_values(var$attributes)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.attribute_values(var$attributes)
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.command.html b/docs/reference/opal.command.html
index 0f88509d..4f419a6e 100644
--- a/docs/reference/opal.command.html
+++ b/docs/reference/opal.command.html
@@ -69,7 +69,7 @@ Get an asynchronous command
- opal.command(opal, id, wait = FALSE)
+ opal.command(opal, id, wait = FALSE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command(o, '1234')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.command_result.html b/docs/reference/opal.command_result.html
index 5289b55a..35bc7964 100644
--- a/docs/reference/opal.command_result.html
+++ b/docs/reference/opal.command_result.html
@@ -71,7 +71,7 @@ Get result of an asynchronous command
- opal.command_result(opal, id, wait = FALSE)
+ opal.command_result(opal, id, wait = FALSE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_result(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_result(o, '1234')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.command_rm.html b/docs/reference/opal.command_rm.html
index c43351fa..e7fea6bb 100644
--- a/docs/reference/opal.command_rm.html
+++ b/docs/reference/opal.command_rm.html
@@ -69,7 +69,7 @@ Remove an asynchronous command
- opal.command_rm(opal, id)
+ opal.command_rm(opal, id)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_rm(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_rm(o, '1234')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.commands.html b/docs/reference/opal.commands.html
index f184c2a2..e5067c0f 100644
--- a/docs/reference/opal.commands.html
+++ b/docs/reference/opal.commands.html
@@ -69,7 +69,7 @@ List the asynchronous commands
- opal.commands(opal, df = TRUE)
+ opal.commands(opal, df = TRUE)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands(o)
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.commands_rm.html b/docs/reference/opal.commands_rm.html
index a79be20b..dad19270 100644
--- a/docs/reference/opal.commands_rm.html
+++ b/docs/reference/opal.commands_rm.html
@@ -69,7 +69,7 @@ Remove all asynchronous commands
- opal.commands_rm(opal)
+ opal.commands_rm(opal)
@@ -89,11 +89,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands_rm(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands_rm(o)
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/opal.datasource.html b/docs/reference/opal.datasource.html
index db4e3140..18ec94fc 100644
--- a/docs/reference/opal.datasource.html
+++ b/docs/reference/opal.datasource.html
@@ -69,7 +69,7 @@ Get a datasource
- opal.datasource(opal, datasource)
+ opal.datasource(opal, datasource)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasource(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasource(o, 'CNSIM')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.datasources.html b/docs/reference/opal.datasources.html
index 2c0c3136..b541b556 100644
--- a/docs/reference/opal.datasources.html
+++ b/docs/reference/opal.datasources.html
@@ -69,7 +69,7 @@ Get datasources
- opal.datasources(opal, df = TRUE)
+ opal.datasources(opal, df = TRUE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasources(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasources(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.delete.html b/docs/reference/opal.delete.html
index 9acf1da1..97b75ae3 100644
--- a/docs/reference/opal.delete.html
+++ b/docs/reference/opal.delete.html
@@ -69,7 +69,7 @@ Generic REST resource deletion.
- opal.delete(opal, ..., query = list(), callback = NULL)
+ opal.delete(opal, ..., query = list(), callback = NULL)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.delete(o, 'some', 'resource')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.delete(o, 'some', 'resource')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.execute.html b/docs/reference/opal.execute.html
index 244ade02..f91dcca6 100644
--- a/docs/reference/opal.execute.html
+++ b/docs/reference/opal.execute.html
@@ -69,7 +69,7 @@ Execute a R script
- opal.execute(opal, script, async = FALSE)
+ opal.execute(opal, script, async = FALSE)
@@ -97,12 +97,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute(o, "x <- 'foo'")
-opal.execute(o, "ls()")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute(o, "x <- 'foo'")
+opal.execute(o, "ls()")
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/opal.execute.source.html b/docs/reference/opal.execute.source.html
index 9ad4eef0..f512ffb2 100644
--- a/docs/reference/opal.execute.source.html
+++ b/docs/reference/opal.execute.source.html
@@ -69,7 +69,7 @@ Execute a R file script
- opal.execute.source(opal, path, async = FALSE)
+ opal.execute.source(opal, path, async = FALSE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute.source(o, "myscript.R")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute.source(o, "myscript.R")
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.file.html b/docs/reference/opal.file.html
index 074023d1..72a13d97 100644
--- a/docs/reference/opal.file.html
+++ b/docs/reference/opal.file.html
@@ -69,7 +69,7 @@ Get file content
- opal.file(opal, path, key = NULL)
+ opal.file(opal, path, key = NULL)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.file(o, '/home/administrator/joins/join-src-3.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.file(o, '/home/administrator/joins/join-src-3.csv')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.file_cp.html b/docs/reference/opal.file_cp.html
index c895e41c..33bb18fd 100644
--- a/docs/reference/opal.file_cp.html
+++ b/docs/reference/opal.file_cp.html
@@ -69,7 +69,7 @@ Copy a file
- opal.file_cp(opal, source, destination)
+ opal.file_cp(opal, source, destination)
@@ -104,14 +104,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# copy a file to another folder
-opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# copy recursively a folder to another folder
-opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# copy a file to another folder
+opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# copy recursively a folder to another folder
+opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.file_download.html b/docs/reference/opal.file_download.html
index dde0cba7..e6770678 100644
--- a/docs/reference/opal.file_download.html
+++ b/docs/reference/opal.file_download.html
@@ -69,7 +69,7 @@ Download a file
- opal.file_download(opal, source, destination = NULL, key = NULL)
+ opal.file_download(opal, source, destination = NULL, key = NULL)
@@ -108,19 +108,19 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# download a file
-opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
-# download a file encrypted by a key: resulting file is a zip with an encrypted content
-opal.file_download(o, '/home/administrator/export/some-data.csv',
- destination='some-data.zip', key='AZF57893FBDE')
-# download, create destination folder and rename file
-opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
-# download a folder
-opal.file_download(o, '/home/administrator/export', 'export.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# download a file
+opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
+# download a file encrypted by a key: resulting file is a zip with an encrypted content
+opal.file_download(o, '/home/administrator/export/some-data.csv',
+ destination='some-data.zip', key='AZF57893FBDE')
+# download, create destination folder and rename file
+opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
+# download a folder
+opal.file_download(o, '/home/administrator/export', 'export.zip')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.file_ls.html b/docs/reference/opal.file_ls.html
index c57e02da..8664df11 100644
--- a/docs/reference/opal.file_ls.html
+++ b/docs/reference/opal.file_ls.html
@@ -69,7 +69,7 @@ List content of a folder
- opal.file_ls(opal, path)
+ opal.file_ls(opal, path)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# list content of a folder
-opal.file_ls(o, '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# list content of a folder
+opal.file_ls(o, '/home/administrator')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.file_mkdir.html b/docs/reference/opal.file_mkdir.html
index 0ed72ad7..d15743df 100644
--- a/docs/reference/opal.file_mkdir.html
+++ b/docs/reference/opal.file_mkdir.html
@@ -71,7 +71,7 @@ Make a folder
- opal.file_mkdir(opal, path, parents = FALSE)
+ opal.file_mkdir(opal, path, parents = FALSE)
@@ -106,12 +106,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.file_mkdir_tmp.html b/docs/reference/opal.file_mkdir_tmp.html
index 396c04ff..8e187fcb 100644
--- a/docs/reference/opal.file_mkdir_tmp.html
+++ b/docs/reference/opal.file_mkdir_tmp.html
@@ -69,7 +69,7 @@ Make a temporary folder
- opal.file_mkdir_tmp(opal)
+ opal.file_mkdir_tmp(opal)
@@ -102,12 +102,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-path <- opal.file_mkdir_tmp(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+path <- opal.file_mkdir_tmp(o)
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/opal.file_mv.html b/docs/reference/opal.file_mv.html
index fc322297..1d6874df 100644
--- a/docs/reference/opal.file_mv.html
+++ b/docs/reference/opal.file_mv.html
@@ -69,7 +69,7 @@ Move and/or rename a file
- opal.file_mv(opal, source, destination)
+ opal.file_mv(opal, source, destination)
@@ -104,18 +104,18 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# move a file to another folder
-opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/administrator/export/some-data.csv')
-# move and rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/userx/deliverables/some-data.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# move a file to another folder
+opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/administrator/export/some-data.csv')
+# move and rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/userx/deliverables/some-data.csv')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.file_read.html b/docs/reference/opal.file_read.html
index 64f4982d..1807b28c 100644
--- a/docs/reference/opal.file_read.html
+++ b/docs/reference/opal.file_read.html
@@ -69,7 +69,7 @@ Read a file
- opal.file_read(opal, source, destination)
+ opal.file_read(opal, source, destination)
@@ -104,16 +104,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# read into folder
-opal.file_read(o,"DatabaseTest.sav", "/tmp")
-# read and rename
-opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
-# user home expansion
-opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# read into folder
+opal.file_read(o,"DatabaseTest.sav", "/tmp")
+# read and rename
+opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
+# user home expansion
+opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.file_rm.html b/docs/reference/opal.file_rm.html
index a23dee2e..5d79795c 100644
--- a/docs/reference/opal.file_rm.html
+++ b/docs/reference/opal.file_rm.html
@@ -69,7 +69,7 @@ Remove a file
- opal.file_rm(opal, path)
+ opal.file_rm(opal, path)
@@ -100,14 +100,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# remove a file
-opal.file_rm(o, '/home/administrator/export/some-data.csv')
-# remove recursively a folder
-opal.file_rm(o, '/home/administrator/export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# remove a file
+opal.file_rm(o, '/home/administrator/export/some-data.csv')
+# remove recursively a folder
+opal.file_rm(o, '/home/administrator/export')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/opal.file_unzip.html b/docs/reference/opal.file_unzip.html
index 66eaea32..a695dfec 100644
--- a/docs/reference/opal.file_unzip.html
+++ b/docs/reference/opal.file_unzip.html
@@ -69,7 +69,7 @@ Unzip a zip archive file
- opal.file_unzip(opal, source, destination, key = NULL)
+ opal.file_unzip(opal, source, destination, key = NULL)
@@ -114,12 +114,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# unzip
-path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# unzip
+path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.file_upload.html b/docs/reference/opal.file_upload.html
index 83a6426c..70c2faea 100644
--- a/docs/reference/opal.file_upload.html
+++ b/docs/reference/opal.file_upload.html
@@ -71,7 +71,7 @@ Upload a file or a folder
- opal.file_upload(opal, source, destination, all.files = TRUE)
+ opal.file_upload(opal, source, destination, all.files = TRUE)
@@ -111,14 +111,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# upload a file
-opal.file_upload(o, 'some_data.csv', '/home/administrator')
-# upload a folder
-opal.file_upload(o, 'some_data', '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# upload a file
+opal.file_upload(o, 'some_data.csv', '/home/administrator')
+# upload a folder
+opal.file_upload(o, 'some_data', '/home/administrator')
+opal.logout(o)
+}
@@ -133,7 +133,7 @@ Examples
diff --git a/docs/reference/opal.file_write.html b/docs/reference/opal.file_write.html
index a1bfb19d..f0835d11 100644
--- a/docs/reference/opal.file_write.html
+++ b/docs/reference/opal.file_write.html
@@ -69,7 +69,7 @@ Write a file
- opal.file_write(opal, source, destination = NULL)
+ opal.file_write(opal, source, destination = NULL)
@@ -104,16 +104,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# user home expansion
-opal.file_write(o, "~/spss/DatabaseTest.sav")
-# rename file
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
-# create sub-folder
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# user home expansion
+opal.file_write(o, "~/spss/DatabaseTest.sav")
+# rename file
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
+# create sub-folder
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.get.html b/docs/reference/opal.get.html
index 19e0f260..f83d5cb9 100644
--- a/docs/reference/opal.get.html
+++ b/docs/reference/opal.get.html
@@ -69,14 +69,14 @@ Generic REST resource getter.
- opal.get(
- opal,
- ...,
- query = list(),
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)
+ opal.get(
+ opal,
+ ...,
+ query = list(),
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)
@@ -115,11 +115,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.get(o, 'project', 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.get(o, 'project', 'CNSIM')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.load_package.html b/docs/reference/opal.load_package.html
index 15e9967f..cba05243 100644
--- a/docs/reference/opal.load_package.html
+++ b/docs/reference/opal.load_package.html
@@ -69,7 +69,7 @@ Load package
- opal.load_package(opal, pkg)
+ opal.load_package(opal, pkg)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.load_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.load_package(o, 'stats')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.login.html b/docs/reference/opal.login.html
index f9523698..549cdc71 100644
--- a/docs/reference/opal.login.html
+++ b/docs/reference/opal.login.html
@@ -73,15 +73,15 @@ Opal login
-
+
@@ -132,44 +132,44 @@ See also
Examples
- if (FALSE) {
-#### The below examples illustrate the different ways to login in opal ####
-
-# explicite username/password login
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
- # explicite personal access token login
-o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login using options and user credentials
-options(opal.username = 'administrator',
- opal.password = 'password',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using options and personal access token
-options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using ssl key pair
-options(opal.opts = list(
- sslcert = 'my-publickey.pem',
- sslkey = 'my-privatekey.pem'))
-o <- opal.login(url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login with a R server profile
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org', profile = 'default')
-opal.logout(o)
-}
+ if (FALSE) {
+#### The below examples illustrate the different ways to login in opal ####
+
+# explicite username/password login
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+ # explicite personal access token login
+o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login using options and user credentials
+options(opal.username = 'administrator',
+ opal.password = 'password',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using options and personal access token
+options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using ssl key pair
+options(opal.opts = list(
+ sslcert = 'my-publickey.pem',
+ sslkey = 'my-privatekey.pem'))
+o <- opal.login(url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login with a R server profile
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org', profile = 'default')
+opal.logout(o)
+}
@@ -184,7 +184,7 @@ Examples
diff --git a/docs/reference/opal.logout.html b/docs/reference/opal.logout.html
index e64f3e86..b91868aa 100644
--- a/docs/reference/opal.logout.html
+++ b/docs/reference/opal.logout.html
@@ -69,7 +69,7 @@ Logout from Opal(s)
- opal.logout(opal, save = FALSE)
+ opal.logout(opal, save = FALSE)
@@ -91,10 +91,10 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+}
@@ -109,7 +109,7 @@ Examples
diff --git a/docs/reference/opal.perms.html b/docs/reference/opal.perms.html
new file mode 100644
index 00000000..aab233ff
--- /dev/null
+++ b/docs/reference/opal.perms.html
@@ -0,0 +1,154 @@
+
+Get the permissions of a subject — opal.perms • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the permissions of a subject. If the subject is a user, the permissions of
+the groups to which the user belongs are also added to the result.
+
+
+
+ opal.perms(opal, subject, type = "user")
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- subject
+A subject identifier: user or group name.
- type
+The type of subject: user (default) or group.
+
+ Value
+
+
+A data.frame with columns: subject, type, target (path to the opal object to which
+the permission applies), target_type and perm (the permission name)
+
+
+ See also
+ Other table functions:
+opal.resource_view_create(),
+opal.resource_view_reconnect(),
+opal.table_create(),
+opal.table_delete(),
+opal.table_dictionary_get(),
+opal.table_dictionary_update(),
+opal.table_exists(),
+opal.table_export(),
+opal.table_get(),
+opal.table_import(),
+opal.table_perm_add(),
+opal.table_perm_delete(),
+opal.table_perm(),
+opal.table_save(),
+opal.table_truncate(),
+opal.table_view_create(),
+opal.table_view_update()
+
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.perms(o, 'andrei')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/opal.post.html b/docs/reference/opal.post.html
index d93bb6bf..f7d80068 100644
--- a/docs/reference/opal.post.html
+++ b/docs/reference/opal.post.html
@@ -69,16 +69,16 @@ Generic REST resource creation.
- opal.post(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)
+ opal.post(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)
@@ -125,11 +125,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.post(o, 'some', 'resources', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.post(o, 'some', 'resources', body = '{"some":"value"}')
+opal.logout(o)
+}
@@ -144,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.profiles.html b/docs/reference/opal.profiles.html
index 067273c2..1e96f85c 100644
--- a/docs/reference/opal.profiles.html
+++ b/docs/reference/opal.profiles.html
@@ -71,7 +71,7 @@ List R profiles
- opal.profiles(opal, df = TRUE)
+ opal.profiles(opal, df = TRUE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.profiles(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.project.html b/docs/reference/opal.project.html
index cd3a4f68..3e6b4a16 100644
--- a/docs/reference/opal.project.html
+++ b/docs/reference/opal.project.html
@@ -69,7 +69,7 @@ Get a project
- opal.project(opal, project)
+ opal.project(opal, project)
@@ -94,11 +94,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project(o, 'datashield')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project(o, 'datashield')
+opal.logout(o)
+}
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/opal.project_backup.html b/docs/reference/opal.project_backup.html
index 9fe7543f..58bf4b6e 100644
--- a/docs/reference/opal.project_backup.html
+++ b/docs/reference/opal.project_backup.html
@@ -75,14 +75,14 @@ Backup a project
- opal.project_backup(
- opal,
- project,
- archive,
- viewsAsTables = FALSE,
- override = TRUE,
- wait = TRUE
-)
+ opal.project_backup(
+ opal,
+ project,
+ archive,
+ viewsAsTables = FALSE,
+ override = TRUE,
+ wait = TRUE
+)
@@ -120,12 +120,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
-opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
+opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
+opal.logout(o)
+}
@@ -140,7 +140,7 @@ Examples
diff --git a/docs/reference/opal.project_command.html b/docs/reference/opal.project_command.html
index 13740837..9e6c5e62 100644
--- a/docs/reference/opal.project_command.html
+++ b/docs/reference/opal.project_command.html
@@ -69,7 +69,7 @@ Get project task
- opal.project_command(opal, project, id)
+ opal.project_command(opal, project, id)
@@ -95,12 +95,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
-opal.project_command(opal, 'GREENSPACE', id)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
+opal.project_command(opal, 'GREENSPACE', id)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.project_create.html b/docs/reference/opal.project_create.html
index 2524037d..d1eb8488 100644
--- a/docs/reference/opal.project_create.html
+++ b/docs/reference/opal.project_create.html
@@ -69,15 +69,15 @@ Create a project
- opal.project_create(
- opal,
- project,
- database = NULL,
- title = NULL,
- description = NULL,
- tags = NULL,
- exportFolder = NULL
-)
+ opal.project_create(
+ opal,
+ project,
+ database = NULL,
+ title = NULL,
+ description = NULL,
+ tags = NULL,
+ exportFolder = NULL
+)
@@ -124,16 +124,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with named database
-opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
-# with default database
-opal.project_create(o, 'test_default_db', database = TRUE)
-# no database, for views and resources only
-opal.project_create(o, 'test_no_db')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with named database
+opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
+# with default database
+opal.project_create(o, 'test_default_db', database = TRUE)
+# no database, for views and resources only
+opal.project_create(o, 'test_no_db')
+opal.logout(o)
+}
@@ -148,7 +148,7 @@ Examples
diff --git a/docs/reference/opal.project_delete.html b/docs/reference/opal.project_delete.html
index 0975b5d4..249dfdd3 100644
--- a/docs/reference/opal.project_delete.html
+++ b/docs/reference/opal.project_delete.html
@@ -69,7 +69,7 @@ Delete a project
- opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
+ opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
@@ -102,11 +102,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_delete(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_delete(o, 'test')
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/opal.project_exists.html b/docs/reference/opal.project_exists.html
index 2d217cab..10266208 100644
--- a/docs/reference/opal.project_exists.html
+++ b/docs/reference/opal.project_exists.html
@@ -69,7 +69,7 @@ Check a project exists
- opal.project_exists(opal, project)
+ opal.project_exists(opal, project)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_exists(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_exists(o, 'test')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.project_perm.html b/docs/reference/opal.project_perm.html
index 07a974c3..abba6946 100644
--- a/docs/reference/opal.project_perm.html
+++ b/docs/reference/opal.project_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a project
- opal.project_perm(opal, project)
+ opal.project_perm(opal, project)
@@ -91,13 +91,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.project_perm_add.html b/docs/reference/opal.project_perm_add.html
index 1fd19072..e134d7b0 100644
--- a/docs/reference/opal.project_perm_add.html
+++ b/docs/reference/opal.project_perm_add.html
@@ -69,13 +69,13 @@ Add or update a permission on a project
- opal.project_perm_add(
- opal,
- project,
- subject,
- type = "user",
- permission = "administrate"
-)
+ opal.project_perm_add(
+ opal,
+ project,
+ subject,
+ type = "user",
+ permission = "administrate"
+)
@@ -103,13 +103,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.project_perm_delete.html b/docs/reference/opal.project_perm_delete.html
index 8a290c35..885e9c53 100644
--- a/docs/reference/opal.project_perm_delete.html
+++ b/docs/reference/opal.project_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a project
- opal.project_perm_delete(opal, project, subject, type = "user")
+ opal.project_perm_delete(opal, project, subject, type = "user")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/opal.project_restore.html b/docs/reference/opal.project_restore.html
index 76c5f138..8f4c0d05 100644
--- a/docs/reference/opal.project_restore.html
+++ b/docs/reference/opal.project_restore.html
@@ -75,14 +75,14 @@ Restore a project
- opal.project_restore(
- opal,
- project,
- archive,
- key = NULL,
- override = TRUE,
- wait = TRUE
-)
+ opal.project_restore(
+ opal,
+ project,
+ archive,
+ key = NULL,
+ override = TRUE,
+ wait = TRUE
+)
@@ -120,15 +120,15 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# create the project to restore, with the default database (to store tables)
-opal.project_create(o, 'GREENSPACE2', database = TRUE)
-# upload backup zip and launch restore task
-opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
-opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# create the project to restore, with the default database (to store tables)
+opal.project_create(o, 'GREENSPACE2', database = TRUE)
+# upload backup zip and launch restore task
+opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
+opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
+opal.logout(o)
+}
@@ -143,7 +143,7 @@ Examples
diff --git a/docs/reference/opal.projects.html b/docs/reference/opal.projects.html
index e8d51a41..73e9e973 100644
--- a/docs/reference/opal.projects.html
+++ b/docs/reference/opal.projects.html
@@ -69,7 +69,7 @@ Get projects
- opal.projects(opal, df = TRUE)
+ opal.projects(opal, df = TRUE)
@@ -94,11 +94,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects(o)
+opal.logout(o)
+}
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/opal.projects_databases.html b/docs/reference/opal.projects_databases.html
index 45f818b3..2a9dc9f0 100644
--- a/docs/reference/opal.projects_databases.html
+++ b/docs/reference/opal.projects_databases.html
@@ -69,7 +69,7 @@ Get projects databases
- opal.projects_databases(opal)
+ opal.projects_databases(opal)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects_databases(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects_databases(o)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.put.html b/docs/reference/opal.put.html
index de59ef78..1622010c 100644
--- a/docs/reference/opal.put.html
+++ b/docs/reference/opal.put.html
@@ -69,14 +69,14 @@ Generic REST resource update.
- opal.put(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- callback = NULL
-)
+ opal.put(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ callback = NULL
+)
@@ -115,11 +115,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.report.html b/docs/reference/opal.report.html
index eaf6c399..efc8d7c1 100644
--- a/docs/reference/opal.report.html
+++ b/docs/reference/opal.report.html
@@ -69,13 +69,13 @@ Opal report
- opal.report(
- input,
- output = NULL,
- progress = FALSE,
- verbose = FALSE,
- boot_style = NULL
-)
+ opal.report(
+ input,
+ output = NULL,
+ progress = FALSE,
+ verbose = FALSE,
+ boot_style = NULL
+)
@@ -103,9 +103,9 @@ Arguments
Examples
- if (FALSE) {
-opal.report('input.Rmd', 'report', progress=TRUE)
-}
+ if (FALSE) {
+opal.report('input.Rmd', 'report', progress=TRUE)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.report_md.html b/docs/reference/opal.report_md.html
index ad0cadd5..50a44df1 100644
--- a/docs/reference/opal.report_md.html
+++ b/docs/reference/opal.report_md.html
@@ -69,7 +69,7 @@ Turn a R markdown file to html.
- opal.report_md(inputFile, progress, verbose)
+ opal.report_md(inputFile, progress, verbose)
@@ -85,7 +85,7 @@ Turn a R markdown file to html.
diff --git a/docs/reference/opal.resource.html b/docs/reference/opal.resource.html
index 8040add0..128ece62 100644
--- a/docs/reference/opal.resource.html
+++ b/docs/reference/opal.resource.html
@@ -69,7 +69,7 @@ Get a resource reference of a project
- opal.resource(opal, project, resource)
+ opal.resource(opal, project, resource)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.resource_create.html b/docs/reference/opal.resource_create.html
index a7f47634..9ed343f2 100644
--- a/docs/reference/opal.resource_create.html
+++ b/docs/reference/opal.resource_create.html
@@ -69,17 +69,17 @@ Create a resource reference in a project
- opal.resource_create(
- opal,
- project,
- name,
- url,
- description = NULL,
- format = NULL,
- package = NULL,
- identity = NULL,
- secret = NULL
-)
+ opal.resource_create(
+ opal,
+ project,
+ name,
+ url,
+ description = NULL,
+ format = NULL,
+ package = NULL,
+ identity = NULL,
+ secret = NULL
+)
@@ -139,13 +139,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_create(o, 'RSRC', 'CNSIM4',
- url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
- format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_create(o, 'RSRC', 'CNSIM4',
+ url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
+ format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
+opal.logout(o)
+}
@@ -160,7 +160,7 @@ Examples
diff --git a/docs/reference/opal.resource_delete.html b/docs/reference/opal.resource_delete.html
index 41eee541..a3e48fb8 100644
--- a/docs/reference/opal.resource_delete.html
+++ b/docs/reference/opal.resource_delete.html
@@ -69,7 +69,7 @@ Delete a resource reference
- opal.resource_delete(opal, project, resource, silent = TRUE)
+ opal.resource_delete(opal, project, resource, silent = TRUE)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_delete(o, "RSRC", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_delete(o, "RSRC", "CNSIM4")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.resource_exists.html b/docs/reference/opal.resource_exists.html
index 7a5852e1..700fd693 100644
--- a/docs/reference/opal.resource_exists.html
+++ b/docs/reference/opal.resource_exists.html
@@ -69,7 +69,7 @@ Check a resource reference exists
- opal.resource_exists(opal, project, resource)
+ opal.resource_exists(opal, project, resource)
@@ -111,11 +111,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_exists(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_exists(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.resource_extension_create.html b/docs/reference/opal.resource_extension_create.html
index c0a045fe..1c8013c4 100644
--- a/docs/reference/opal.resource_extension_create.html
+++ b/docs/reference/opal.resource_extension_create.html
@@ -69,16 +69,16 @@ Create an extended resource reference in a project
- opal.resource_extension_create(
- opal,
- project,
- name,
- provider,
- factory,
- parameters,
- description = NULL,
- credentials = NULL
-)
+ opal.resource_extension_create(
+ opal,
+ project,
+ name,
+ provider,
+ factory,
+ parameters,
+ description = NULL,
+ credentials = NULL
+)
@@ -134,21 +134,21 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
- provider = 'dsOmics', factory = 'ga4gh-htsget',
- parameters = list(
- host = 'https://htsget.ga4gh.org',
- sample = '1000genomes.phase1.chr1',
- reference = '1',
- start = '1',
- end = '100000',
- format = 'GA4GHVCF'
- )
-)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
+ provider = 'dsOmics', factory = 'ga4gh-htsget',
+ parameters = list(
+ host = 'https://htsget.ga4gh.org',
+ sample = '1000genomes.phase1.chr1',
+ reference = '1',
+ start = '1',
+ end = '100000',
+ format = 'GA4GHVCF'
+ )
+)
+opal.logout(o)
+}
@@ -163,7 +163,7 @@ Examples
diff --git a/docs/reference/opal.resource_get.html b/docs/reference/opal.resource_get.html
index ae00707a..80a02871 100644
--- a/docs/reference/opal.resource_get.html
+++ b/docs/reference/opal.resource_get.html
@@ -69,7 +69,7 @@ Get the resource object of a project
- opal.resource_get(opal, project, resource)
+ opal.resource_get(opal, project, resource)
@@ -105,17 +105,17 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
-# then interpret locally the resource object (load the appropriate R packages)
-library(resourcer)
-# coerce to a data.frame
-as.data.frame(res)
-# or get the resource client object for low-level interactions
-rescli <- resourcer::newResourceClient(res)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
+# then interpret locally the resource object (load the appropriate R packages)
+library(resourcer)
+# coerce to a data.frame
+as.data.frame(res)
+# or get the resource client object for low-level interactions
+rescli <- resourcer::newResourceClient(res)
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm.html b/docs/reference/opal.resource_perm.html
index e6856cab..d97e7fef 100644
--- a/docs/reference/opal.resource_perm.html
+++ b/docs/reference/opal.resource_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a resource
- opal.resource_perm(opal, project, resource)
+ opal.resource_perm(opal, project, resource)
@@ -111,13 +111,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -132,7 +132,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm_add.html b/docs/reference/opal.resource_perm_add.html
index 9c3d1438..6ad84919 100644
--- a/docs/reference/opal.resource_perm_add.html
+++ b/docs/reference/opal.resource_perm_add.html
@@ -69,14 +69,14 @@ Add or update a permission on a resource
- opal.resource_perm_add(
- opal,
- project,
- resource,
- subject,
- type = "user",
- permission
-)
+ opal.resource_perm_add(
+ opal,
+ project,
+ resource,
+ subject,
+ type = "user",
+ permission
+)
@@ -125,13 +125,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -146,7 +146,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm_delete.html b/docs/reference/opal.resource_perm_delete.html
index df299ed2..541396ce 100644
--- a/docs/reference/opal.resource_perm_delete.html
+++ b/docs/reference/opal.resource_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a resource
- opal.resource_perm_delete(opal, project, resource, subject, type = "user")
+ opal.resource_perm_delete(opal, project, resource, subject, type = "user")
@@ -113,13 +113,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.resource_view_create.html b/docs/reference/opal.resource_view_create.html
index d653a1cf..f3a7a1f2 100644
--- a/docs/reference/opal.resource_view_create.html
+++ b/docs/reference/opal.resource_view_create.html
@@ -73,15 +73,15 @@ Create an Opal view over a resource reference
- opal.resource_view_create(
- opal,
- project,
- table,
- resource,
- type = "Participant",
- idColumn = NULL,
- profile = NULL
-)
+ opal.resource_view_create(
+ opal,
+ project,
+ table,
+ resource,
+ type = "Participant",
+ idColumn = NULL,
+ profile = NULL
+)
@@ -119,6 +119,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
@@ -139,14 +140,14 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
- resource = "RSRC.FEMALE_2439", idColumn = "Name")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
+ resource = "RSRC.FEMALE_2439", idColumn = "Name")
+opal.logout(o)
+}
@@ -161,7 +162,7 @@ Examples
diff --git a/docs/reference/opal.resource_view_reconnect.html b/docs/reference/opal.resource_view_reconnect.html
index e8650b92..06f03a44 100644
--- a/docs/reference/opal.resource_view_reconnect.html
+++ b/docs/reference/opal.resource_view_reconnect.html
@@ -73,7 +73,7 @@ Reconnect an Opal view to its underlying resource
- opal.resource_view_reconnect(opal, project, table)
+ opal.resource_view_reconnect(opal, project, table)
@@ -93,6 +93,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.table_create(),
opal.table_delete(),
@@ -113,14 +114,14 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-# re-initialize the view's connection to the resource
-opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+# re-initialize the view's connection to the resource
+opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
+opal.logout(o)
+}
@@ -135,7 +136,7 @@ Examples
diff --git a/docs/reference/opal.resources.html b/docs/reference/opal.resources.html
index 305236d9..1219e1b9 100644
--- a/docs/reference/opal.resources.html
+++ b/docs/reference/opal.resources.html
@@ -69,7 +69,7 @@ Get the resource references of a project
- opal.resources(opal, project, df = TRUE)
+ opal.resources(opal, project, df = TRUE)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources(o, 'RSRC')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources(o, 'RSRC')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm.html b/docs/reference/opal.resources_perm.html
index ba3302b2..c53289ba 100644
--- a/docs/reference/opal.resources_perm.html
+++ b/docs/reference/opal.resources_perm.html
@@ -69,7 +69,7 @@ Get the permissions on any resource
- opal.resources_perm(opal, project)
+ opal.resources_perm(opal, project)
@@ -107,13 +107,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm_add.html b/docs/reference/opal.resources_perm_add.html
index 1a4a38e2..f1c870b4 100644
--- a/docs/reference/opal.resources_perm_add.html
+++ b/docs/reference/opal.resources_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on any resource
- opal.resources_perm_add(opal, project, subject, type = "user", permission)
+ opal.resources_perm_add(opal, project, subject, type = "user", permission)
@@ -114,13 +114,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm_delete.html b/docs/reference/opal.resources_perm_delete.html
index e7c09535..5c093566 100644
--- a/docs/reference/opal.resources_perm_delete.html
+++ b/docs/reference/opal.resources_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from any resource
- opal.resources_perm_delete(opal, project, subject, type = "user")
+ opal.resources_perm_delete(opal, project, subject, type = "user")
@@ -109,13 +109,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM', 'CNSIM1')
-opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM', 'CNSIM1')
+opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.rm.html b/docs/reference/opal.rm.html
index f444e41c..728ec6d4 100644
--- a/docs/reference/opal.rm.html
+++ b/docs/reference/opal.rm.html
@@ -69,7 +69,7 @@ Remove a R symbol (deprecated)
- opal.rm(opal, symbol)
+ opal.rm(opal, symbol)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.rm(o, 'D')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.sql.html b/docs/reference/opal.sql.html
index 41f13417..5fa1f9b8 100644
--- a/docs/reference/opal.sql.html
+++ b/docs/reference/opal.sql.html
@@ -75,7 +75,7 @@ Execute a SQL query on tables
- opal.sql(opal, query, project = NULL, id.name = "_id")
+ opal.sql(opal, query, project = NULL, id.name = "_id")
@@ -106,23 +106,23 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from CNSIM1
- where LAB_HDL is not null
- group by GENDER',
- 'CNSIM')
-# without project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from `CNSIM.CNSIM1`
- where LAB_HDL is not null
- group by GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from CNSIM1
+ where LAB_HDL is not null
+ group by GENDER',
+ 'CNSIM')
+# without project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from `CNSIM.CNSIM1`
+ where LAB_HDL is not null
+ group by GENDER')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/opal.sql_history.html b/docs/reference/opal.sql_history.html
index ff53d0db..1bd338f2 100644
--- a/docs/reference/opal.sql_history.html
+++ b/docs/reference/opal.sql_history.html
@@ -71,14 +71,14 @@ SQL query execution history
- opal.sql_history(
- opal,
- project = NULL,
- offset = 0,
- limit = 100,
- user = NULL,
- df = TRUE
-)
+ opal.sql_history(
+ opal,
+ project = NULL,
+ offset = 0,
+ limit = 100,
+ user = NULL,
+ df = TRUE
+)
@@ -118,16 +118,16 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql_history(o, 'CNSIM')
-# without project context
-opal.sql_history(o, NA)
-# with or without project context
-opal.sql_history(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql_history(o, 'CNSIM')
+# without project context
+opal.sql_history(o, NA)
+# with or without project context
+opal.sql_history(o)
+opal.logout(o)
+}
@@ -142,7 +142,7 @@ Examples
diff --git a/docs/reference/opal.symbol_import.html b/docs/reference/opal.symbol_import.html
index ae50bd82..5ee219a5 100644
--- a/docs/reference/opal.symbol_import.html
+++ b/docs/reference/opal.symbol_import.html
@@ -71,16 +71,16 @@ Import a tibble
- opal.symbol_import(
- opal,
- symbol,
- project,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)
+ opal.symbol_import(
+ opal,
+ symbol,
+ project,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)
@@ -128,11 +128,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_import(o, 'D', 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_import(o, 'D', 'test')
+opal.logout(o)
+}
@@ -147,7 +147,7 @@ Examples
diff --git a/docs/reference/opal.symbol_rm.html b/docs/reference/opal.symbol_rm.html
index d0cfd696..6d16a689 100644
--- a/docs/reference/opal.symbol_rm.html
+++ b/docs/reference/opal.symbol_rm.html
@@ -69,7 +69,7 @@ Remove a R symbol
- opal.symbol_rm(opal, symbol)
+ opal.symbol_rm(opal, symbol)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_rm(o, 'D')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.symbol_save.html b/docs/reference/opal.symbol_save.html
index f2a900f1..79035aa9 100644
--- a/docs/reference/opal.symbol_save.html
+++ b/docs/reference/opal.symbol_save.html
@@ -69,7 +69,7 @@ Save a tibble
- opal.symbol_save(opal, symbol, destination)
+ opal.symbol_save(opal, symbol, destination)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_save(o, 'D', 'test.sav')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_save(o, 'D', 'test.sav')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.symbols.html b/docs/reference/opal.symbols.html
index bb88de70..1b7894c4 100644
--- a/docs/reference/opal.symbols.html
+++ b/docs/reference/opal.symbols.html
@@ -69,7 +69,7 @@ List R symbols
- opal.symbols(opal)
+ opal.symbols(opal)
@@ -89,11 +89,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbols(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbols(o)
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/opal.table.html b/docs/reference/opal.table.html
index b4d05790..be03e321 100644
--- a/docs/reference/opal.table.html
+++ b/docs/reference/opal.table.html
@@ -69,7 +69,7 @@ Get a table of a datasource
- opal.table(opal, datasource, table, counts = FALSE)
+ opal.table(opal, datasource, table, counts = FALSE)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.table_create.html b/docs/reference/opal.table_create.html
index 44e433ba..46cf045b 100644
--- a/docs/reference/opal.table_create.html
+++ b/docs/reference/opal.table_create.html
@@ -73,7 +73,7 @@ Create an Opal table or view
- opal.table_create(opal, project, table, type = "Participant", tables = NULL)
+ opal.table_create(opal, project, table, type = "Participant", tables = NULL)
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_delete(),
@@ -122,15 +123,15 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a raw table
-opal.table_create(o, "CNSIM", "CNSIM4")
-# make a view
-opal.table_create(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a raw table
+opal.table_create(o, "CNSIM", "CNSIM4")
+# make a view
+opal.table_create(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
@@ -145,7 +146,7 @@ Examples
diff --git a/docs/reference/opal.table_delete.html b/docs/reference/opal.table_delete.html
index 778f2343..cba12a39 100644
--- a/docs/reference/opal.table_delete.html
+++ b/docs/reference/opal.table_delete.html
@@ -71,7 +71,7 @@ Delete a Opal table
- opal.table_delete(opal, project, table, silent = TRUE)
+ opal.table_delete(opal, project, table, silent = TRUE)
@@ -95,6 +95,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,11 +116,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_delete(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_delete(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -134,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.table_dictionary_get.html b/docs/reference/opal.table_dictionary_get.html
index 95a5c21a..59126cc2 100644
--- a/docs/reference/opal.table_dictionary_get.html
+++ b/docs/reference/opal.table_dictionary_get.html
@@ -69,7 +69,7 @@ Get the dictionary of a Opal table
- opal.table_dictionary_get(opal, project, table)
+ opal.table_dictionary_get(opal, project, table)
@@ -89,6 +89,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -109,11 +110,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -128,7 +129,7 @@ Examples
diff --git a/docs/reference/opal.table_dictionary_update.html b/docs/reference/opal.table_dictionary_update.html
index c2e5bfc5..090a7d91 100644
--- a/docs/reference/opal.table_dictionary_update.html
+++ b/docs/reference/opal.table_dictionary_update.html
@@ -69,13 +69,13 @@ Update the dictionary of a Opal table
- opal.table_dictionary_update(
- opal,
- project,
- table,
- variables,
- categories = NULL
-)
+ opal.table_dictionary_update(
+ opal,
+ project,
+ table,
+ variables,
+ categories = NULL
+)
@@ -104,6 +104,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -124,23 +125,23 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-variables <- tibble::tribble(
- ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
- "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
- "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
- "disp", "decimal", "Disp label", NA, NA, 1, 3
-)
-categories <- tibble::tribble(
- ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
- "cyl", "4", 0, "Four", "Quatre",
- "cyl", "6", 0, "Six", "Six",
- "cyl", "8", 1, "Height", "Huit"
-)
-opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+variables <- tibble::tribble(
+ ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
+ "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
+ "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
+ "disp", "decimal", "Disp label", NA, NA, 1, 3
+)
+categories <- tibble::tribble(
+ ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
+ "cyl", "4", 0, "Four", "Quatre",
+ "cyl", "6", 0, "Six", "Six",
+ "cyl", "8", 1, "Height", "Huit"
+)
+opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
+opal.logout(o)
+}
@@ -155,7 +156,7 @@ Examples
diff --git a/docs/reference/opal.table_exists.html b/docs/reference/opal.table_exists.html
index 10649da8..e4ac20bb 100644
--- a/docs/reference/opal.table_exists.html
+++ b/docs/reference/opal.table_exists.html
@@ -71,7 +71,7 @@ Check a Opal table exists
- opal.table_exists(opal, project, table, view = NA)
+ opal.table_exists(opal, project, table, view = NA)
@@ -96,6 +96,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -116,16 +117,16 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# check table exists
-opal.table_exists(o, "CNSIM", "CNSIM1")
-# check table exists AND is a NOT a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
-# check table exists AND is a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# check table exists
+opal.table_exists(o, "CNSIM", "CNSIM1")
+# check table exists AND is a NOT a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
+# check table exists AND is a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
+opal.logout(o)
+}
@@ -140,7 +141,7 @@ Examples
diff --git a/docs/reference/opal.table_export.html b/docs/reference/opal.table_export.html
index f5eb8c76..5110bb07 100644
--- a/docs/reference/opal.table_export.html
+++ b/docs/reference/opal.table_export.html
@@ -73,15 +73,15 @@ Export a table as a file
- opal.table_export(
- opal,
- project,
- table,
- file,
- identifiers = NULL,
- id.name = "id",
- wait = TRUE
-)
+ opal.table_export(
+ opal,
+ project,
+ table,
+ file,
+ identifiers = NULL,
+ id.name = "id",
+ wait = TRUE
+)
@@ -120,6 +120,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -140,12 +141,12 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
- file = "/home/administrator/cnsim1.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
+ file = "/home/administrator/cnsim1.sav")
+opal.logout(o)
+}
@@ -160,7 +161,7 @@ Examples
diff --git a/docs/reference/opal.table_get.html b/docs/reference/opal.table_get.html
index 8a695e18..50b31621 100644
--- a/docs/reference/opal.table_get.html
+++ b/docs/reference/opal.table_get.html
@@ -73,14 +73,14 @@ Get a Opal table as a tibble
- opal.table_get(
- opal,
- project,
- table,
- id.name = "id",
- variables = NULL,
- missings = TRUE
-)
+ opal.table_get(
+ opal,
+ project,
+ table,
+ id.name = "id",
+ variables = NULL,
+ missings = TRUE
+)
@@ -112,6 +112,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -132,11 +133,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+opal.logout(o)
+}
@@ -151,7 +152,7 @@ Examples
diff --git a/docs/reference/opal.table_import.html b/docs/reference/opal.table_import.html
index e7a050a5..587ba457 100644
--- a/docs/reference/opal.table_import.html
+++ b/docs/reference/opal.table_import.html
@@ -77,17 +77,17 @@ Import a file as table
- opal.table_import(
- opal,
- file,
- project,
- table,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)
+ opal.table_import(
+ opal,
+ file,
+ project,
+ table,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)
@@ -131,6 +131,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -151,11 +152,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
+opal.logout(o)
+}
@@ -170,7 +171,7 @@ Examples
diff --git a/docs/reference/opal.table_perm.html b/docs/reference/opal.table_perm.html
index d6ebf2a3..b007ebba 100644
--- a/docs/reference/opal.table_perm.html
+++ b/docs/reference/opal.table_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a table
- opal.table_perm(opal, project, table)
+ opal.table_perm(opal, project, table)
@@ -95,6 +95,7 @@ Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,13 +116,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -136,7 +137,7 @@ Examples
diff --git a/docs/reference/opal.table_perm_add.html b/docs/reference/opal.table_perm_add.html
index dcd7c7bc..0a6d3975 100644
--- a/docs/reference/opal.table_perm_add.html
+++ b/docs/reference/opal.table_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on a table
- opal.table_perm_add(opal, project, table, subject, type = "user", permission)
+ opal.table_perm_add(opal, project, table, subject, type = "user", permission)
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -143,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.table_perm_delete.html b/docs/reference/opal.table_perm_delete.html
index 8b9b72de..940dd6c6 100644
--- a/docs/reference/opal.table_perm_delete.html
+++ b/docs/reference/opal.table_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a table
- opal.table_perm_delete(opal, project, table, subject, type = "user")
+ opal.table_perm_delete(opal, project, table, subject, type = "user")
@@ -97,6 +97,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -117,13 +118,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -138,7 +139,7 @@ Examples
diff --git a/docs/reference/opal.table_save.html b/docs/reference/opal.table_save.html
index 99d85274..b60ae4ab 100644
--- a/docs/reference/opal.table_save.html
+++ b/docs/reference/opal.table_save.html
@@ -71,18 +71,18 @@ Save a local tibble as a Opal table
- opal.table_save(
- opal,
- tibble,
- project,
- table,
- overwrite = TRUE,
- force = FALSE,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant"
-)
+ opal.table_save(
+ opal,
+ tibble,
+ project,
+ table,
+ overwrite = TRUE,
+ force = FALSE,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant"
+)
@@ -142,6 +142,7 @@ Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -162,15 +163,15 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-# do some (meta)data transformations, then save in opal's database
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
-# or overwrite data only (keep original data dictionary)
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+# do some (meta)data transformations, then save in opal's database
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
+# or overwrite data only (keep original data dictionary)
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
+opal.logout(o)
+}
@@ -185,7 +186,7 @@ Examples
diff --git a/docs/reference/opal.table_truncate.html b/docs/reference/opal.table_truncate.html
index 13487c0d..41394336 100644
--- a/docs/reference/opal.table_truncate.html
+++ b/docs/reference/opal.table_truncate.html
@@ -71,7 +71,7 @@ Truncate a Opal table
- opal.table_truncate(opal, project, table)
+ opal.table_truncate(opal, project, table)
@@ -91,6 +91,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -111,11 +112,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_truncate(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_truncate(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -130,7 +131,7 @@ Examples
diff --git a/docs/reference/opal.table_view_create.html b/docs/reference/opal.table_view_create.html
index 9b40db41..704d8e1c 100644
--- a/docs/reference/opal.table_view_create.html
+++ b/docs/reference/opal.table_view_create.html
@@ -73,7 +73,7 @@ Create an Opal view over tables
- opal.table_view_create(opal, project, table, tables, type = "Participant")
+ opal.table_view_create(opal, project, table, tables, type = "Participant")
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
@@ -143,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.table_view_update.html b/docs/reference/opal.table_view_update.html
index c4892e57..edf8750f 100644
--- a/docs/reference/opal.table_view_update.html
+++ b/docs/reference/opal.table_view_update.html
@@ -73,7 +73,7 @@ Update the table references and the entity filter of an Opal view
- opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
+ opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
@@ -101,6 +101,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -121,28 +122,28 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1"))
-
-# update the table references
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-
-# update the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
-
-# remove the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
-
-# update both the table references and the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
- where = "$('LAB_TSC').ge(5)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1"))
+
+# update the table references
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+
+# update the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
+
+# remove the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
+
+# update both the table references and the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
+ where = "$('LAB_TSC').ge(5)")
+opal.logout(o)
+}
@@ -157,7 +158,7 @@ Examples
diff --git a/docs/reference/opal.tables.html b/docs/reference/opal.tables.html
index da771ccc..3523f1ce 100644
--- a/docs/reference/opal.tables.html
+++ b/docs/reference/opal.tables.html
@@ -69,7 +69,7 @@ Get tables of a datasource
- opal.tables(opal, datasource, counts = FALSE, df = TRUE)
+ opal.tables(opal, datasource, counts = FALSE, df = TRUE)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables(o, 'CNSIM')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm.html b/docs/reference/opal.tables_perm.html
index e401969e..eaf76e27 100644
--- a/docs/reference/opal.tables_perm.html
+++ b/docs/reference/opal.tables_perm.html
@@ -69,7 +69,7 @@ Get the permissions on any table of a project
- opal.tables_perm(opal, project)
+ opal.tables_perm(opal, project)
@@ -91,13 +91,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm_add.html b/docs/reference/opal.tables_perm_add.html
index f9f318fe..34f1092b 100644
--- a/docs/reference/opal.tables_perm_add.html
+++ b/docs/reference/opal.tables_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on any table of a project
- opal.tables_perm_add(opal, project, subject, type = "user", permission)
+ opal.tables_perm_add(opal, project, subject, type = "user", permission)
@@ -97,13 +97,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm_delete.html b/docs/reference/opal.tables_perm_delete.html
index 58317fa1..c6c2bbb4 100644
--- a/docs/reference/opal.tables_perm_delete.html
+++ b/docs/reference/opal.tables_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from any table of a project
- opal.tables_perm_delete(opal, project, subject, type = "user")
+ opal.tables_perm_delete(opal, project, subject, type = "user")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/opal.task.html b/docs/reference/opal.task.html
index 5f63c0bb..9f2abe58 100644
--- a/docs/reference/opal.task.html
+++ b/docs/reference/opal.task.html
@@ -69,7 +69,7 @@ Get a task
- opal.task(opal, id)
+ opal.task(opal, id)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task(o, '1')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.task_cancel.html b/docs/reference/opal.task_cancel.html
index 4d2f68ff..a6d3af66 100644
--- a/docs/reference/opal.task_cancel.html
+++ b/docs/reference/opal.task_cancel.html
@@ -69,7 +69,7 @@ Cancel a task
- opal.task_cancel(opal, id)
+ opal.task_cancel(opal, id)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_cancel(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_cancel(o, '1')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.task_wait.html b/docs/reference/opal.task_wait.html
index e46c9ad1..c75baf8d 100644
--- a/docs/reference/opal.task_wait.html
+++ b/docs/reference/opal.task_wait.html
@@ -69,7 +69,7 @@ Wait for a task to complete.
- opal.task_wait(opal, id, max = NULL)
+ opal.task_wait(opal, id, max = NULL)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_wait(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_wait(o, '1')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.tasks.html b/docs/reference/opal.tasks.html
index b03cca25..bbc1909c 100644
--- a/docs/reference/opal.tasks.html
+++ b/docs/reference/opal.tasks.html
@@ -69,7 +69,7 @@ Get the tasks
- opal.tasks(opal, df = TRUE)
+ opal.tasks(opal, df = TRUE)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tasks(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tasks(o)
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.taxonomies.html b/docs/reference/opal.taxonomies.html
index 6eb7c9fc..7fdeb65c 100644
--- a/docs/reference/opal.taxonomies.html
+++ b/docs/reference/opal.taxonomies.html
@@ -71,7 +71,7 @@ Get taxonomies
- opal.taxonomies(opal, locale = "en", df = TRUE)
+ opal.taxonomies(opal, locale = "en", df = TRUE)
@@ -102,11 +102,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomies(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomies(o)
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy.html b/docs/reference/opal.taxonomy.html
index 588356cb..830f2f20 100644
--- a/docs/reference/opal.taxonomy.html
+++ b/docs/reference/opal.taxonomy.html
@@ -69,7 +69,7 @@ Get a taxonomy
- opal.taxonomy(opal, taxonomy)
+ opal.taxonomy(opal, taxonomy)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_delete.html b/docs/reference/opal.taxonomy_delete.html
index 56a28d51..16c5fe75 100644
--- a/docs/reference/opal.taxonomy_delete.html
+++ b/docs/reference/opal.taxonomy_delete.html
@@ -69,7 +69,7 @@ Delete a taxonomy
- opal.taxonomy_delete(opal, taxonomy)
+ opal.taxonomy_delete(opal, taxonomy)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_delete(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_delete(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_download.html b/docs/reference/opal.taxonomy_download.html
index bde9b7cc..72ddba73 100644
--- a/docs/reference/opal.taxonomy_download.html
+++ b/docs/reference/opal.taxonomy_download.html
@@ -69,7 +69,7 @@ Download a taxonomy file
- opal.taxonomy_download(opal, taxonomy, destination = NULL)
+ opal.taxonomy_download(opal, taxonomy, destination = NULL)
@@ -101,11 +101,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_upload.html b/docs/reference/opal.taxonomy_upload.html
index f64a1c9c..33aa2918 100644
--- a/docs/reference/opal.taxonomy_upload.html
+++ b/docs/reference/opal.taxonomy_upload.html
@@ -71,7 +71,7 @@ Upload a taxonomy file
- opal.taxonomy_upload(opal, path)
+ opal.taxonomy_upload(opal, path)
@@ -98,11 +98,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/opal.terms.html b/docs/reference/opal.terms.html
index 42d3ba1c..4514444d 100644
--- a/docs/reference/opal.terms.html
+++ b/docs/reference/opal.terms.html
@@ -69,7 +69,7 @@ Get the terms of a vocabulary
- opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
+ opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/opal.token.html b/docs/reference/opal.token.html
index 139cfb7f..2b23254c 100644
--- a/docs/reference/opal.token.html
+++ b/docs/reference/opal.token.html
@@ -71,7 +71,7 @@ Get a personal access token
- opal.token(opal, name)
+ opal.token(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_datashield_create.html b/docs/reference/opal.token_datashield_create.html
index 3eb7cd13..2f127a6b 100644
--- a/docs/reference/opal.token_datashield_create.html
+++ b/docs/reference/opal.token_datashield_create.html
@@ -71,7 +71,7 @@ Create a personal access token for Datashield usage
- opal.token_datashield_create(opal, name, projects = NULL)
+ opal.token_datashield_create(opal, name, projects = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_datashield_create(o, 'ds-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_datashield_create(o, 'ds-1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.token_delete.html b/docs/reference/opal.token_delete.html
index 780eb5ed..402a3d26 100644
--- a/docs/reference/opal.token_delete.html
+++ b/docs/reference/opal.token_delete.html
@@ -71,7 +71,7 @@ Delete a personal access token
- opal.token_delete(opal, name)
+ opal.token_delete(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_delete(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_delete(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_r_create.html b/docs/reference/opal.token_r_create.html
index b0b36787..c8222189 100644
--- a/docs/reference/opal.token_r_create.html
+++ b/docs/reference/opal.token_r_create.html
@@ -71,13 +71,13 @@ Create a personal access token for R usage
- opal.token_r_create(
- opal,
- name,
- projects = NULL,
- access = NULL,
- commands = c("export")
-)
+ opal.token_r_create(
+ opal,
+ name,
+ projects = NULL,
+ access = NULL,
+ commands = c("export")
+)
@@ -121,11 +121,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
+opal.logout(o)
+}
@@ -140,7 +140,7 @@ Examples
diff --git a/docs/reference/opal.token_renew.html b/docs/reference/opal.token_renew.html
index 72208339..e11a4f33 100644
--- a/docs/reference/opal.token_renew.html
+++ b/docs/reference/opal.token_renew.html
@@ -71,7 +71,7 @@ Renew an inactive personal access token
- opal.token_renew(opal, name)
+ opal.token_renew(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_renew(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_renew(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_sql_create.html b/docs/reference/opal.token_sql_create.html
index b618980e..d65e177c 100644
--- a/docs/reference/opal.token_sql_create.html
+++ b/docs/reference/opal.token_sql_create.html
@@ -71,7 +71,7 @@ Create a personal access token for SQL usage
- opal.token_sql_create(opal, name, projects = NULL)
+ opal.token_sql_create(opal, name, projects = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_sql_create(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_sql_create(o, 'sql-1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.tokens.html b/docs/reference/opal.tokens.html
index 59d4edfa..703771e5 100644
--- a/docs/reference/opal.tokens.html
+++ b/docs/reference/opal.tokens.html
@@ -71,7 +71,7 @@ Get the personal access tokens
- opal.tokens(opal, df = TRUE)
+ opal.tokens(opal, df = TRUE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tokens(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tokens(o)
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.unload_package.html b/docs/reference/opal.unload_package.html
index cb7ded42..6b5ebac0 100644
--- a/docs/reference/opal.unload_package.html
+++ b/docs/reference/opal.unload_package.html
@@ -69,7 +69,7 @@ Unload package
- opal.unload_package(opal, pkg)
+ opal.unload_package(opal, pkg)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.unload_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.unload_package(o, 'stats')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.valueset.html b/docs/reference/opal.valueset.html
index 7bbd50a4..d0c5c00a 100644
--- a/docs/reference/opal.valueset.html
+++ b/docs/reference/opal.valueset.html
@@ -69,7 +69,7 @@ Get the values of an entity
- opal.valueset(opal, datasource, table, identifier)
+ opal.valueset(opal, datasource, table, identifier)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.variable.html b/docs/reference/opal.variable.html
index 3e2e9155..2269ea5d 100644
--- a/docs/reference/opal.variable.html
+++ b/docs/reference/opal.variable.html
@@ -69,7 +69,7 @@ Get a variable of a table
- opal.variable(opal, datasource, table, variable)
+ opal.variable(opal, datasource, table, variable)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.variable_summary.html b/docs/reference/opal.variable_summary.html
index 75fda252..5686692d 100644
--- a/docs/reference/opal.variable_summary.html
+++ b/docs/reference/opal.variable_summary.html
@@ -69,14 +69,14 @@ Get summary statistics of a variable of a table
- opal.variable_summary(
- opal,
- datasource,
- table,
- variable,
- cached = TRUE,
- nature = NULL
-)
+ opal.variable_summary(
+ opal,
+ datasource,
+ table,
+ variable,
+ cached = TRUE,
+ nature = NULL
+)
@@ -124,11 +124,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
@@ -143,7 +143,7 @@ Examples
diff --git a/docs/reference/opal.variables.html b/docs/reference/opal.variables.html
index e1072df8..3ea90c87 100644
--- a/docs/reference/opal.variables.html
+++ b/docs/reference/opal.variables.html
@@ -69,7 +69,7 @@ Get variables of a table
- opal.variables(opal, datasource, table, locale = "en", df = TRUE)
+ opal.variables(opal, datasource, table, locale = "en", df = TRUE)
@@ -111,11 +111,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variables(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variables(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.version_compare.html b/docs/reference/opal.version_compare.html
index f9a8bc44..b8a11b96 100644
--- a/docs/reference/opal.version_compare.html
+++ b/docs/reference/opal.version_compare.html
@@ -71,7 +71,7 @@ Compare
- opal.version_compare(opal, version)
+ opal.version_compare(opal, version)
@@ -93,11 +93,11 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.version_compare(o, "2.6.0")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.version_compare(o, "2.6.0")
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.vocabularies.html b/docs/reference/opal.vocabularies.html
index 2a4ae4ac..edaf165e 100644
--- a/docs/reference/opal.vocabularies.html
+++ b/docs/reference/opal.vocabularies.html
@@ -69,7 +69,7 @@ Get the vocabularies of a taxonomy
- opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
+ opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabularies(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabularies(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.vocabulary.html b/docs/reference/opal.vocabulary.html
index 8dd847d4..18c471f7 100644
--- a/docs/reference/opal.vocabulary.html
+++ b/docs/reference/opal.vocabulary.html
@@ -69,7 +69,7 @@ Get a taxonomy vocabulary
- opal.vocabulary(opal, taxonomy, vocabulary)
+ opal.vocabulary(opal, taxonomy, vocabulary)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.workspace_restore.html b/docs/reference/opal.workspace_restore.html
index 192c945b..705b823a 100644
--- a/docs/reference/opal.workspace_restore.html
+++ b/docs/reference/opal.workspace_restore.html
@@ -69,7 +69,7 @@ Restore a R workspace from a opal.
- opal.workspace_restore(opal, ws)
+ opal.workspace_restore(opal, ws)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_restore(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_restore(o, 'test')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.workspace_rm.html b/docs/reference/opal.workspace_rm.html
index e33cf1d2..4bce81f9 100644
--- a/docs/reference/opal.workspace_rm.html
+++ b/docs/reference/opal.workspace_rm.html
@@ -69,7 +69,7 @@ Remove a R workspace from a opal.
- opal.workspace_rm(opal, ws, user = NULL)
+ opal.workspace_rm(opal, ws, user = NULL)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_rm(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_rm(o, 'test')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.workspace_save.html b/docs/reference/opal.workspace_save.html
index 074274e0..aa974933 100644
--- a/docs/reference/opal.workspace_save.html
+++ b/docs/reference/opal.workspace_save.html
@@ -69,7 +69,7 @@ Save the current session in a opal R workspace.
- opal.workspace_save(opal, save = TRUE)
+ opal.workspace_save(opal, save = TRUE)
@@ -98,14 +98,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# provide a workspace ID
-opal.workspace_save(o, 'test')
-# or use default one
-id <- opal.workspace_save(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# provide a workspace ID
+opal.workspace_save(o, 'test')
+# or use default one
+id <- opal.workspace_save(o)
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.workspaces.html b/docs/reference/opal.workspaces.html
index 83f92fdc..f4b0c155 100644
--- a/docs/reference/opal.workspaces.html
+++ b/docs/reference/opal.workspaces.html
@@ -69,7 +69,7 @@ Get the R workspaces from a opal.
- opal.workspaces(opal)
+ opal.workspaces(opal)
@@ -88,11 +88,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspaces(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspaces(o)
+opal.logout(o)
+}
@@ -107,7 +107,7 @@ Examples
diff --git a/docs/reference/opalr-package.html b/docs/reference/opalr-package.html
index acf0539c..7a3957ef 100644
--- a/docs/reference/opalr-package.html
+++ b/docs/reference/opalr-package.html
@@ -99,7 +99,7 @@ Author
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index db0185af..5d5b6ce2 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -123,6 +123,12 @@
/reference/dot-verbose.html
+
+ /reference/dsadmin.activity.html
+
+
+ /reference/dsadmin.activity_summary.html
+
/reference/dsadmin.get_method.html
@@ -144,6 +150,9 @@
/reference/dsadmin.installed_package.html
+
+ /reference/dsadmin.log.html
+
/reference/dsadmin.package_description.html
@@ -231,6 +240,12 @@
/reference/index.html
+
+ /reference/oadmin.activity.html
+
+
+ /reference/oadmin.activity_summary.html
+
/reference/oadmin.install_bioconductor_package.html
@@ -258,6 +273,15 @@
/reference/oadmin.installed_packages.html
+
+ /reference/oadmin.log.html
+
+
+ /reference/oadmin.log_rest.html
+
+
+ /reference/oadmin.log_sql.html
+
/reference/oadmin.package_description.html
@@ -426,6 +450,9 @@
/reference/opal.logout.html
+
+ /reference/opal.perms.html
+
/reference/opal.post.html
.getRSessionId(opal).getRSessionId(opal)Get all R session in Opal.
-
+
@@ -85,7 +85,7 @@ .getSessions(opal).getSessions(opal)Get all R session in Opal.
diff --git a/docs/reference/dot-handleError.html b/docs/reference/dot-handleError.html index 3f25f7b3..10a4a4d6 100644 --- a/docs/reference/dot-handleError.html +++ b/docs/reference/dot-handleError.html @@ -69,7 +69,7 @@Handle error response
-
+
@@ -85,7 +85,7 @@ .handleError(opal, response).handleError(opal, response)Handle error response
diff --git a/docs/reference/dot-handleResponse.html b/docs/reference/dot-handleResponse.html index 135a5f63..812aabe6 100644 --- a/docs/reference/dot-handleResponse.html +++ b/docs/reference/dot-handleResponse.html @@ -69,7 +69,7 @@Default request response handler.
-
+
@@ -85,7 +85,7 @@ .handleResponse(opal, response).handleResponse(opal, response)Default request response handler.
diff --git a/docs/reference/dot-handleResponseLocation.html b/docs/reference/dot-handleResponseLocation.html index 2aa7fa4a..1a9c550a 100644 --- a/docs/reference/dot-handleResponseLocation.html +++ b/docs/reference/dot-handleResponseLocation.html @@ -69,7 +69,7 @@Default request response Location handler.
-
+
@@ -85,7 +85,7 @@ .handleResponseLocation(opal, response).handleResponseLocation(opal, response)Default request response Location handler.
diff --git a/docs/reference/dot-handleResponseOrCallback.html b/docs/reference/dot-handleResponseOrCallback.html index 1c19cded..fd75863d 100644 --- a/docs/reference/dot-handleResponseOrCallback.html +++ b/docs/reference/dot-handleResponseOrCallback.html @@ -69,7 +69,7 @@Process response with default handler or the provided one
-
+
@@ -85,7 +85,7 @@ .handleResponseOrCallback(opal, response, callback = NULL).handleResponseOrCallback(opal, response, callback = NULL)Process response with default handler or the provided one
diff --git a/docs/reference/dot-is.verbose.html b/docs/reference/dot-is.verbose.html index f3462be7..ddaab2ed 100644 --- a/docs/reference/dot-is.verbose.html +++ b/docs/reference/dot-is.verbose.html @@ -69,7 +69,7 @@Verbose option
-
+
@@ -85,7 +85,7 @@ .is.verbose().is.verbose()Verbose option
diff --git a/docs/reference/dot-isContentEmpty.html b/docs/reference/dot-isContentEmpty.html index 2ca189f6..88320efd 100644 --- a/docs/reference/dot-isContentEmpty.html +++ b/docs/reference/dot-isContentEmpty.html @@ -69,7 +69,7 @@Check if response content is empty.
-
+
@@ -85,7 +85,7 @@ .isContentEmpty(content).isContentEmpty(content)Check if response content is empty.
diff --git a/docs/reference/dot-listToJson.html b/docs/reference/dot-listToJson.html index 9c4d2140..c0bd2195 100644 --- a/docs/reference/dot-listToJson.html +++ b/docs/reference/dot-listToJson.html @@ -69,7 +69,7 @@Simple transformation function of a list into a JSON object/array.
-
+
@@ -85,7 +85,7 @@ .listToJson(l).listToJson(l)Simple transformation function of a list into a JSON object/array.
diff --git a/docs/reference/dot-newProgress.html b/docs/reference/dot-newProgress.html index cdfa936f..c801ff16 100644 --- a/docs/reference/dot-newProgress.html +++ b/docs/reference/dot-newProgress.html @@ -69,12 +69,12 @@Create a new progress instance with default settings.
-
+
@@ -90,7 +90,7 @@ .newProgress(
- format = " :what [:bar] :percent /:elapsed",
- clear = getOption("opal.progress.clear", FALSE),
- total,
- width = 100
-).newProgress(
+ format = " :what [:bar] :percent /:elapsed",
+ clear = getOption("opal.progress.clear", FALSE),
+ total,
+ width = 100
+)Create a new progress instance with default settings.
diff --git a/docs/reference/dot-newSession.html b/docs/reference/dot-newSession.html index a3d04f33..b15cdaa4 100644 --- a/docs/reference/dot-newSession.html +++ b/docs/reference/dot-newSession.html @@ -69,7 +69,7 @@Create a new R session in Opal.
-
+
@@ -85,7 +85,7 @@ .newSession(opal, restore = NULL, profile = NULL).newSession(opal, restore = NULL, profile = NULL)Create a new R session in Opal.
diff --git a/docs/reference/dot-opal.login.html b/docs/reference/dot-opal.login.html index cf5be580..a2d29cf6 100644 --- a/docs/reference/dot-opal.login.html +++ b/docs/reference/dot-opal.login.html @@ -69,15 +69,15 @@Create the opal object
-
+
@@ -93,7 +93,7 @@ .opal.login(
- username,
- password,
- token,
- url,
- opts = list(),
- profile = profile,
- restore = NULL
-).opal.login(
+ username,
+ password,
+ token,
+ url,
+ opts = list(),
+ profile = profile,
+ restore = NULL
+)Create the opal object
diff --git a/docs/reference/dot-rmOpalSession.html b/docs/reference/dot-rmOpalSession.html index bfd20a01..a29f9e94 100644 --- a/docs/reference/dot-rmOpalSession.html +++ b/docs/reference/dot-rmOpalSession.html @@ -69,7 +69,7 @@Remove a Opal session (logout)
-
+
@@ -85,7 +85,7 @@ .rmOpalSession(opal).rmOpalSession(opal)Remove a Opal session (logout)
diff --git a/docs/reference/dot-rmRSession.html b/docs/reference/dot-rmRSession.html index b521882a..827d5ccb 100644 --- a/docs/reference/dot-rmRSession.html +++ b/docs/reference/dot-rmRSession.html @@ -69,7 +69,7 @@Remove a R session from Opal.
-
+
@@ -85,7 +85,7 @@ .rmRSession(opal, save = FALSE).rmRSession(opal, save = FALSE)Remove a R session from Opal.
diff --git a/docs/reference/dot-select.html b/docs/reference/dot-select.html index 43f6c002..13df65cb 100644 --- a/docs/reference/dot-select.html +++ b/docs/reference/dot-select.html @@ -69,7 +69,7 @@Returns a list r such that r[[i]] == l[[i]][field] for all i:length(l)
-
+
@@ -85,7 +85,7 @@ .select(l, field).select(l, field)Returns a list r such that r[[i]] == l[[i]][field] for all i:length(l)
diff --git a/docs/reference/dot-tickProgress.html b/docs/reference/dot-tickProgress.html index 46e06caa..0777056f 100644 --- a/docs/reference/dot-tickProgress.html +++ b/docs/reference/dot-tickProgress.html @@ -69,7 +69,7 @@Output the progress status if option "datashield.progress" is allows to.
@@ -85,7 +85,7 @@Output the progress status if option "datashield.progress" is allows to.
diff --git a/docs/reference/dot-tokenHeader.html b/docs/reference/dot-tokenHeader.html index e6d91a46..a6265701 100644 --- a/docs/reference/dot-tokenHeader.html +++ b/docs/reference/dot-tokenHeader.html @@ -69,7 +69,7 @@Constructs the value for the X-Opal-Auth header
-
+
@@ -85,7 +85,7 @@ .tokenHeader(token).tokenHeader(token)Constructs the value for the X-Opal-Auth header
diff --git a/docs/reference/dot-url.html b/docs/reference/dot-url.html index 6f7da3b7..41bd1de4 100644 --- a/docs/reference/dot-url.html +++ b/docs/reference/dot-url.html @@ -69,7 +69,7 @@Utility method to build urls. Concatenates all arguments and adds a '/' sepa
- .url(opal, ...)
+ .url(opal, ...)
@@ -85,7 +85,7 @@ Utility method to build urls. Concatenates all arguments and adds a '/' sepa
diff --git a/docs/reference/dot-verbose.html b/docs/reference/dot-verbose.html
index f47a65e5..3cf22c86 100644
--- a/docs/reference/dot-verbose.html
+++ b/docs/reference/dot-verbose.html
@@ -69,7 +69,7 @@ Verbose flag
- .verbose()
+ .verbose()
@@ -85,7 +85,7 @@ Verbose flag
diff --git a/docs/reference/dsadmin.activity.html b/docs/reference/dsadmin.activity.html
new file mode 100644
index 00000000..a0d1cc75
--- /dev/null
+++ b/docs/reference/dsadmin.activity.html
@@ -0,0 +1,146 @@
+
+Get DataSHIELD activity — dsadmin.activity • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded DataSHIELD session metrics.
+
+
+
+ dsadmin.activity(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+dsadmin.activity(o)
+# user and profile specific session metrics
+dsadmin.activity(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+dsadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.activity_summary.html b/docs/reference/dsadmin.activity_summary.html
new file mode 100644
index 00000000..c291b9fe
--- /dev/null
+++ b/docs/reference/dsadmin.activity_summary.html
@@ -0,0 +1,146 @@
+
+Get DataSHIELD activity summary — dsadmin.activity_summary • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded DataSHIELD session metrics, grouped by profile and user.
+
+
+
+ dsadmin.activity_summary(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+dsadmin.activity_summary(o)
+# user and profile specific session metrics
+dsadmin.activity_summary(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+dsadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.get_method.html b/docs/reference/dsadmin.get_method.html
index 35d8bada..7e0286ab 100644
--- a/docs/reference/dsadmin.get_method.html
+++ b/docs/reference/dsadmin.get_method.html
@@ -69,7 +69,7 @@ Get a DataSHIELD method
- dsadmin.get_method(opal, name, type = "aggregate", profile = NULL)
+ dsadmin.get_method(opal, name, type = "aggregate", profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_method(o, 'class')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_method(o, 'class')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.get_methods.html b/docs/reference/dsadmin.get_methods.html
index eb9d116f..332bd2e6 100644
--- a/docs/reference/dsadmin.get_methods.html
+++ b/docs/reference/dsadmin.get_methods.html
@@ -69,7 +69,7 @@ Get DataSHIELD methods
- dsadmin.get_methods(opal, type = "aggregate", profile = NULL)
+ dsadmin.get_methods(opal, type = "aggregate", profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_methods(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_methods(o)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.get_options.html b/docs/reference/dsadmin.get_options.html
index 41b6d38f..936afd9a 100644
--- a/docs/reference/dsadmin.get_options.html
+++ b/docs/reference/dsadmin.get_options.html
@@ -69,7 +69,7 @@ Get the DataSHIELD options
- dsadmin.get_options(opal, profile = NULL)
+ dsadmin.get_options(opal, profile = NULL)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_options(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_options(o)
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_github_package.html b/docs/reference/dsadmin.install_github_package.html
index 3cd61327..9cac06c4 100644
--- a/docs/reference/dsadmin.install_github_package.html
+++ b/docs/reference/dsadmin.install_github_package.html
@@ -69,13 +69,13 @@ Install a DataSHIELD package from GitHub
- dsadmin.install_github_package(
- opal,
- pkg,
- username = "datashield",
- ref = "master",
- profile = NULL
-)
+ dsadmin.install_github_package(
+ opal,
+ pkg,
+ username = "datashield",
+ ref = "master",
+ profile = NULL
+)
@@ -132,11 +132,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge')
+opal.logout(o)
+}
@@ -151,7 +151,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_local_package.html b/docs/reference/dsadmin.install_local_package.html
index a1a1c76d..d1a6d9a2 100644
--- a/docs/reference/dsadmin.install_local_package.html
+++ b/docs/reference/dsadmin.install_local_package.html
@@ -71,7 +71,7 @@ Install a DataSHIELD package from a local archive file
- dsadmin.install_local_package(opal, path, profile = NULL)
+ dsadmin.install_local_package(opal, path, profile = NULL)
@@ -114,14 +114,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# install a pre-built local archive file
-dsadmin.install_local_package(o, '~/dsExposome_1.0.0.tar.gz')
-# or build archive file from local package source (in current working folder)
-dsadmin.install_local_package(o, devtools::build())
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# install a pre-built local archive file
+dsadmin.install_local_package(o, '~/dsExposome_1.0.0.tar.gz')
+# or build archive file from local package source (in current working folder)
+dsadmin.install_local_package(o, devtools::build())
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/dsadmin.install_package.html b/docs/reference/dsadmin.install_package.html
index 5a0c9ad1..904d1231 100644
--- a/docs/reference/dsadmin.install_package.html
+++ b/docs/reference/dsadmin.install_package.html
@@ -69,13 +69,13 @@ Install a DataSHIELD package
- dsadmin.install_package(
- opal,
- pkg,
- githubusername = NULL,
- ref = NULL,
- profile = NULL
-)
+ dsadmin.install_package(
+ opal,
+ pkg,
+ githubusername = NULL,
+ ref = NULL,
+ profile = NULL
+)
@@ -132,11 +132,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.install_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.install_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -151,7 +151,7 @@ Examples
diff --git a/docs/reference/dsadmin.installed_package.html b/docs/reference/dsadmin.installed_package.html
index 65240b16..d4e1e5f8 100644
--- a/docs/reference/dsadmin.installed_package.html
+++ b/docs/reference/dsadmin.installed_package.html
@@ -69,7 +69,7 @@ Check DataSHIELD package
- dsadmin.installed_package(opal, pkg, profile = NULL)
+ dsadmin.installed_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.installed_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.installed_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/dsadmin.log.html b/docs/reference/dsadmin.log.html
new file mode 100644
index 00000000..76fcc36d
--- /dev/null
+++ b/docs/reference/dsadmin.log.html
@@ -0,0 +1,155 @@
+
+Get DataSHIELD logs — dsadmin.log • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ The DataSHIELD log is structured as follows:
+
+
+
+ dsadmin.log(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+ Details
+ Common fields
timestamp: when action is logged
version: not used
message: human readable message
logger_name: name of the log channel
thread_name: java thread name
level: log level (TRACE, DEBUG, INFO, WARN, ERROR)
level_value: log level numeric value
ip: ip origin of the request, when available
ds_id: unique DS session ID
ds_profile: DS profile name (available after the R server session is created, can be after authentication)
username: DS user name
r_duration: time spent by the remote R server action (all except PARSE)
r_size: R result serialized object size in bytes
ds_action: DS operation (OPEN, CLOSE, PARSE, ASSIGN, AGGREGATE, LS, RM, WS_SAVE, WS_RESTORE)
DS operations fields
OPEN: DS session opened (note: happens after successful authentication as R server session creation is deferred)
CLOSE: DS session closed
PARSE: R expression parsed
ds_map: DS function mappings used in the R parser, separated by semicolons when several functions are called
ds_script_in: R script as sent by DS user
ds_script_out: R script rewritten by opal, to be evaluated
ASSIGN:
ds_symbol: assigned symbol name
ds_table: table name that is assigned
ds_resource: resource name that is assigned
ds_eval: assign R expression that is evaluated
AGGREGATE:
ds_eval: aggregate R expression that is evaluated
LS: R symbols listed
RM: R symbol removed
ds_symbol: symbol name to remove
WS_SAVE:
ds_ws: workspace name
WS_RESTORE:
ds_ws: workspace name
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.log(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.package_description.html b/docs/reference/dsadmin.package_description.html
index 3351e46a..29694b5b 100644
--- a/docs/reference/dsadmin.package_description.html
+++ b/docs/reference/dsadmin.package_description.html
@@ -69,7 +69,7 @@ Get DataSHIELD package description
- dsadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
+ dsadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
@@ -117,11 +117,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_description(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_description(o, 'dsBase')
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/dsadmin.package_descriptions.html b/docs/reference/dsadmin.package_descriptions.html
index 5fb8ebc9..7707a023 100644
--- a/docs/reference/dsadmin.package_descriptions.html
+++ b/docs/reference/dsadmin.package_descriptions.html
@@ -69,7 +69,7 @@ Get DataSHIELD package descriptions
- dsadmin.package_descriptions(opal, fields = NULL, df = TRUE, profile = NULL)
+ dsadmin.package_descriptions(opal, fields = NULL, df = TRUE, profile = NULL)
@@ -123,11 +123,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_descriptions(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_descriptions(o)
+opal.logout(o)
+}
@@ -142,7 +142,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm.html b/docs/reference/dsadmin.perm.html
index c397d495..50f5957c 100644
--- a/docs/reference/dsadmin.perm.html
+++ b/docs/reference/dsadmin.perm.html
@@ -69,7 +69,7 @@ Get the DataSHIELD permissions
- dsadmin.perm(opal)
+ dsadmin.perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm_add.html b/docs/reference/dsadmin.perm_add.html
index 832ce0ce..e17b5796 100644
--- a/docs/reference/dsadmin.perm_add.html
+++ b/docs/reference/dsadmin.perm_add.html
@@ -69,7 +69,7 @@ Add or update a DataSHIELD permission
- dsadmin.perm_add(opal, subject, type = "user", permission)
+ dsadmin.perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/dsadmin.perm_delete.html b/docs/reference/dsadmin.perm_delete.html
index 91a12ac8..a5ce771c 100644
--- a/docs/reference/dsadmin.perm_delete.html
+++ b/docs/reference/dsadmin.perm_delete.html
@@ -69,7 +69,7 @@ Delete a DataSHIELD permission
- dsadmin.perm_delete(opal, subject, type = "user")
+ dsadmin.perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile.html b/docs/reference/dsadmin.profile.html
index d16b82ac..d8859752 100644
--- a/docs/reference/dsadmin.profile.html
+++ b/docs/reference/dsadmin.profile.html
@@ -73,7 +73,7 @@ Get a DataSHIELD profile
- dsadmin.profile(opal, name)
+ dsadmin.profile(opal, name)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile(o, name = 'default')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile(o, name = 'default')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_access.html b/docs/reference/dsadmin.profile_access.html
index b23f41c7..64ad8674 100644
--- a/docs/reference/dsadmin.profile_access.html
+++ b/docs/reference/dsadmin.profile_access.html
@@ -73,7 +73,7 @@ Restrict or open access to a DataSHIELD profile
- dsadmin.profile_access(opal, name, restricted = TRUE)
+ dsadmin.profile_access(opal, name, restricted = TRUE)
@@ -108,12 +108,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_access(o, name = 'survival', restricted = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_access(o, name = 'survival', restricted = TRUE)
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_create.html b/docs/reference/dsadmin.profile_create.html
index 5f5fb762..e377a2b7 100644
--- a/docs/reference/dsadmin.profile_create.html
+++ b/docs/reference/dsadmin.profile_create.html
@@ -69,7 +69,7 @@ Create a DataSHIELD profile
- dsadmin.profile_create(opal, name, cluster = "default", rParser = NULL)
+ dsadmin.profile_create(opal, name, cluster = "default", rParser = NULL)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_delete.html b/docs/reference/dsadmin.profile_delete.html
index 8bb60e74..de86336c 100644
--- a/docs/reference/dsadmin.profile_delete.html
+++ b/docs/reference/dsadmin.profile_delete.html
@@ -69,7 +69,7 @@ Delete a DataSHIELD profile
- dsadmin.profile_delete(opal, name)
+ dsadmin.profile_delete(opal, name)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_delete(o, name = 'survival')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_delete(o, name = 'survival')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_enable.html b/docs/reference/dsadmin.profile_enable.html
index 8901ed93..36ba9503 100644
--- a/docs/reference/dsadmin.profile_enable.html
+++ b/docs/reference/dsadmin.profile_enable.html
@@ -69,7 +69,7 @@ Enable or disable a DataSHIELD profile
- dsadmin.profile_enable(opal, name, enabled = TRUE)
+ dsadmin.profile_enable(opal, name, enabled = TRUE)
@@ -104,12 +104,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_enable(o, name = 'survival', enabled = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_enable(o, name = 'survival', enabled = TRUE)
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_exists.html b/docs/reference/dsadmin.profile_exists.html
index e5c19c97..5ea51e86 100644
--- a/docs/reference/dsadmin.profile_exists.html
+++ b/docs/reference/dsadmin.profile_exists.html
@@ -69,7 +69,7 @@ Check a DataSHIELD profile exists
- dsadmin.profile_exists(opal, name)
+ dsadmin.profile_exists(opal, name)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-if (!dsadmin.profile_exists(o, name = 'survival'))
- dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+if (!dsadmin.profile_exists(o, name = 'survival'))
+ dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_init.html b/docs/reference/dsadmin.profile_init.html
index 1d117fad..ad4fc311 100644
--- a/docs/reference/dsadmin.profile_init.html
+++ b/docs/reference/dsadmin.profile_init.html
@@ -73,7 +73,7 @@ Initialize a DataSHIELD profile
- dsadmin.profile_init(opal, name, packages = NULL)
+ dsadmin.profile_init(opal, name, packages = NULL)
@@ -108,12 +108,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_init(o, name = 'survival', packages = c('dsSurvival'))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_init(o, name = 'survival', packages = c('dsSurvival'))
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm.html b/docs/reference/dsadmin.profile_perm.html
index ea1913ac..3f90f5de 100644
--- a/docs/reference/dsadmin.profile_perm.html
+++ b/docs/reference/dsadmin.profile_perm.html
@@ -69,7 +69,7 @@ Get the permissions of a DataSHIELD profile
- dsadmin.profile_perm(opal, name)
+ dsadmin.profile_perm(opal, name)
@@ -106,13 +106,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm_add.html b/docs/reference/dsadmin.profile_perm_add.html
index 5aa4f324..e9b60807 100644
--- a/docs/reference/dsadmin.profile_perm_add.html
+++ b/docs/reference/dsadmin.profile_perm_add.html
@@ -71,13 +71,13 @@ Add or update a permission on a DataSHIELD profile
- dsadmin.profile_perm_add(
- opal,
- name,
- subject,
- type = "user",
- permission = "use"
-)
+ dsadmin.profile_perm_add(
+ opal,
+ name,
+ subject,
+ type = "user",
+ permission = "use"
+)
@@ -120,13 +120,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -141,7 +141,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_perm_delete.html b/docs/reference/dsadmin.profile_perm_delete.html
index 5b218b2b..8d2fa69a 100644
--- a/docs/reference/dsadmin.profile_perm_delete.html
+++ b/docs/reference/dsadmin.profile_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a DataSHIELD profile
- dsadmin.profile_perm_delete(opal, name, subject, type = "user")
+ dsadmin.profile_perm_delete(opal, name, subject, type = "user")
@@ -108,13 +108,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/dsadmin.profile_rparser.html b/docs/reference/dsadmin.profile_rparser.html
index f24c5242..bf9617df 100644
--- a/docs/reference/dsadmin.profile_rparser.html
+++ b/docs/reference/dsadmin.profile_rparser.html
@@ -69,7 +69,7 @@ Set or remove the R parser version of a DataSHIELD profile
- dsadmin.profile_rparser(opal, name, rParser = NULL)
+ dsadmin.profile_rparser(opal, name, rParser = NULL)
@@ -105,15 +105,15 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-# apply R parser version v2
-dsadmin.profile_rparser(o, name = 'survival', rParser = 'v2')
-# apply system's default R parser version
-dsadmin.profile_rparser(o, name = 'survival')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+# apply R parser version v2
+dsadmin.profile_rparser(o, name = 'survival', rParser = 'v2')
+# apply system's default R parser version
+dsadmin.profile_rparser(o, name = 'survival')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/dsadmin.profiles.html b/docs/reference/dsadmin.profiles.html
index 7f97e3ad..2ab7201f 100644
--- a/docs/reference/dsadmin.profiles.html
+++ b/docs/reference/dsadmin.profiles.html
@@ -69,7 +69,7 @@ Get DataSHIELD profiles
- dsadmin.profiles(opal, df = TRUE)
+ dsadmin.profiles(opal, df = TRUE)
@@ -106,11 +106,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_descriptions(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_descriptions(o)
+opal.logout(o)
+}
@@ -125,7 +125,7 @@ Examples
diff --git a/docs/reference/dsadmin.publish_package.html b/docs/reference/dsadmin.publish_package.html
index 1aed7d0b..db0a16e3 100644
--- a/docs/reference/dsadmin.publish_package.html
+++ b/docs/reference/dsadmin.publish_package.html
@@ -69,7 +69,7 @@ Publish DataSHIELD package settings
- dsadmin.publish_package(opal, pkg, profile = NULL)
+ dsadmin.publish_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.publish_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.publish_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/dsadmin.remove_package.html b/docs/reference/dsadmin.remove_package.html
index a696d968..11d7e1d3 100644
--- a/docs/reference/dsadmin.remove_package.html
+++ b/docs/reference/dsadmin.remove_package.html
@@ -69,7 +69,7 @@ Remove DataSHIELD package
- dsadmin.remove_package(opal, pkg, profile = NULL)
+ dsadmin.remove_package(opal, pkg, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.remove_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.remove_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_method.html b/docs/reference/dsadmin.rm_method.html
index cca7bb9e..b2d596b8 100644
--- a/docs/reference/dsadmin.rm_method.html
+++ b/docs/reference/dsadmin.rm_method.html
@@ -69,7 +69,7 @@ Remove DataSHIELD method
- dsadmin.rm_method(opal, name, type = "aggregate", profile = NULL)
+ dsadmin.rm_method(opal, name, type = "aggregate", profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_method(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_method(o, 'foo')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_methods.html b/docs/reference/dsadmin.rm_methods.html
index 2532751f..470d8498 100644
--- a/docs/reference/dsadmin.rm_methods.html
+++ b/docs/reference/dsadmin.rm_methods.html
@@ -69,7 +69,7 @@ Remove DataSHIELD methods.
- dsadmin.rm_methods(opal, type = NULL, profile = NULL)
+ dsadmin.rm_methods(opal, type = NULL, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_methods(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_methods(o)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_option.html b/docs/reference/dsadmin.rm_option.html
index 64995c5f..1b4ed85b 100644
--- a/docs/reference/dsadmin.rm_option.html
+++ b/docs/reference/dsadmin.rm_option.html
@@ -69,7 +69,7 @@ Remove a DataSHIELD option
- dsadmin.rm_option(opal, name, profile = NULL)
+ dsadmin.rm_option(opal, name, profile = NULL)
@@ -112,11 +112,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_option(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_option(o, 'foo')
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_options.html b/docs/reference/dsadmin.rm_options.html
index 80414f34..2e4e1b38 100644
--- a/docs/reference/dsadmin.rm_options.html
+++ b/docs/reference/dsadmin.rm_options.html
@@ -69,7 +69,7 @@ Remove all DataSHIELD options
- dsadmin.rm_options(opal, profile = NULL)
+ dsadmin.rm_options(opal, profile = NULL)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_options(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_options(o, 'foo')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/dsadmin.rm_package_methods.html b/docs/reference/dsadmin.rm_package_methods.html
index 26a699ef..f86188d4 100644
--- a/docs/reference/dsadmin.rm_package_methods.html
+++ b/docs/reference/dsadmin.rm_package_methods.html
@@ -69,7 +69,7 @@ Remove DataSHIELD package methods
- dsadmin.rm_package_methods(opal, pkg, type = NULL, profile = NULL)
+ dsadmin.rm_package_methods(opal, pkg, type = NULL, profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_package_methods(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_package_methods(o, 'dsBase')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_method.html b/docs/reference/dsadmin.set_method.html
index ab7bc9ff..a1287cc2 100644
--- a/docs/reference/dsadmin.set_method.html
+++ b/docs/reference/dsadmin.set_method.html
@@ -69,14 +69,14 @@ Set DataSHIELD method
- dsadmin.set_method(
- opal,
- name,
- func = NULL,
- path = NULL,
- type = "aggregate",
- profile = NULL
-)
+ dsadmin.set_method(
+ opal,
+ name,
+ func = NULL,
+ path = NULL,
+ type = "aggregate",
+ profile = NULL
+)
@@ -131,14 +131,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# as a package's function
-dsadmin.set_method(o, 'foo', func = 'base::mean')
-# as a custom function
-dsadmin.set_method(o, 'foo', func = function(x) { base::mean(x) })
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# as a package's function
+dsadmin.set_method(o, 'foo', func = 'base::mean')
+# as a custom function
+dsadmin.set_method(o, 'foo', func = function(x) { base::mean(x) })
+opal.logout(o)
+}
@@ -153,7 +153,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_option.html b/docs/reference/dsadmin.set_option.html
index fa661b5b..af2b415b 100644
--- a/docs/reference/dsadmin.set_option.html
+++ b/docs/reference/dsadmin.set_option.html
@@ -69,7 +69,7 @@ Set DataSHIELD option
- dsadmin.set_option(opal, name, value, profile = NULL)
+ dsadmin.set_option(opal, name, value, profile = NULL)
@@ -116,11 +116,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.set_option(o, 'foo', 'bar')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.set_option(o, 'foo', 'bar')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/dsadmin.set_package_methods.html b/docs/reference/dsadmin.set_package_methods.html
index 663ff9fd..91a0f0e5 100644
--- a/docs/reference/dsadmin.set_package_methods.html
+++ b/docs/reference/dsadmin.set_package_methods.html
@@ -69,7 +69,7 @@ Set DataSHIELD package methods
- dsadmin.set_package_methods(opal, pkg, type = NULL, profile = NULL)
+ dsadmin.set_package_methods(opal, pkg, type = NULL, profile = NULL)
@@ -122,11 +122,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.set_package_methods(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.set_package_methods(o, 'dsBase')
+opal.logout(o)
+}
@@ -141,7 +141,7 @@ Examples
diff --git a/docs/reference/dsadmin.unpublish_package.html b/docs/reference/dsadmin.unpublish_package.html
index 59177cb6..2f4cb561 100644
--- a/docs/reference/dsadmin.unpublish_package.html
+++ b/docs/reference/dsadmin.unpublish_package.html
@@ -69,7 +69,7 @@ Unpublish DataSHIELD package settings
- dsadmin.unpublish_package(opal, pkg, profile = NULL)
+ dsadmin.unpublish_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.unpublish_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.unpublish_package(o, 'dsBase')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 7b8fa952..1410bfd7 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -86,6 +86,14 @@ All functions dictionary.inspect()
Inspect the dictionary of a tibble
+
+
+ Get DataSHIELD activity
+
+
+ Get DataSHIELD activity summary
@@ -114,6 +122,10 @@ All functions dsadmin.installed_package()
Check DataSHIELD package
+
+
+ Get DataSHIELD logs
@@ -226,6 +238,14 @@ All functions dsadmin.unpublish_package()
Unpublish DataSHIELD package settings
+
+
+ Get R activity
+
+
+ Get R activity summary
@@ -262,6 +282,18 @@ All functions oadmin.installed_packages()
List installed packages
+
+
+ Get Opal main logs
+
+
+ Get Opal REST API logs
+
+
+ Get Opal SQL API logs
@@ -486,6 +518,10 @@ All functions opal.logout()
Logout from Opal(s)
+
+
+ Get the permissions of a subject
@@ -847,7 +883,7 @@ All functions
diff --git a/docs/reference/oadmin.activity.html b/docs/reference/oadmin.activity.html
new file mode 100644
index 00000000..a11491b6
--- /dev/null
+++ b/docs/reference/oadmin.activity.html
@@ -0,0 +1,146 @@
+
+Get R activity — oadmin.activity • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics.
+
+
+
+ oadmin.activity(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity(o)
+# user and profile specific session metrics
+oadmin.activity(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.activity_summary.html b/docs/reference/oadmin.activity_summary.html
new file mode 100644
index 00000000..a8159421
--- /dev/null
+++ b/docs/reference/oadmin.activity_summary.html
@@ -0,0 +1,146 @@
+
+Get R activity summary — oadmin.activity_summary • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics, grouped by profile and user.
+
+
+
+ oadmin.activity_summary(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity_summary(o)
+# user and profile specific session metrics
+oadmin.activity_summary(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.install_bioconductor_package.html b/docs/reference/oadmin.install_bioconductor_package.html
index adde90ec..2c0551ed 100644
--- a/docs/reference/oadmin.install_bioconductor_package.html
+++ b/docs/reference/oadmin.install_bioconductor_package.html
@@ -69,7 +69,7 @@ Install a package from Bioconductor
- oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
+ oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_bioconductor_package(o, 'GWASTools')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_bioconductor_package(o, 'GWASTools')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.install_cran_package.html b/docs/reference/oadmin.install_cran_package.html
index 3e7e3a18..d229933e 100644
--- a/docs/reference/oadmin.install_cran_package.html
+++ b/docs/reference/oadmin.install_cran_package.html
@@ -69,7 +69,7 @@ Install a package from CRAN
- oadmin.install_cran_package(opal, pkg, profile = NULL)
+ oadmin.install_cran_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_cran_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_cran_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.install_devtools.html b/docs/reference/oadmin.install_devtools.html
index 3f2bc53c..79b175d3 100644
--- a/docs/reference/oadmin.install_devtools.html
+++ b/docs/reference/oadmin.install_devtools.html
@@ -69,7 +69,7 @@ Install devtools package
- oadmin.install_devtools(opal, profile = NULL)
+ oadmin.install_devtools(opal, profile = NULL)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_devtools(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.install_github_package.html b/docs/reference/oadmin.install_github_package.html
index 496f0075..ae130887 100644
--- a/docs/reference/oadmin.install_github_package.html
+++ b/docs/reference/oadmin.install_github_package.html
@@ -69,13 +69,13 @@ Install a package from GitHub
- oadmin.install_github_package(
- opal,
- pkg,
- username = getOption("github.user"),
- ref = "master",
- profile = NULL
-)
+ oadmin.install_github_package(
+ opal,
+ pkg,
+ username = getOption("github.user"),
+ ref = "master",
+ profile = NULL
+)
@@ -117,11 +117,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_github_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_github_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/oadmin.install_local_package.html b/docs/reference/oadmin.install_local_package.html
index 17ddc429..9ddb56c3 100644
--- a/docs/reference/oadmin.install_local_package.html
+++ b/docs/reference/oadmin.install_local_package.html
@@ -71,7 +71,7 @@ Install a package from a local archive file
- oadmin.install_local_package(opal, path, profile = NULL)
+ oadmin.install_local_package(opal, path, profile = NULL)
@@ -105,14 +105,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# install a pre-built local archive file
-oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
-# or build archive file from local package source (in current working folder)
-oadmin.install_local_package(o, devtools::build())
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# install a pre-built local archive file
+oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
+# or build archive file from local package source (in current working folder)
+oadmin.install_local_package(o, devtools::build())
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/oadmin.install_package.html b/docs/reference/oadmin.install_package.html
index 0b2c26c5..7539e7fc 100644
--- a/docs/reference/oadmin.install_package.html
+++ b/docs/reference/oadmin.install_package.html
@@ -69,7 +69,7 @@ Install CRAN package
- oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
+ oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
@@ -113,11 +113,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_package(o, 'xxx')
+opal.logout(o)
+}
@@ -132,7 +132,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_devtools.html b/docs/reference/oadmin.installed_devtools.html
index eaf1b900..a90063c1 100644
--- a/docs/reference/oadmin.installed_devtools.html
+++ b/docs/reference/oadmin.installed_devtools.html
@@ -69,7 +69,7 @@ Check devtools package
- oadmin.installed_devtools(opal, profile = NULL)
+ oadmin.installed_devtools(opal, profile = NULL)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_devtools(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_package.html b/docs/reference/oadmin.installed_package.html
index 604bd8ef..aa802b54 100644
--- a/docs/reference/oadmin.installed_package.html
+++ b/docs/reference/oadmin.installed_package.html
@@ -69,7 +69,7 @@ Check package is installed
- oadmin.installed_package(opal, pkg, profile = NULL)
+ oadmin.installed_package(opal, pkg, profile = NULL)
@@ -109,12 +109,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_package(o, 'xxx')
-oadmin.installed_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_package(o, 'xxx')
+oadmin.installed_package(o, 'stats')
+opal.logout(o)
+}
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_packages.html b/docs/reference/oadmin.installed_packages.html
index 2bc6bfc8..2034f299 100644
--- a/docs/reference/oadmin.installed_packages.html
+++ b/docs/reference/oadmin.installed_packages.html
@@ -69,7 +69,7 @@ List installed packages
- oadmin.installed_packages(opal, profile = NULL)
+ oadmin.installed_packages(opal, profile = NULL)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_packages(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_packages(o)
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/oadmin.log.html b/docs/reference/oadmin.log.html
new file mode 100644
index 00000000..2204fa48
--- /dev/null
+++ b/docs/reference/oadmin.log.html
@@ -0,0 +1,118 @@
+
+Get Opal main logs — oadmin.log • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal main logs
+
+
+
+ oadmin.log(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.log_rest.html b/docs/reference/oadmin.log_rest.html
new file mode 100644
index 00000000..fd2f9ef2
--- /dev/null
+++ b/docs/reference/oadmin.log_rest.html
@@ -0,0 +1,118 @@
+
+Get Opal REST API logs — oadmin.log_rest • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal REST API logs
+
+
+
+ oadmin.log_rest(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_rest(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.log_sql.html b/docs/reference/oadmin.log_sql.html
new file mode 100644
index 00000000..0dc4fae5
--- /dev/null
+++ b/docs/reference/oadmin.log_sql.html
@@ -0,0 +1,118 @@
+
+Get Opal SQL API logs — oadmin.log_sql • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal SQL API logs
+
+
+
+ oadmin.log_sql(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_sql(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.package_description.html b/docs/reference/oadmin.package_description.html
index d07d871e..d402b336 100644
--- a/docs/reference/oadmin.package_description.html
+++ b/docs/reference/oadmin.package_description.html
@@ -69,7 +69,7 @@ Get package description
- oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
+ oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.package_description(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.package_description(o, 'stats')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/oadmin.perm.html b/docs/reference/oadmin.perm.html
index b61d3e13..20a30ecc 100644
--- a/docs/reference/oadmin.perm.html
+++ b/docs/reference/oadmin.perm.html
@@ -69,7 +69,7 @@ Get the R permissions (deprecated)
- oadmin.perm(opal)
+ oadmin.perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.perm_add.html b/docs/reference/oadmin.perm_add.html
index b3a39610..df43a7c7 100644
--- a/docs/reference/oadmin.perm_add.html
+++ b/docs/reference/oadmin.perm_add.html
@@ -69,7 +69,7 @@ Add or update a R permission (deprecated)
- oadmin.perm_add(opal, subject, type = "user", permission)
+ oadmin.perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.perm_delete.html b/docs/reference/oadmin.perm_delete.html
index f629e6fc..fa8fa4de 100644
--- a/docs/reference/oadmin.perm_delete.html
+++ b/docs/reference/oadmin.perm_delete.html
@@ -69,7 +69,7 @@ Delete a R permission (deprecated)
- oadmin.perm_delete(opal, subject, type = "user")
+ oadmin.perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm.html b/docs/reference/oadmin.r_perm.html
index 4bae064d..12b32d20 100644
--- a/docs/reference/oadmin.r_perm.html
+++ b/docs/reference/oadmin.r_perm.html
@@ -69,7 +69,7 @@ Get the R permissions
- oadmin.r_perm(opal)
+ oadmin.r_perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm_add.html b/docs/reference/oadmin.r_perm_add.html
index 06ec844e..fc74abf1 100644
--- a/docs/reference/oadmin.r_perm_add.html
+++ b/docs/reference/oadmin.r_perm_add.html
@@ -69,7 +69,7 @@ Add or update a R permission
- oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
+ oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm_delete.html b/docs/reference/oadmin.r_perm_delete.html
index c68d1ff5..01177602 100644
--- a/docs/reference/oadmin.r_perm_delete.html
+++ b/docs/reference/oadmin.r_perm_delete.html
@@ -69,7 +69,7 @@ Delete a R permission
- oadmin.r_perm_delete(opal, subject, type = "user")
+ oadmin.r_perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.remove_package.html b/docs/reference/oadmin.remove_package.html
index 7d9fd447..0953b827 100644
--- a/docs/reference/oadmin.remove_package.html
+++ b/docs/reference/oadmin.remove_package.html
@@ -69,7 +69,7 @@ Remove package
- oadmin.remove_package(opal, pkg, profile = NULL)
+ oadmin.remove_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.remove_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.remove_package(o, 'xxx')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.system_metrics.html b/docs/reference/oadmin.system_metrics.html
index 4e5ba20e..9eb7d54a 100644
--- a/docs/reference/oadmin.system_metrics.html
+++ b/docs/reference/oadmin.system_metrics.html
@@ -81,7 +81,7 @@ Get system metrics
- oadmin.system_metrics(opal)
+ oadmin.system_metrics(opal)
@@ -93,11 +93,11 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_metrics(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_metrics(o)
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm.html b/docs/reference/oadmin.system_perm.html
index a858025b..5cc5a542 100644
--- a/docs/reference/oadmin.system_perm.html
+++ b/docs/reference/oadmin.system_perm.html
@@ -69,7 +69,7 @@ Get the System permissions
- oadmin.system_perm(opal)
+ oadmin.system_perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm_add.html b/docs/reference/oadmin.system_perm_add.html
index 8b06fd5e..ecc56a90 100644
--- a/docs/reference/oadmin.system_perm_add.html
+++ b/docs/reference/oadmin.system_perm_add.html
@@ -69,7 +69,7 @@ Add or update a System permission
- oadmin.system_perm_add(opal, subject, type = "user", permission)
+ oadmin.system_perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm_delete.html b/docs/reference/oadmin.system_perm_delete.html
index c78fc7d4..5268feec 100644
--- a/docs/reference/oadmin.system_perm_delete.html
+++ b/docs/reference/oadmin.system_perm_delete.html
@@ -69,7 +69,7 @@ Delete a System permission
- oadmin.system_perm_delete(opal, subject, type = "user")
+ oadmin.system_perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.user_add.html b/docs/reference/oadmin.user_add.html
index e5a58e5b..1b82c9b6 100644
--- a/docs/reference/oadmin.user_add.html
+++ b/docs/reference/oadmin.user_add.html
@@ -69,7 +69,7 @@ Add a user
- oadmin.user_add(opal, name, groups = NULL, password = NULL)
+ oadmin.user_add(opal, name, groups = NULL, password = NULL)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/oadmin.user_delete.html b/docs/reference/oadmin.user_delete.html
index 123be6e5..1ae1cb20 100644
--- a/docs/reference/oadmin.user_delete.html
+++ b/docs/reference/oadmin.user_delete.html
@@ -69,7 +69,7 @@ Delete a user
- oadmin.user_delete(opal, name)
+ oadmin.user_delete(opal, name)
@@ -96,12 +96,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_delete(o, "foo")
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/oadmin.user_enable.html b/docs/reference/oadmin.user_enable.html
index 1b531f3a..5b480d04 100644
--- a/docs/reference/oadmin.user_enable.html
+++ b/docs/reference/oadmin.user_enable.html
@@ -69,7 +69,7 @@ Enable a user
- oadmin.user_enable(opal, name, enabled = TRUE)
+ oadmin.user_enable(opal, name, enabled = TRUE)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_enable(o, "foo", enabled = FALSE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_enable(o, "foo", enabled = FALSE)
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/oadmin.user_exists.html b/docs/reference/oadmin.user_exists.html
index e05a1f79..fad76e33 100644
--- a/docs/reference/oadmin.user_exists.html
+++ b/docs/reference/oadmin.user_exists.html
@@ -71,7 +71,7 @@ Check user exists
- oadmin.user_exists(opal, name)
+ oadmin.user_exists(opal, name)
@@ -98,12 +98,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-if (!oadmin.user_exists(o, "foo"))
- oadmin.user_add(o, "foo", password = "bar123")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+if (!oadmin.user_exists(o, "foo"))
+ oadmin.user_add(o, "foo", password = "bar123")
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.user_profile_delete.html b/docs/reference/oadmin.user_profile_delete.html
index e1aab115..2e585266 100644
--- a/docs/reference/oadmin.user_profile_delete.html
+++ b/docs/reference/oadmin.user_profile_delete.html
@@ -75,7 +75,7 @@ Delete a user profile
- oadmin.user_profile_delete(opal, name)
+ oadmin.user_profile_delete(opal, name)
@@ -102,12 +102,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_profile_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_profile_delete(o, "foo")
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.user_profiles.html b/docs/reference/oadmin.user_profiles.html
index 2c1e5a94..f23f1669 100644
--- a/docs/reference/oadmin.user_profiles.html
+++ b/docs/reference/oadmin.user_profiles.html
@@ -71,7 +71,7 @@ Get user profiles
- oadmin.user_profiles(opal, df = TRUE)
+ oadmin.user_profiles(opal, df = TRUE)
@@ -98,11 +98,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.user_profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.user_profiles(o)
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/oadmin.user_reset_password.html b/docs/reference/oadmin.user_reset_password.html
index 7bc446ae..75e27675 100644
--- a/docs/reference/oadmin.user_reset_password.html
+++ b/docs/reference/oadmin.user_reset_password.html
@@ -69,7 +69,7 @@ Reset user password
- oadmin.user_reset_password(opal, name, password = NULL)
+ oadmin.user_reset_password(opal, name, password = NULL)
@@ -100,13 +100,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_reset_password(o, "foo", password = "password1234")
-oadmin.user_rm(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_reset_password(o, "foo", password = "password1234")
+oadmin.user_rm(o, "foo")
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/oadmin.users.html b/docs/reference/oadmin.users.html
index e16383d7..f7a3388e 100644
--- a/docs/reference/oadmin.users.html
+++ b/docs/reference/oadmin.users.html
@@ -69,7 +69,7 @@ Get the users
- oadmin.users(opal, df = TRUE)
+ oadmin.users(opal, df = TRUE)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.users(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.users(o)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.annotate.html b/docs/reference/opal.annotate.html
index f8b0529c..d0970046 100644
--- a/docs/reference/opal.annotate.html
+++ b/docs/reference/opal.annotate.html
@@ -71,7 +71,7 @@ Apply the annotations to a Opal table
- opal.annotate(opal, datasource, table, annotations)
+ opal.annotate(opal, datasource, table, annotations)
@@ -111,12 +111,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/opal.annotations.html b/docs/reference/opal.annotations.html
index 54727239..9f6b17eb 100644
--- a/docs/reference/opal.annotations.html
+++ b/docs/reference/opal.annotations.html
@@ -69,7 +69,7 @@ Get the annotations of a Opal table
- opal.annotations(opal, datasource, table)
+ opal.annotations(opal, datasource, table)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.as_md_table.html b/docs/reference/opal.as_md_table.html
index e37dd66e..b6b4c121 100644
--- a/docs/reference/opal.as_md_table.html
+++ b/docs/reference/opal.as_md_table.html
@@ -69,14 +69,14 @@ Array to Markdown
-
+
@@ -108,11 +108,11 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/opal.assign.data.html b/docs/reference/opal.assign.data.html
index e7b39e90..2be27522 100644
--- a/docs/reference/opal.assign.data.html
+++ b/docs/reference/opal.assign.data.html
@@ -69,7 +69,7 @@ Data assignment
- opal.assign.data(opal, symbol, value, async = FALSE)
+ opal.assign.data(opal, symbol, value, async = FALSE)
@@ -102,16 +102,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# push an arbitrary data frame to the R server
-opal.assign.data(o, "D", mtcars)
-# push an arbitrary vector to the R server
-opal.assign.data(o, "C", mtcars$cyl)
-# push a string
-opal.assign.data(o, "S", "Hello!")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# push an arbitrary data frame to the R server
+opal.assign.data(o, "D", mtcars)
+# push an arbitrary vector to the R server
+opal.assign.data(o, "C", mtcars$cyl)
+# push a string
+opal.assign.data(o, "S", "Hello!")
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.assign.html b/docs/reference/opal.assign.html
index c0c14727..83bab276 100644
--- a/docs/reference/opal.assign.html
+++ b/docs/reference/opal.assign.html
@@ -69,17 +69,17 @@ Data or expression assignment
- opal.assign(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- async = FALSE
-)
+ opal.assign(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ async = FALSE
+)
@@ -132,21 +132,21 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-# push an arbitrary data frame to the R server
-#opal.assign(o, "D", mtcars)
-# push an arbitrary vector to the R server
-#opal.assign(o, "C", mtcars$cyl)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+# push an arbitrary data frame to the R server
+#opal.assign(o, "D", mtcars)
+# push an arbitrary vector to the R server
+#opal.assign(o, "C", mtcars$cyl)
+opal.logout(o)
+}
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/opal.assign.resource.html b/docs/reference/opal.assign.resource.html
index 649d475e..b06c3fee 100644
--- a/docs/reference/opal.assign.resource.html
+++ b/docs/reference/opal.assign.resource.html
@@ -69,7 +69,7 @@ Resource assignment
- opal.assign.resource(opal, symbol, value, async = FALSE)
+ opal.assign.resource(opal, symbol, value, async = FALSE)
@@ -102,13 +102,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a resource and make some operation on it
-opal.assign.resource(o, "D", "datashield.cram1")
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a resource and make some operation on it
+opal.assign.resource(o, "D", "datashield.cram1")
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.assign.script.html b/docs/reference/opal.assign.script.html
index ce2ee8a8..4826146e 100644
--- a/docs/reference/opal.assign.script.html
+++ b/docs/reference/opal.assign.script.html
@@ -69,7 +69,7 @@ R script assignment
- opal.assign.script(opal, symbol, value, async = FALSE)
+ opal.assign.script(opal, symbol, value, async = FALSE)
@@ -102,13 +102,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.assign.table.html b/docs/reference/opal.assign.table.html
index f23b63b9..b853219b 100644
--- a/docs/reference/opal.assign.table.html
+++ b/docs/reference/opal.assign.table.html
@@ -69,18 +69,18 @@ Data assignment to a data.frame
- opal.assign.table(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- class = "data.frame",
- async = FALSE
-)
+ opal.assign.table(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ class = "data.frame",
+ async = FALSE
+)
@@ -137,19 +137,19 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-opal.execute(o, "colnames(D)")
-# assign a table CNSIM1 with a identifiers column
-opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
-opal.execute(o, "colnames(H)")
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-opal.execute(o, "colnames(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+opal.execute(o, "colnames(D)")
+# assign a table CNSIM1 with a identifiers column
+opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
+opal.execute(o, "colnames(H)")
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+opal.execute(o, "colnames(D)")
+opal.logout(o)
+}
@@ -164,7 +164,7 @@ Examples
diff --git a/docs/reference/opal.assign.table.tibble.html b/docs/reference/opal.assign.table.tibble.html
index 95dc04a3..e508e729 100644
--- a/docs/reference/opal.assign.table.tibble.html
+++ b/docs/reference/opal.assign.table.tibble.html
@@ -69,18 +69,18 @@ Data assignment to a tibble
- opal.assign.table.tibble(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = "id",
- with.factors = FALSE,
- updated.name = NULL,
- async = FALSE
-)
+ opal.assign.table.tibble(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = "id",
+ with.factors = FALSE,
+ updated.name = NULL,
+ async = FALSE
+)
@@ -137,13 +137,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a table and make some operation on it
-opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a table and make some operation on it
+opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
@@ -158,7 +158,7 @@ Examples
diff --git a/docs/reference/opal.attribute_values.html b/docs/reference/opal.attribute_values.html
index dd1b1537..98a94106 100644
--- a/docs/reference/opal.attribute_values.html
+++ b/docs/reference/opal.attribute_values.html
@@ -69,7 +69,7 @@ Get a vector of attribute values
- opal.attribute_values(attributes, namespace = NULL, name = "label")
+ opal.attribute_values(attributes, namespace = NULL, name = "label")
@@ -103,12 +103,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.attribute_values(var$attributes)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.attribute_values(var$attributes)
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.command.html b/docs/reference/opal.command.html
index 0f88509d..4f419a6e 100644
--- a/docs/reference/opal.command.html
+++ b/docs/reference/opal.command.html
@@ -69,7 +69,7 @@ Get an asynchronous command
- opal.command(opal, id, wait = FALSE)
+ opal.command(opal, id, wait = FALSE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command(o, '1234')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.command_result.html b/docs/reference/opal.command_result.html
index 5289b55a..35bc7964 100644
--- a/docs/reference/opal.command_result.html
+++ b/docs/reference/opal.command_result.html
@@ -71,7 +71,7 @@ Get result of an asynchronous command
- opal.command_result(opal, id, wait = FALSE)
+ opal.command_result(opal, id, wait = FALSE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_result(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_result(o, '1234')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.command_rm.html b/docs/reference/opal.command_rm.html
index c43351fa..e7fea6bb 100644
--- a/docs/reference/opal.command_rm.html
+++ b/docs/reference/opal.command_rm.html
@@ -69,7 +69,7 @@ Remove an asynchronous command
- opal.command_rm(opal, id)
+ opal.command_rm(opal, id)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_rm(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_rm(o, '1234')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.commands.html b/docs/reference/opal.commands.html
index f184c2a2..e5067c0f 100644
--- a/docs/reference/opal.commands.html
+++ b/docs/reference/opal.commands.html
@@ -69,7 +69,7 @@ List the asynchronous commands
- opal.commands(opal, df = TRUE)
+ opal.commands(opal, df = TRUE)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands(o)
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.commands_rm.html b/docs/reference/opal.commands_rm.html
index a79be20b..dad19270 100644
--- a/docs/reference/opal.commands_rm.html
+++ b/docs/reference/opal.commands_rm.html
@@ -69,7 +69,7 @@ Remove all asynchronous commands
- opal.commands_rm(opal)
+ opal.commands_rm(opal)
@@ -89,11 +89,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands_rm(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands_rm(o)
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/opal.datasource.html b/docs/reference/opal.datasource.html
index db4e3140..18ec94fc 100644
--- a/docs/reference/opal.datasource.html
+++ b/docs/reference/opal.datasource.html
@@ -69,7 +69,7 @@ Get a datasource
- opal.datasource(opal, datasource)
+ opal.datasource(opal, datasource)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasource(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasource(o, 'CNSIM')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.datasources.html b/docs/reference/opal.datasources.html
index 2c0c3136..b541b556 100644
--- a/docs/reference/opal.datasources.html
+++ b/docs/reference/opal.datasources.html
@@ -69,7 +69,7 @@ Get datasources
- opal.datasources(opal, df = TRUE)
+ opal.datasources(opal, df = TRUE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasources(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasources(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.delete.html b/docs/reference/opal.delete.html
index 9acf1da1..97b75ae3 100644
--- a/docs/reference/opal.delete.html
+++ b/docs/reference/opal.delete.html
@@ -69,7 +69,7 @@ Generic REST resource deletion.
- opal.delete(opal, ..., query = list(), callback = NULL)
+ opal.delete(opal, ..., query = list(), callback = NULL)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.delete(o, 'some', 'resource')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.delete(o, 'some', 'resource')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.execute.html b/docs/reference/opal.execute.html
index 244ade02..f91dcca6 100644
--- a/docs/reference/opal.execute.html
+++ b/docs/reference/opal.execute.html
@@ -69,7 +69,7 @@ Execute a R script
- opal.execute(opal, script, async = FALSE)
+ opal.execute(opal, script, async = FALSE)
@@ -97,12 +97,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute(o, "x <- 'foo'")
-opal.execute(o, "ls()")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute(o, "x <- 'foo'")
+opal.execute(o, "ls()")
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/opal.execute.source.html b/docs/reference/opal.execute.source.html
index 9ad4eef0..f512ffb2 100644
--- a/docs/reference/opal.execute.source.html
+++ b/docs/reference/opal.execute.source.html
@@ -69,7 +69,7 @@ Execute a R file script
- opal.execute.source(opal, path, async = FALSE)
+ opal.execute.source(opal, path, async = FALSE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute.source(o, "myscript.R")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute.source(o, "myscript.R")
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.file.html b/docs/reference/opal.file.html
index 074023d1..72a13d97 100644
--- a/docs/reference/opal.file.html
+++ b/docs/reference/opal.file.html
@@ -69,7 +69,7 @@ Get file content
- opal.file(opal, path, key = NULL)
+ opal.file(opal, path, key = NULL)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.file(o, '/home/administrator/joins/join-src-3.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.file(o, '/home/administrator/joins/join-src-3.csv')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.file_cp.html b/docs/reference/opal.file_cp.html
index c895e41c..33bb18fd 100644
--- a/docs/reference/opal.file_cp.html
+++ b/docs/reference/opal.file_cp.html
@@ -69,7 +69,7 @@ Copy a file
- opal.file_cp(opal, source, destination)
+ opal.file_cp(opal, source, destination)
@@ -104,14 +104,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# copy a file to another folder
-opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# copy recursively a folder to another folder
-opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# copy a file to another folder
+opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# copy recursively a folder to another folder
+opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.file_download.html b/docs/reference/opal.file_download.html
index dde0cba7..e6770678 100644
--- a/docs/reference/opal.file_download.html
+++ b/docs/reference/opal.file_download.html
@@ -69,7 +69,7 @@ Download a file
- opal.file_download(opal, source, destination = NULL, key = NULL)
+ opal.file_download(opal, source, destination = NULL, key = NULL)
@@ -108,19 +108,19 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# download a file
-opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
-# download a file encrypted by a key: resulting file is a zip with an encrypted content
-opal.file_download(o, '/home/administrator/export/some-data.csv',
- destination='some-data.zip', key='AZF57893FBDE')
-# download, create destination folder and rename file
-opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
-# download a folder
-opal.file_download(o, '/home/administrator/export', 'export.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# download a file
+opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
+# download a file encrypted by a key: resulting file is a zip with an encrypted content
+opal.file_download(o, '/home/administrator/export/some-data.csv',
+ destination='some-data.zip', key='AZF57893FBDE')
+# download, create destination folder and rename file
+opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
+# download a folder
+opal.file_download(o, '/home/administrator/export', 'export.zip')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.file_ls.html b/docs/reference/opal.file_ls.html
index c57e02da..8664df11 100644
--- a/docs/reference/opal.file_ls.html
+++ b/docs/reference/opal.file_ls.html
@@ -69,7 +69,7 @@ List content of a folder
- opal.file_ls(opal, path)
+ opal.file_ls(opal, path)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# list content of a folder
-opal.file_ls(o, '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# list content of a folder
+opal.file_ls(o, '/home/administrator')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.file_mkdir.html b/docs/reference/opal.file_mkdir.html
index 0ed72ad7..d15743df 100644
--- a/docs/reference/opal.file_mkdir.html
+++ b/docs/reference/opal.file_mkdir.html
@@ -71,7 +71,7 @@ Make a folder
- opal.file_mkdir(opal, path, parents = FALSE)
+ opal.file_mkdir(opal, path, parents = FALSE)
@@ -106,12 +106,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.file_mkdir_tmp.html b/docs/reference/opal.file_mkdir_tmp.html
index 396c04ff..8e187fcb 100644
--- a/docs/reference/opal.file_mkdir_tmp.html
+++ b/docs/reference/opal.file_mkdir_tmp.html
@@ -69,7 +69,7 @@ Make a temporary folder
- opal.file_mkdir_tmp(opal)
+ opal.file_mkdir_tmp(opal)
@@ -102,12 +102,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-path <- opal.file_mkdir_tmp(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+path <- opal.file_mkdir_tmp(o)
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/opal.file_mv.html b/docs/reference/opal.file_mv.html
index fc322297..1d6874df 100644
--- a/docs/reference/opal.file_mv.html
+++ b/docs/reference/opal.file_mv.html
@@ -69,7 +69,7 @@ Move and/or rename a file
- opal.file_mv(opal, source, destination)
+ opal.file_mv(opal, source, destination)
@@ -104,18 +104,18 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# move a file to another folder
-opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/administrator/export/some-data.csv')
-# move and rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/userx/deliverables/some-data.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# move a file to another folder
+opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/administrator/export/some-data.csv')
+# move and rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/userx/deliverables/some-data.csv')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.file_read.html b/docs/reference/opal.file_read.html
index 64f4982d..1807b28c 100644
--- a/docs/reference/opal.file_read.html
+++ b/docs/reference/opal.file_read.html
@@ -69,7 +69,7 @@ Read a file
- opal.file_read(opal, source, destination)
+ opal.file_read(opal, source, destination)
@@ -104,16 +104,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# read into folder
-opal.file_read(o,"DatabaseTest.sav", "/tmp")
-# read and rename
-opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
-# user home expansion
-opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# read into folder
+opal.file_read(o,"DatabaseTest.sav", "/tmp")
+# read and rename
+opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
+# user home expansion
+opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.file_rm.html b/docs/reference/opal.file_rm.html
index a23dee2e..5d79795c 100644
--- a/docs/reference/opal.file_rm.html
+++ b/docs/reference/opal.file_rm.html
@@ -69,7 +69,7 @@ Remove a file
- opal.file_rm(opal, path)
+ opal.file_rm(opal, path)
@@ -100,14 +100,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# remove a file
-opal.file_rm(o, '/home/administrator/export/some-data.csv')
-# remove recursively a folder
-opal.file_rm(o, '/home/administrator/export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# remove a file
+opal.file_rm(o, '/home/administrator/export/some-data.csv')
+# remove recursively a folder
+opal.file_rm(o, '/home/administrator/export')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/opal.file_unzip.html b/docs/reference/opal.file_unzip.html
index 66eaea32..a695dfec 100644
--- a/docs/reference/opal.file_unzip.html
+++ b/docs/reference/opal.file_unzip.html
@@ -69,7 +69,7 @@ Unzip a zip archive file
- opal.file_unzip(opal, source, destination, key = NULL)
+ opal.file_unzip(opal, source, destination, key = NULL)
@@ -114,12 +114,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# unzip
-path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# unzip
+path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.file_upload.html b/docs/reference/opal.file_upload.html
index 83a6426c..70c2faea 100644
--- a/docs/reference/opal.file_upload.html
+++ b/docs/reference/opal.file_upload.html
@@ -71,7 +71,7 @@ Upload a file or a folder
- opal.file_upload(opal, source, destination, all.files = TRUE)
+ opal.file_upload(opal, source, destination, all.files = TRUE)
@@ -111,14 +111,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# upload a file
-opal.file_upload(o, 'some_data.csv', '/home/administrator')
-# upload a folder
-opal.file_upload(o, 'some_data', '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# upload a file
+opal.file_upload(o, 'some_data.csv', '/home/administrator')
+# upload a folder
+opal.file_upload(o, 'some_data', '/home/administrator')
+opal.logout(o)
+}
@@ -133,7 +133,7 @@ Examples
diff --git a/docs/reference/opal.file_write.html b/docs/reference/opal.file_write.html
index a1bfb19d..f0835d11 100644
--- a/docs/reference/opal.file_write.html
+++ b/docs/reference/opal.file_write.html
@@ -69,7 +69,7 @@ Write a file
- opal.file_write(opal, source, destination = NULL)
+ opal.file_write(opal, source, destination = NULL)
@@ -104,16 +104,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# user home expansion
-opal.file_write(o, "~/spss/DatabaseTest.sav")
-# rename file
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
-# create sub-folder
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# user home expansion
+opal.file_write(o, "~/spss/DatabaseTest.sav")
+# rename file
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
+# create sub-folder
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.get.html b/docs/reference/opal.get.html
index 19e0f260..f83d5cb9 100644
--- a/docs/reference/opal.get.html
+++ b/docs/reference/opal.get.html
@@ -69,14 +69,14 @@ Generic REST resource getter.
- opal.get(
- opal,
- ...,
- query = list(),
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)
+ opal.get(
+ opal,
+ ...,
+ query = list(),
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)
@@ -115,11 +115,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.get(o, 'project', 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.get(o, 'project', 'CNSIM')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.load_package.html b/docs/reference/opal.load_package.html
index 15e9967f..cba05243 100644
--- a/docs/reference/opal.load_package.html
+++ b/docs/reference/opal.load_package.html
@@ -69,7 +69,7 @@ Load package
- opal.load_package(opal, pkg)
+ opal.load_package(opal, pkg)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.load_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.load_package(o, 'stats')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.login.html b/docs/reference/opal.login.html
index f9523698..549cdc71 100644
--- a/docs/reference/opal.login.html
+++ b/docs/reference/opal.login.html
@@ -73,15 +73,15 @@ Opal login
-
+
@@ -132,44 +132,44 @@ See also
Examples
- if (FALSE) {
-#### The below examples illustrate the different ways to login in opal ####
-
-# explicite username/password login
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
- # explicite personal access token login
-o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login using options and user credentials
-options(opal.username = 'administrator',
- opal.password = 'password',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using options and personal access token
-options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using ssl key pair
-options(opal.opts = list(
- sslcert = 'my-publickey.pem',
- sslkey = 'my-privatekey.pem'))
-o <- opal.login(url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login with a R server profile
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org', profile = 'default')
-opal.logout(o)
-}
+ if (FALSE) {
+#### The below examples illustrate the different ways to login in opal ####
+
+# explicite username/password login
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+ # explicite personal access token login
+o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login using options and user credentials
+options(opal.username = 'administrator',
+ opal.password = 'password',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using options and personal access token
+options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using ssl key pair
+options(opal.opts = list(
+ sslcert = 'my-publickey.pem',
+ sslkey = 'my-privatekey.pem'))
+o <- opal.login(url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login with a R server profile
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org', profile = 'default')
+opal.logout(o)
+}
@@ -184,7 +184,7 @@ Examples
diff --git a/docs/reference/opal.logout.html b/docs/reference/opal.logout.html
index e64f3e86..b91868aa 100644
--- a/docs/reference/opal.logout.html
+++ b/docs/reference/opal.logout.html
@@ -69,7 +69,7 @@ Logout from Opal(s)
- opal.logout(opal, save = FALSE)
+ opal.logout(opal, save = FALSE)
@@ -91,10 +91,10 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+}
@@ -109,7 +109,7 @@ Examples
diff --git a/docs/reference/opal.perms.html b/docs/reference/opal.perms.html
new file mode 100644
index 00000000..aab233ff
--- /dev/null
+++ b/docs/reference/opal.perms.html
@@ -0,0 +1,154 @@
+
+Get the permissions of a subject — opal.perms • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the permissions of a subject. If the subject is a user, the permissions of
+the groups to which the user belongs are also added to the result.
+
+
+
+ opal.perms(opal, subject, type = "user")
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- subject
+A subject identifier: user or group name.
- type
+The type of subject: user (default) or group.
+
+ Value
+
+
+A data.frame with columns: subject, type, target (path to the opal object to which
+the permission applies), target_type and perm (the permission name)
+
+
+ See also
+ Other table functions:
+opal.resource_view_create(),
+opal.resource_view_reconnect(),
+opal.table_create(),
+opal.table_delete(),
+opal.table_dictionary_get(),
+opal.table_dictionary_update(),
+opal.table_exists(),
+opal.table_export(),
+opal.table_get(),
+opal.table_import(),
+opal.table_perm_add(),
+opal.table_perm_delete(),
+opal.table_perm(),
+opal.table_save(),
+opal.table_truncate(),
+opal.table_view_create(),
+opal.table_view_update()
+
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.perms(o, 'andrei')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/opal.post.html b/docs/reference/opal.post.html
index d93bb6bf..f7d80068 100644
--- a/docs/reference/opal.post.html
+++ b/docs/reference/opal.post.html
@@ -69,16 +69,16 @@ Generic REST resource creation.
- opal.post(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)
+ opal.post(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)
@@ -125,11 +125,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.post(o, 'some', 'resources', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.post(o, 'some', 'resources', body = '{"some":"value"}')
+opal.logout(o)
+}
@@ -144,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.profiles.html b/docs/reference/opal.profiles.html
index 067273c2..1e96f85c 100644
--- a/docs/reference/opal.profiles.html
+++ b/docs/reference/opal.profiles.html
@@ -71,7 +71,7 @@ List R profiles
- opal.profiles(opal, df = TRUE)
+ opal.profiles(opal, df = TRUE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.profiles(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.project.html b/docs/reference/opal.project.html
index cd3a4f68..3e6b4a16 100644
--- a/docs/reference/opal.project.html
+++ b/docs/reference/opal.project.html
@@ -69,7 +69,7 @@ Get a project
- opal.project(opal, project)
+ opal.project(opal, project)
@@ -94,11 +94,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project(o, 'datashield')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project(o, 'datashield')
+opal.logout(o)
+}
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/opal.project_backup.html b/docs/reference/opal.project_backup.html
index 9fe7543f..58bf4b6e 100644
--- a/docs/reference/opal.project_backup.html
+++ b/docs/reference/opal.project_backup.html
@@ -75,14 +75,14 @@ Backup a project
- opal.project_backup(
- opal,
- project,
- archive,
- viewsAsTables = FALSE,
- override = TRUE,
- wait = TRUE
-)
+ opal.project_backup(
+ opal,
+ project,
+ archive,
+ viewsAsTables = FALSE,
+ override = TRUE,
+ wait = TRUE
+)
@@ -120,12 +120,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
-opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
+opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
+opal.logout(o)
+}
@@ -140,7 +140,7 @@ Examples
diff --git a/docs/reference/opal.project_command.html b/docs/reference/opal.project_command.html
index 13740837..9e6c5e62 100644
--- a/docs/reference/opal.project_command.html
+++ b/docs/reference/opal.project_command.html
@@ -69,7 +69,7 @@ Get project task
- opal.project_command(opal, project, id)
+ opal.project_command(opal, project, id)
@@ -95,12 +95,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
-opal.project_command(opal, 'GREENSPACE', id)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
+opal.project_command(opal, 'GREENSPACE', id)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.project_create.html b/docs/reference/opal.project_create.html
index 2524037d..d1eb8488 100644
--- a/docs/reference/opal.project_create.html
+++ b/docs/reference/opal.project_create.html
@@ -69,15 +69,15 @@ Create a project
- opal.project_create(
- opal,
- project,
- database = NULL,
- title = NULL,
- description = NULL,
- tags = NULL,
- exportFolder = NULL
-)
+ opal.project_create(
+ opal,
+ project,
+ database = NULL,
+ title = NULL,
+ description = NULL,
+ tags = NULL,
+ exportFolder = NULL
+)
@@ -124,16 +124,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with named database
-opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
-# with default database
-opal.project_create(o, 'test_default_db', database = TRUE)
-# no database, for views and resources only
-opal.project_create(o, 'test_no_db')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with named database
+opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
+# with default database
+opal.project_create(o, 'test_default_db', database = TRUE)
+# no database, for views and resources only
+opal.project_create(o, 'test_no_db')
+opal.logout(o)
+}
@@ -148,7 +148,7 @@ Examples
diff --git a/docs/reference/opal.project_delete.html b/docs/reference/opal.project_delete.html
index 0975b5d4..249dfdd3 100644
--- a/docs/reference/opal.project_delete.html
+++ b/docs/reference/opal.project_delete.html
@@ -69,7 +69,7 @@ Delete a project
- opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
+ opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
@@ -102,11 +102,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_delete(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_delete(o, 'test')
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/opal.project_exists.html b/docs/reference/opal.project_exists.html
index 2d217cab..10266208 100644
--- a/docs/reference/opal.project_exists.html
+++ b/docs/reference/opal.project_exists.html
@@ -69,7 +69,7 @@ Check a project exists
- opal.project_exists(opal, project)
+ opal.project_exists(opal, project)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_exists(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_exists(o, 'test')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.project_perm.html b/docs/reference/opal.project_perm.html
index 07a974c3..abba6946 100644
--- a/docs/reference/opal.project_perm.html
+++ b/docs/reference/opal.project_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a project
- opal.project_perm(opal, project)
+ opal.project_perm(opal, project)
@@ -91,13 +91,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.project_perm_add.html b/docs/reference/opal.project_perm_add.html
index 1fd19072..e134d7b0 100644
--- a/docs/reference/opal.project_perm_add.html
+++ b/docs/reference/opal.project_perm_add.html
@@ -69,13 +69,13 @@ Add or update a permission on a project
- opal.project_perm_add(
- opal,
- project,
- subject,
- type = "user",
- permission = "administrate"
-)
+ opal.project_perm_add(
+ opal,
+ project,
+ subject,
+ type = "user",
+ permission = "administrate"
+)
@@ -103,13 +103,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.project_perm_delete.html b/docs/reference/opal.project_perm_delete.html
index 8a290c35..885e9c53 100644
--- a/docs/reference/opal.project_perm_delete.html
+++ b/docs/reference/opal.project_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a project
- opal.project_perm_delete(opal, project, subject, type = "user")
+ opal.project_perm_delete(opal, project, subject, type = "user")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/opal.project_restore.html b/docs/reference/opal.project_restore.html
index 76c5f138..8f4c0d05 100644
--- a/docs/reference/opal.project_restore.html
+++ b/docs/reference/opal.project_restore.html
@@ -75,14 +75,14 @@ Restore a project
- opal.project_restore(
- opal,
- project,
- archive,
- key = NULL,
- override = TRUE,
- wait = TRUE
-)
+ opal.project_restore(
+ opal,
+ project,
+ archive,
+ key = NULL,
+ override = TRUE,
+ wait = TRUE
+)
@@ -120,15 +120,15 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# create the project to restore, with the default database (to store tables)
-opal.project_create(o, 'GREENSPACE2', database = TRUE)
-# upload backup zip and launch restore task
-opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
-opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# create the project to restore, with the default database (to store tables)
+opal.project_create(o, 'GREENSPACE2', database = TRUE)
+# upload backup zip and launch restore task
+opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
+opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
+opal.logout(o)
+}
@@ -143,7 +143,7 @@ Examples
diff --git a/docs/reference/opal.projects.html b/docs/reference/opal.projects.html
index e8d51a41..73e9e973 100644
--- a/docs/reference/opal.projects.html
+++ b/docs/reference/opal.projects.html
@@ -69,7 +69,7 @@ Get projects
- opal.projects(opal, df = TRUE)
+ opal.projects(opal, df = TRUE)
@@ -94,11 +94,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects(o)
+opal.logout(o)
+}
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/opal.projects_databases.html b/docs/reference/opal.projects_databases.html
index 45f818b3..2a9dc9f0 100644
--- a/docs/reference/opal.projects_databases.html
+++ b/docs/reference/opal.projects_databases.html
@@ -69,7 +69,7 @@ Get projects databases
- opal.projects_databases(opal)
+ opal.projects_databases(opal)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects_databases(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects_databases(o)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.put.html b/docs/reference/opal.put.html
index de59ef78..1622010c 100644
--- a/docs/reference/opal.put.html
+++ b/docs/reference/opal.put.html
@@ -69,14 +69,14 @@ Generic REST resource update.
- opal.put(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- callback = NULL
-)
+ opal.put(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ callback = NULL
+)
@@ -115,11 +115,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.report.html b/docs/reference/opal.report.html
index eaf6c399..efc8d7c1 100644
--- a/docs/reference/opal.report.html
+++ b/docs/reference/opal.report.html
@@ -69,13 +69,13 @@ Opal report
- opal.report(
- input,
- output = NULL,
- progress = FALSE,
- verbose = FALSE,
- boot_style = NULL
-)
+ opal.report(
+ input,
+ output = NULL,
+ progress = FALSE,
+ verbose = FALSE,
+ boot_style = NULL
+)
@@ -103,9 +103,9 @@ Arguments
Examples
- if (FALSE) {
-opal.report('input.Rmd', 'report', progress=TRUE)
-}
+ if (FALSE) {
+opal.report('input.Rmd', 'report', progress=TRUE)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.report_md.html b/docs/reference/opal.report_md.html
index ad0cadd5..50a44df1 100644
--- a/docs/reference/opal.report_md.html
+++ b/docs/reference/opal.report_md.html
@@ -69,7 +69,7 @@ Turn a R markdown file to html.
- opal.report_md(inputFile, progress, verbose)
+ opal.report_md(inputFile, progress, verbose)
@@ -85,7 +85,7 @@ Turn a R markdown file to html.
diff --git a/docs/reference/opal.resource.html b/docs/reference/opal.resource.html
index 8040add0..128ece62 100644
--- a/docs/reference/opal.resource.html
+++ b/docs/reference/opal.resource.html
@@ -69,7 +69,7 @@ Get a resource reference of a project
- opal.resource(opal, project, resource)
+ opal.resource(opal, project, resource)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.resource_create.html b/docs/reference/opal.resource_create.html
index a7f47634..9ed343f2 100644
--- a/docs/reference/opal.resource_create.html
+++ b/docs/reference/opal.resource_create.html
@@ -69,17 +69,17 @@ Create a resource reference in a project
- opal.resource_create(
- opal,
- project,
- name,
- url,
- description = NULL,
- format = NULL,
- package = NULL,
- identity = NULL,
- secret = NULL
-)
+ opal.resource_create(
+ opal,
+ project,
+ name,
+ url,
+ description = NULL,
+ format = NULL,
+ package = NULL,
+ identity = NULL,
+ secret = NULL
+)
@@ -139,13 +139,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_create(o, 'RSRC', 'CNSIM4',
- url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
- format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_create(o, 'RSRC', 'CNSIM4',
+ url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
+ format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
+opal.logout(o)
+}
@@ -160,7 +160,7 @@ Examples
diff --git a/docs/reference/opal.resource_delete.html b/docs/reference/opal.resource_delete.html
index 41eee541..a3e48fb8 100644
--- a/docs/reference/opal.resource_delete.html
+++ b/docs/reference/opal.resource_delete.html
@@ -69,7 +69,7 @@ Delete a resource reference
- opal.resource_delete(opal, project, resource, silent = TRUE)
+ opal.resource_delete(opal, project, resource, silent = TRUE)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_delete(o, "RSRC", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_delete(o, "RSRC", "CNSIM4")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.resource_exists.html b/docs/reference/opal.resource_exists.html
index 7a5852e1..700fd693 100644
--- a/docs/reference/opal.resource_exists.html
+++ b/docs/reference/opal.resource_exists.html
@@ -69,7 +69,7 @@ Check a resource reference exists
- opal.resource_exists(opal, project, resource)
+ opal.resource_exists(opal, project, resource)
@@ -111,11 +111,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_exists(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_exists(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.resource_extension_create.html b/docs/reference/opal.resource_extension_create.html
index c0a045fe..1c8013c4 100644
--- a/docs/reference/opal.resource_extension_create.html
+++ b/docs/reference/opal.resource_extension_create.html
@@ -69,16 +69,16 @@ Create an extended resource reference in a project
- opal.resource_extension_create(
- opal,
- project,
- name,
- provider,
- factory,
- parameters,
- description = NULL,
- credentials = NULL
-)
+ opal.resource_extension_create(
+ opal,
+ project,
+ name,
+ provider,
+ factory,
+ parameters,
+ description = NULL,
+ credentials = NULL
+)
@@ -134,21 +134,21 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
- provider = 'dsOmics', factory = 'ga4gh-htsget',
- parameters = list(
- host = 'https://htsget.ga4gh.org',
- sample = '1000genomes.phase1.chr1',
- reference = '1',
- start = '1',
- end = '100000',
- format = 'GA4GHVCF'
- )
-)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
+ provider = 'dsOmics', factory = 'ga4gh-htsget',
+ parameters = list(
+ host = 'https://htsget.ga4gh.org',
+ sample = '1000genomes.phase1.chr1',
+ reference = '1',
+ start = '1',
+ end = '100000',
+ format = 'GA4GHVCF'
+ )
+)
+opal.logout(o)
+}
@@ -163,7 +163,7 @@ Examples
diff --git a/docs/reference/opal.resource_get.html b/docs/reference/opal.resource_get.html
index ae00707a..80a02871 100644
--- a/docs/reference/opal.resource_get.html
+++ b/docs/reference/opal.resource_get.html
@@ -69,7 +69,7 @@ Get the resource object of a project
- opal.resource_get(opal, project, resource)
+ opal.resource_get(opal, project, resource)
@@ -105,17 +105,17 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
-# then interpret locally the resource object (load the appropriate R packages)
-library(resourcer)
-# coerce to a data.frame
-as.data.frame(res)
-# or get the resource client object for low-level interactions
-rescli <- resourcer::newResourceClient(res)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
+# then interpret locally the resource object (load the appropriate R packages)
+library(resourcer)
+# coerce to a data.frame
+as.data.frame(res)
+# or get the resource client object for low-level interactions
+rescli <- resourcer::newResourceClient(res)
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm.html b/docs/reference/opal.resource_perm.html
index e6856cab..d97e7fef 100644
--- a/docs/reference/opal.resource_perm.html
+++ b/docs/reference/opal.resource_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a resource
- opal.resource_perm(opal, project, resource)
+ opal.resource_perm(opal, project, resource)
@@ -111,13 +111,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -132,7 +132,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm_add.html b/docs/reference/opal.resource_perm_add.html
index 9c3d1438..6ad84919 100644
--- a/docs/reference/opal.resource_perm_add.html
+++ b/docs/reference/opal.resource_perm_add.html
@@ -69,14 +69,14 @@ Add or update a permission on a resource
- opal.resource_perm_add(
- opal,
- project,
- resource,
- subject,
- type = "user",
- permission
-)
+ opal.resource_perm_add(
+ opal,
+ project,
+ resource,
+ subject,
+ type = "user",
+ permission
+)
@@ -125,13 +125,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -146,7 +146,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm_delete.html b/docs/reference/opal.resource_perm_delete.html
index df299ed2..541396ce 100644
--- a/docs/reference/opal.resource_perm_delete.html
+++ b/docs/reference/opal.resource_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a resource
- opal.resource_perm_delete(opal, project, resource, subject, type = "user")
+ opal.resource_perm_delete(opal, project, resource, subject, type = "user")
@@ -113,13 +113,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.resource_view_create.html b/docs/reference/opal.resource_view_create.html
index d653a1cf..f3a7a1f2 100644
--- a/docs/reference/opal.resource_view_create.html
+++ b/docs/reference/opal.resource_view_create.html
@@ -73,15 +73,15 @@ Create an Opal view over a resource reference
- opal.resource_view_create(
- opal,
- project,
- table,
- resource,
- type = "Participant",
- idColumn = NULL,
- profile = NULL
-)
+ opal.resource_view_create(
+ opal,
+ project,
+ table,
+ resource,
+ type = "Participant",
+ idColumn = NULL,
+ profile = NULL
+)
@@ -119,6 +119,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
@@ -139,14 +140,14 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
- resource = "RSRC.FEMALE_2439", idColumn = "Name")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
+ resource = "RSRC.FEMALE_2439", idColumn = "Name")
+opal.logout(o)
+}
@@ -161,7 +162,7 @@ Examples
diff --git a/docs/reference/opal.resource_view_reconnect.html b/docs/reference/opal.resource_view_reconnect.html
index e8650b92..06f03a44 100644
--- a/docs/reference/opal.resource_view_reconnect.html
+++ b/docs/reference/opal.resource_view_reconnect.html
@@ -73,7 +73,7 @@ Reconnect an Opal view to its underlying resource
- opal.resource_view_reconnect(opal, project, table)
+ opal.resource_view_reconnect(opal, project, table)
@@ -93,6 +93,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.table_create(),
opal.table_delete(),
@@ -113,14 +114,14 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-# re-initialize the view's connection to the resource
-opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+# re-initialize the view's connection to the resource
+opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
+opal.logout(o)
+}
@@ -135,7 +136,7 @@ Examples
diff --git a/docs/reference/opal.resources.html b/docs/reference/opal.resources.html
index 305236d9..1219e1b9 100644
--- a/docs/reference/opal.resources.html
+++ b/docs/reference/opal.resources.html
@@ -69,7 +69,7 @@ Get the resource references of a project
- opal.resources(opal, project, df = TRUE)
+ opal.resources(opal, project, df = TRUE)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources(o, 'RSRC')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources(o, 'RSRC')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm.html b/docs/reference/opal.resources_perm.html
index ba3302b2..c53289ba 100644
--- a/docs/reference/opal.resources_perm.html
+++ b/docs/reference/opal.resources_perm.html
@@ -69,7 +69,7 @@ Get the permissions on any resource
- opal.resources_perm(opal, project)
+ opal.resources_perm(opal, project)
@@ -107,13 +107,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm_add.html b/docs/reference/opal.resources_perm_add.html
index 1a4a38e2..f1c870b4 100644
--- a/docs/reference/opal.resources_perm_add.html
+++ b/docs/reference/opal.resources_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on any resource
- opal.resources_perm_add(opal, project, subject, type = "user", permission)
+ opal.resources_perm_add(opal, project, subject, type = "user", permission)
@@ -114,13 +114,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm_delete.html b/docs/reference/opal.resources_perm_delete.html
index e7c09535..5c093566 100644
--- a/docs/reference/opal.resources_perm_delete.html
+++ b/docs/reference/opal.resources_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from any resource
- opal.resources_perm_delete(opal, project, subject, type = "user")
+ opal.resources_perm_delete(opal, project, subject, type = "user")
@@ -109,13 +109,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM', 'CNSIM1')
-opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM', 'CNSIM1')
+opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.rm.html b/docs/reference/opal.rm.html
index f444e41c..728ec6d4 100644
--- a/docs/reference/opal.rm.html
+++ b/docs/reference/opal.rm.html
@@ -69,7 +69,7 @@ Remove a R symbol (deprecated)
- opal.rm(opal, symbol)
+ opal.rm(opal, symbol)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.rm(o, 'D')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.sql.html b/docs/reference/opal.sql.html
index 41f13417..5fa1f9b8 100644
--- a/docs/reference/opal.sql.html
+++ b/docs/reference/opal.sql.html
@@ -75,7 +75,7 @@ Execute a SQL query on tables
- opal.sql(opal, query, project = NULL, id.name = "_id")
+ opal.sql(opal, query, project = NULL, id.name = "_id")
@@ -106,23 +106,23 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from CNSIM1
- where LAB_HDL is not null
- group by GENDER',
- 'CNSIM')
-# without project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from `CNSIM.CNSIM1`
- where LAB_HDL is not null
- group by GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from CNSIM1
+ where LAB_HDL is not null
+ group by GENDER',
+ 'CNSIM')
+# without project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from `CNSIM.CNSIM1`
+ where LAB_HDL is not null
+ group by GENDER')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/opal.sql_history.html b/docs/reference/opal.sql_history.html
index ff53d0db..1bd338f2 100644
--- a/docs/reference/opal.sql_history.html
+++ b/docs/reference/opal.sql_history.html
@@ -71,14 +71,14 @@ SQL query execution history
- opal.sql_history(
- opal,
- project = NULL,
- offset = 0,
- limit = 100,
- user = NULL,
- df = TRUE
-)
+ opal.sql_history(
+ opal,
+ project = NULL,
+ offset = 0,
+ limit = 100,
+ user = NULL,
+ df = TRUE
+)
@@ -118,16 +118,16 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql_history(o, 'CNSIM')
-# without project context
-opal.sql_history(o, NA)
-# with or without project context
-opal.sql_history(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql_history(o, 'CNSIM')
+# without project context
+opal.sql_history(o, NA)
+# with or without project context
+opal.sql_history(o)
+opal.logout(o)
+}
@@ -142,7 +142,7 @@ Examples
diff --git a/docs/reference/opal.symbol_import.html b/docs/reference/opal.symbol_import.html
index ae50bd82..5ee219a5 100644
--- a/docs/reference/opal.symbol_import.html
+++ b/docs/reference/opal.symbol_import.html
@@ -71,16 +71,16 @@ Import a tibble
- opal.symbol_import(
- opal,
- symbol,
- project,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)
+ opal.symbol_import(
+ opal,
+ symbol,
+ project,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)
@@ -128,11 +128,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_import(o, 'D', 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_import(o, 'D', 'test')
+opal.logout(o)
+}
@@ -147,7 +147,7 @@ Examples
diff --git a/docs/reference/opal.symbol_rm.html b/docs/reference/opal.symbol_rm.html
index d0cfd696..6d16a689 100644
--- a/docs/reference/opal.symbol_rm.html
+++ b/docs/reference/opal.symbol_rm.html
@@ -69,7 +69,7 @@ Remove a R symbol
- opal.symbol_rm(opal, symbol)
+ opal.symbol_rm(opal, symbol)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_rm(o, 'D')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.symbol_save.html b/docs/reference/opal.symbol_save.html
index f2a900f1..79035aa9 100644
--- a/docs/reference/opal.symbol_save.html
+++ b/docs/reference/opal.symbol_save.html
@@ -69,7 +69,7 @@ Save a tibble
- opal.symbol_save(opal, symbol, destination)
+ opal.symbol_save(opal, symbol, destination)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_save(o, 'D', 'test.sav')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_save(o, 'D', 'test.sav')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.symbols.html b/docs/reference/opal.symbols.html
index bb88de70..1b7894c4 100644
--- a/docs/reference/opal.symbols.html
+++ b/docs/reference/opal.symbols.html
@@ -69,7 +69,7 @@ List R symbols
- opal.symbols(opal)
+ opal.symbols(opal)
@@ -89,11 +89,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbols(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbols(o)
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/opal.table.html b/docs/reference/opal.table.html
index b4d05790..be03e321 100644
--- a/docs/reference/opal.table.html
+++ b/docs/reference/opal.table.html
@@ -69,7 +69,7 @@ Get a table of a datasource
- opal.table(opal, datasource, table, counts = FALSE)
+ opal.table(opal, datasource, table, counts = FALSE)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.table_create.html b/docs/reference/opal.table_create.html
index 44e433ba..46cf045b 100644
--- a/docs/reference/opal.table_create.html
+++ b/docs/reference/opal.table_create.html
@@ -73,7 +73,7 @@ Create an Opal table or view
- opal.table_create(opal, project, table, type = "Participant", tables = NULL)
+ opal.table_create(opal, project, table, type = "Participant", tables = NULL)
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_delete(),
@@ -122,15 +123,15 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a raw table
-opal.table_create(o, "CNSIM", "CNSIM4")
-# make a view
-opal.table_create(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a raw table
+opal.table_create(o, "CNSIM", "CNSIM4")
+# make a view
+opal.table_create(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
@@ -145,7 +146,7 @@ Examples
diff --git a/docs/reference/opal.table_delete.html b/docs/reference/opal.table_delete.html
index 778f2343..cba12a39 100644
--- a/docs/reference/opal.table_delete.html
+++ b/docs/reference/opal.table_delete.html
@@ -71,7 +71,7 @@ Delete a Opal table
- opal.table_delete(opal, project, table, silent = TRUE)
+ opal.table_delete(opal, project, table, silent = TRUE)
@@ -95,6 +95,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,11 +116,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_delete(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_delete(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -134,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.table_dictionary_get.html b/docs/reference/opal.table_dictionary_get.html
index 95a5c21a..59126cc2 100644
--- a/docs/reference/opal.table_dictionary_get.html
+++ b/docs/reference/opal.table_dictionary_get.html
@@ -69,7 +69,7 @@ Get the dictionary of a Opal table
- opal.table_dictionary_get(opal, project, table)
+ opal.table_dictionary_get(opal, project, table)
@@ -89,6 +89,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -109,11 +110,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -128,7 +129,7 @@ Examples
diff --git a/docs/reference/opal.table_dictionary_update.html b/docs/reference/opal.table_dictionary_update.html
index c2e5bfc5..090a7d91 100644
--- a/docs/reference/opal.table_dictionary_update.html
+++ b/docs/reference/opal.table_dictionary_update.html
@@ -69,13 +69,13 @@ Update the dictionary of a Opal table
- opal.table_dictionary_update(
- opal,
- project,
- table,
- variables,
- categories = NULL
-)
+ opal.table_dictionary_update(
+ opal,
+ project,
+ table,
+ variables,
+ categories = NULL
+)
@@ -104,6 +104,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -124,23 +125,23 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-variables <- tibble::tribble(
- ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
- "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
- "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
- "disp", "decimal", "Disp label", NA, NA, 1, 3
-)
-categories <- tibble::tribble(
- ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
- "cyl", "4", 0, "Four", "Quatre",
- "cyl", "6", 0, "Six", "Six",
- "cyl", "8", 1, "Height", "Huit"
-)
-opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+variables <- tibble::tribble(
+ ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
+ "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
+ "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
+ "disp", "decimal", "Disp label", NA, NA, 1, 3
+)
+categories <- tibble::tribble(
+ ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
+ "cyl", "4", 0, "Four", "Quatre",
+ "cyl", "6", 0, "Six", "Six",
+ "cyl", "8", 1, "Height", "Huit"
+)
+opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
+opal.logout(o)
+}
@@ -155,7 +156,7 @@ Examples
diff --git a/docs/reference/opal.table_exists.html b/docs/reference/opal.table_exists.html
index 10649da8..e4ac20bb 100644
--- a/docs/reference/opal.table_exists.html
+++ b/docs/reference/opal.table_exists.html
@@ -71,7 +71,7 @@ Check a Opal table exists
- opal.table_exists(opal, project, table, view = NA)
+ opal.table_exists(opal, project, table, view = NA)
@@ -96,6 +96,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -116,16 +117,16 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# check table exists
-opal.table_exists(o, "CNSIM", "CNSIM1")
-# check table exists AND is a NOT a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
-# check table exists AND is a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# check table exists
+opal.table_exists(o, "CNSIM", "CNSIM1")
+# check table exists AND is a NOT a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
+# check table exists AND is a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
+opal.logout(o)
+}
@@ -140,7 +141,7 @@ Examples
diff --git a/docs/reference/opal.table_export.html b/docs/reference/opal.table_export.html
index f5eb8c76..5110bb07 100644
--- a/docs/reference/opal.table_export.html
+++ b/docs/reference/opal.table_export.html
@@ -73,15 +73,15 @@ Export a table as a file
- opal.table_export(
- opal,
- project,
- table,
- file,
- identifiers = NULL,
- id.name = "id",
- wait = TRUE
-)
+ opal.table_export(
+ opal,
+ project,
+ table,
+ file,
+ identifiers = NULL,
+ id.name = "id",
+ wait = TRUE
+)
@@ -120,6 +120,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -140,12 +141,12 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
- file = "/home/administrator/cnsim1.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
+ file = "/home/administrator/cnsim1.sav")
+opal.logout(o)
+}
@@ -160,7 +161,7 @@ Examples
diff --git a/docs/reference/opal.table_get.html b/docs/reference/opal.table_get.html
index 8a695e18..50b31621 100644
--- a/docs/reference/opal.table_get.html
+++ b/docs/reference/opal.table_get.html
@@ -73,14 +73,14 @@ Get a Opal table as a tibble
- opal.table_get(
- opal,
- project,
- table,
- id.name = "id",
- variables = NULL,
- missings = TRUE
-)
+ opal.table_get(
+ opal,
+ project,
+ table,
+ id.name = "id",
+ variables = NULL,
+ missings = TRUE
+)
@@ -112,6 +112,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -132,11 +133,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+opal.logout(o)
+}
@@ -151,7 +152,7 @@ Examples
diff --git a/docs/reference/opal.table_import.html b/docs/reference/opal.table_import.html
index e7a050a5..587ba457 100644
--- a/docs/reference/opal.table_import.html
+++ b/docs/reference/opal.table_import.html
@@ -77,17 +77,17 @@ Import a file as table
- opal.table_import(
- opal,
- file,
- project,
- table,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)
+ opal.table_import(
+ opal,
+ file,
+ project,
+ table,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)
@@ -131,6 +131,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -151,11 +152,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
+opal.logout(o)
+}
@@ -170,7 +171,7 @@ Examples
diff --git a/docs/reference/opal.table_perm.html b/docs/reference/opal.table_perm.html
index d6ebf2a3..b007ebba 100644
--- a/docs/reference/opal.table_perm.html
+++ b/docs/reference/opal.table_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a table
- opal.table_perm(opal, project, table)
+ opal.table_perm(opal, project, table)
@@ -95,6 +95,7 @@ Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,13 +116,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -136,7 +137,7 @@ Examples
diff --git a/docs/reference/opal.table_perm_add.html b/docs/reference/opal.table_perm_add.html
index dcd7c7bc..0a6d3975 100644
--- a/docs/reference/opal.table_perm_add.html
+++ b/docs/reference/opal.table_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on a table
- opal.table_perm_add(opal, project, table, subject, type = "user", permission)
+ opal.table_perm_add(opal, project, table, subject, type = "user", permission)
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -143,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.table_perm_delete.html b/docs/reference/opal.table_perm_delete.html
index 8b9b72de..940dd6c6 100644
--- a/docs/reference/opal.table_perm_delete.html
+++ b/docs/reference/opal.table_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a table
- opal.table_perm_delete(opal, project, table, subject, type = "user")
+ opal.table_perm_delete(opal, project, table, subject, type = "user")
@@ -97,6 +97,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -117,13 +118,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -138,7 +139,7 @@ Examples
diff --git a/docs/reference/opal.table_save.html b/docs/reference/opal.table_save.html
index 99d85274..b60ae4ab 100644
--- a/docs/reference/opal.table_save.html
+++ b/docs/reference/opal.table_save.html
@@ -71,18 +71,18 @@ Save a local tibble as a Opal table
- opal.table_save(
- opal,
- tibble,
- project,
- table,
- overwrite = TRUE,
- force = FALSE,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant"
-)
+ opal.table_save(
+ opal,
+ tibble,
+ project,
+ table,
+ overwrite = TRUE,
+ force = FALSE,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant"
+)
@@ -142,6 +142,7 @@ Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -162,15 +163,15 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-# do some (meta)data transformations, then save in opal's database
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
-# or overwrite data only (keep original data dictionary)
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+# do some (meta)data transformations, then save in opal's database
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
+# or overwrite data only (keep original data dictionary)
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
+opal.logout(o)
+}
@@ -185,7 +186,7 @@ Examples
diff --git a/docs/reference/opal.table_truncate.html b/docs/reference/opal.table_truncate.html
index 13487c0d..41394336 100644
--- a/docs/reference/opal.table_truncate.html
+++ b/docs/reference/opal.table_truncate.html
@@ -71,7 +71,7 @@ Truncate a Opal table
- opal.table_truncate(opal, project, table)
+ opal.table_truncate(opal, project, table)
@@ -91,6 +91,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -111,11 +112,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_truncate(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_truncate(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -130,7 +131,7 @@ Examples
diff --git a/docs/reference/opal.table_view_create.html b/docs/reference/opal.table_view_create.html
index 9b40db41..704d8e1c 100644
--- a/docs/reference/opal.table_view_create.html
+++ b/docs/reference/opal.table_view_create.html
@@ -73,7 +73,7 @@ Create an Opal view over tables
- opal.table_view_create(opal, project, table, tables, type = "Participant")
+ opal.table_view_create(opal, project, table, tables, type = "Participant")
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
@@ -143,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.table_view_update.html b/docs/reference/opal.table_view_update.html
index c4892e57..edf8750f 100644
--- a/docs/reference/opal.table_view_update.html
+++ b/docs/reference/opal.table_view_update.html
@@ -73,7 +73,7 @@ Update the table references and the entity filter of an Opal view
- opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
+ opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
@@ -101,6 +101,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -121,28 +122,28 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1"))
-
-# update the table references
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-
-# update the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
-
-# remove the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
-
-# update both the table references and the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
- where = "$('LAB_TSC').ge(5)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1"))
+
+# update the table references
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+
+# update the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
+
+# remove the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
+
+# update both the table references and the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
+ where = "$('LAB_TSC').ge(5)")
+opal.logout(o)
+}
@@ -157,7 +158,7 @@ Examples
diff --git a/docs/reference/opal.tables.html b/docs/reference/opal.tables.html
index da771ccc..3523f1ce 100644
--- a/docs/reference/opal.tables.html
+++ b/docs/reference/opal.tables.html
@@ -69,7 +69,7 @@ Get tables of a datasource
- opal.tables(opal, datasource, counts = FALSE, df = TRUE)
+ opal.tables(opal, datasource, counts = FALSE, df = TRUE)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables(o, 'CNSIM')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm.html b/docs/reference/opal.tables_perm.html
index e401969e..eaf76e27 100644
--- a/docs/reference/opal.tables_perm.html
+++ b/docs/reference/opal.tables_perm.html
@@ -69,7 +69,7 @@ Get the permissions on any table of a project
- opal.tables_perm(opal, project)
+ opal.tables_perm(opal, project)
@@ -91,13 +91,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm_add.html b/docs/reference/opal.tables_perm_add.html
index f9f318fe..34f1092b 100644
--- a/docs/reference/opal.tables_perm_add.html
+++ b/docs/reference/opal.tables_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on any table of a project
- opal.tables_perm_add(opal, project, subject, type = "user", permission)
+ opal.tables_perm_add(opal, project, subject, type = "user", permission)
@@ -97,13 +97,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm_delete.html b/docs/reference/opal.tables_perm_delete.html
index 58317fa1..c6c2bbb4 100644
--- a/docs/reference/opal.tables_perm_delete.html
+++ b/docs/reference/opal.tables_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from any table of a project
- opal.tables_perm_delete(opal, project, subject, type = "user")
+ opal.tables_perm_delete(opal, project, subject, type = "user")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/opal.task.html b/docs/reference/opal.task.html
index 5f63c0bb..9f2abe58 100644
--- a/docs/reference/opal.task.html
+++ b/docs/reference/opal.task.html
@@ -69,7 +69,7 @@ Get a task
- opal.task(opal, id)
+ opal.task(opal, id)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task(o, '1')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.task_cancel.html b/docs/reference/opal.task_cancel.html
index 4d2f68ff..a6d3af66 100644
--- a/docs/reference/opal.task_cancel.html
+++ b/docs/reference/opal.task_cancel.html
@@ -69,7 +69,7 @@ Cancel a task
- opal.task_cancel(opal, id)
+ opal.task_cancel(opal, id)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_cancel(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_cancel(o, '1')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.task_wait.html b/docs/reference/opal.task_wait.html
index e46c9ad1..c75baf8d 100644
--- a/docs/reference/opal.task_wait.html
+++ b/docs/reference/opal.task_wait.html
@@ -69,7 +69,7 @@ Wait for a task to complete.
- opal.task_wait(opal, id, max = NULL)
+ opal.task_wait(opal, id, max = NULL)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_wait(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_wait(o, '1')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.tasks.html b/docs/reference/opal.tasks.html
index b03cca25..bbc1909c 100644
--- a/docs/reference/opal.tasks.html
+++ b/docs/reference/opal.tasks.html
@@ -69,7 +69,7 @@ Get the tasks
- opal.tasks(opal, df = TRUE)
+ opal.tasks(opal, df = TRUE)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tasks(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tasks(o)
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.taxonomies.html b/docs/reference/opal.taxonomies.html
index 6eb7c9fc..7fdeb65c 100644
--- a/docs/reference/opal.taxonomies.html
+++ b/docs/reference/opal.taxonomies.html
@@ -71,7 +71,7 @@ Get taxonomies
- opal.taxonomies(opal, locale = "en", df = TRUE)
+ opal.taxonomies(opal, locale = "en", df = TRUE)
@@ -102,11 +102,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomies(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomies(o)
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy.html b/docs/reference/opal.taxonomy.html
index 588356cb..830f2f20 100644
--- a/docs/reference/opal.taxonomy.html
+++ b/docs/reference/opal.taxonomy.html
@@ -69,7 +69,7 @@ Get a taxonomy
- opal.taxonomy(opal, taxonomy)
+ opal.taxonomy(opal, taxonomy)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_delete.html b/docs/reference/opal.taxonomy_delete.html
index 56a28d51..16c5fe75 100644
--- a/docs/reference/opal.taxonomy_delete.html
+++ b/docs/reference/opal.taxonomy_delete.html
@@ -69,7 +69,7 @@ Delete a taxonomy
- opal.taxonomy_delete(opal, taxonomy)
+ opal.taxonomy_delete(opal, taxonomy)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_delete(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_delete(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_download.html b/docs/reference/opal.taxonomy_download.html
index bde9b7cc..72ddba73 100644
--- a/docs/reference/opal.taxonomy_download.html
+++ b/docs/reference/opal.taxonomy_download.html
@@ -69,7 +69,7 @@ Download a taxonomy file
- opal.taxonomy_download(opal, taxonomy, destination = NULL)
+ opal.taxonomy_download(opal, taxonomy, destination = NULL)
@@ -101,11 +101,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_upload.html b/docs/reference/opal.taxonomy_upload.html
index f64a1c9c..33aa2918 100644
--- a/docs/reference/opal.taxonomy_upload.html
+++ b/docs/reference/opal.taxonomy_upload.html
@@ -71,7 +71,7 @@ Upload a taxonomy file
- opal.taxonomy_upload(opal, path)
+ opal.taxonomy_upload(opal, path)
@@ -98,11 +98,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/opal.terms.html b/docs/reference/opal.terms.html
index 42d3ba1c..4514444d 100644
--- a/docs/reference/opal.terms.html
+++ b/docs/reference/opal.terms.html
@@ -69,7 +69,7 @@ Get the terms of a vocabulary
- opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
+ opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/opal.token.html b/docs/reference/opal.token.html
index 139cfb7f..2b23254c 100644
--- a/docs/reference/opal.token.html
+++ b/docs/reference/opal.token.html
@@ -71,7 +71,7 @@ Get a personal access token
- opal.token(opal, name)
+ opal.token(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_datashield_create.html b/docs/reference/opal.token_datashield_create.html
index 3eb7cd13..2f127a6b 100644
--- a/docs/reference/opal.token_datashield_create.html
+++ b/docs/reference/opal.token_datashield_create.html
@@ -71,7 +71,7 @@ Create a personal access token for Datashield usage
- opal.token_datashield_create(opal, name, projects = NULL)
+ opal.token_datashield_create(opal, name, projects = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_datashield_create(o, 'ds-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_datashield_create(o, 'ds-1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.token_delete.html b/docs/reference/opal.token_delete.html
index 780eb5ed..402a3d26 100644
--- a/docs/reference/opal.token_delete.html
+++ b/docs/reference/opal.token_delete.html
@@ -71,7 +71,7 @@ Delete a personal access token
- opal.token_delete(opal, name)
+ opal.token_delete(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_delete(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_delete(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_r_create.html b/docs/reference/opal.token_r_create.html
index b0b36787..c8222189 100644
--- a/docs/reference/opal.token_r_create.html
+++ b/docs/reference/opal.token_r_create.html
@@ -71,13 +71,13 @@ Create a personal access token for R usage
- opal.token_r_create(
- opal,
- name,
- projects = NULL,
- access = NULL,
- commands = c("export")
-)
+ opal.token_r_create(
+ opal,
+ name,
+ projects = NULL,
+ access = NULL,
+ commands = c("export")
+)
@@ -121,11 +121,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
+opal.logout(o)
+}
@@ -140,7 +140,7 @@ Examples
diff --git a/docs/reference/opal.token_renew.html b/docs/reference/opal.token_renew.html
index 72208339..e11a4f33 100644
--- a/docs/reference/opal.token_renew.html
+++ b/docs/reference/opal.token_renew.html
@@ -71,7 +71,7 @@ Renew an inactive personal access token
- opal.token_renew(opal, name)
+ opal.token_renew(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_renew(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_renew(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_sql_create.html b/docs/reference/opal.token_sql_create.html
index b618980e..d65e177c 100644
--- a/docs/reference/opal.token_sql_create.html
+++ b/docs/reference/opal.token_sql_create.html
@@ -71,7 +71,7 @@ Create a personal access token for SQL usage
- opal.token_sql_create(opal, name, projects = NULL)
+ opal.token_sql_create(opal, name, projects = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_sql_create(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_sql_create(o, 'sql-1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.tokens.html b/docs/reference/opal.tokens.html
index 59d4edfa..703771e5 100644
--- a/docs/reference/opal.tokens.html
+++ b/docs/reference/opal.tokens.html
@@ -71,7 +71,7 @@ Get the personal access tokens
- opal.tokens(opal, df = TRUE)
+ opal.tokens(opal, df = TRUE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tokens(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tokens(o)
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.unload_package.html b/docs/reference/opal.unload_package.html
index cb7ded42..6b5ebac0 100644
--- a/docs/reference/opal.unload_package.html
+++ b/docs/reference/opal.unload_package.html
@@ -69,7 +69,7 @@ Unload package
- opal.unload_package(opal, pkg)
+ opal.unload_package(opal, pkg)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.unload_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.unload_package(o, 'stats')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.valueset.html b/docs/reference/opal.valueset.html
index 7bbd50a4..d0c5c00a 100644
--- a/docs/reference/opal.valueset.html
+++ b/docs/reference/opal.valueset.html
@@ -69,7 +69,7 @@ Get the values of an entity
- opal.valueset(opal, datasource, table, identifier)
+ opal.valueset(opal, datasource, table, identifier)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.variable.html b/docs/reference/opal.variable.html
index 3e2e9155..2269ea5d 100644
--- a/docs/reference/opal.variable.html
+++ b/docs/reference/opal.variable.html
@@ -69,7 +69,7 @@ Get a variable of a table
- opal.variable(opal, datasource, table, variable)
+ opal.variable(opal, datasource, table, variable)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.variable_summary.html b/docs/reference/opal.variable_summary.html
index 75fda252..5686692d 100644
--- a/docs/reference/opal.variable_summary.html
+++ b/docs/reference/opal.variable_summary.html
@@ -69,14 +69,14 @@ Get summary statistics of a variable of a table
- opal.variable_summary(
- opal,
- datasource,
- table,
- variable,
- cached = TRUE,
- nature = NULL
-)
+ opal.variable_summary(
+ opal,
+ datasource,
+ table,
+ variable,
+ cached = TRUE,
+ nature = NULL
+)
@@ -124,11 +124,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
@@ -143,7 +143,7 @@ Examples
diff --git a/docs/reference/opal.variables.html b/docs/reference/opal.variables.html
index e1072df8..3ea90c87 100644
--- a/docs/reference/opal.variables.html
+++ b/docs/reference/opal.variables.html
@@ -69,7 +69,7 @@ Get variables of a table
- opal.variables(opal, datasource, table, locale = "en", df = TRUE)
+ opal.variables(opal, datasource, table, locale = "en", df = TRUE)
@@ -111,11 +111,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variables(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variables(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.version_compare.html b/docs/reference/opal.version_compare.html
index f9a8bc44..b8a11b96 100644
--- a/docs/reference/opal.version_compare.html
+++ b/docs/reference/opal.version_compare.html
@@ -71,7 +71,7 @@ Compare
- opal.version_compare(opal, version)
+ opal.version_compare(opal, version)
@@ -93,11 +93,11 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.version_compare(o, "2.6.0")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.version_compare(o, "2.6.0")
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.vocabularies.html b/docs/reference/opal.vocabularies.html
index 2a4ae4ac..edaf165e 100644
--- a/docs/reference/opal.vocabularies.html
+++ b/docs/reference/opal.vocabularies.html
@@ -69,7 +69,7 @@ Get the vocabularies of a taxonomy
- opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
+ opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabularies(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabularies(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.vocabulary.html b/docs/reference/opal.vocabulary.html
index 8dd847d4..18c471f7 100644
--- a/docs/reference/opal.vocabulary.html
+++ b/docs/reference/opal.vocabulary.html
@@ -69,7 +69,7 @@ Get a taxonomy vocabulary
- opal.vocabulary(opal, taxonomy, vocabulary)
+ opal.vocabulary(opal, taxonomy, vocabulary)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.workspace_restore.html b/docs/reference/opal.workspace_restore.html
index 192c945b..705b823a 100644
--- a/docs/reference/opal.workspace_restore.html
+++ b/docs/reference/opal.workspace_restore.html
@@ -69,7 +69,7 @@ Restore a R workspace from a opal.
- opal.workspace_restore(opal, ws)
+ opal.workspace_restore(opal, ws)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_restore(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_restore(o, 'test')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.workspace_rm.html b/docs/reference/opal.workspace_rm.html
index e33cf1d2..4bce81f9 100644
--- a/docs/reference/opal.workspace_rm.html
+++ b/docs/reference/opal.workspace_rm.html
@@ -69,7 +69,7 @@ Remove a R workspace from a opal.
- opal.workspace_rm(opal, ws, user = NULL)
+ opal.workspace_rm(opal, ws, user = NULL)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_rm(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_rm(o, 'test')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.workspace_save.html b/docs/reference/opal.workspace_save.html
index 074274e0..aa974933 100644
--- a/docs/reference/opal.workspace_save.html
+++ b/docs/reference/opal.workspace_save.html
@@ -69,7 +69,7 @@ Save the current session in a opal R workspace.
- opal.workspace_save(opal, save = TRUE)
+ opal.workspace_save(opal, save = TRUE)
@@ -98,14 +98,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# provide a workspace ID
-opal.workspace_save(o, 'test')
-# or use default one
-id <- opal.workspace_save(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# provide a workspace ID
+opal.workspace_save(o, 'test')
+# or use default one
+id <- opal.workspace_save(o)
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.workspaces.html b/docs/reference/opal.workspaces.html
index 83f92fdc..f4b0c155 100644
--- a/docs/reference/opal.workspaces.html
+++ b/docs/reference/opal.workspaces.html
@@ -69,7 +69,7 @@ Get the R workspaces from a opal.
- opal.workspaces(opal)
+ opal.workspaces(opal)
@@ -88,11 +88,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspaces(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspaces(o)
+opal.logout(o)
+}
@@ -107,7 +107,7 @@ Examples
diff --git a/docs/reference/opalr-package.html b/docs/reference/opalr-package.html
index acf0539c..7a3957ef 100644
--- a/docs/reference/opalr-package.html
+++ b/docs/reference/opalr-package.html
@@ -99,7 +99,7 @@ Author
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index db0185af..5d5b6ce2 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -123,6 +123,12 @@
/reference/dot-verbose.html
+
+ /reference/dsadmin.activity.html
+
+
+ /reference/dsadmin.activity_summary.html
+
/reference/dsadmin.get_method.html
@@ -144,6 +150,9 @@
/reference/dsadmin.installed_package.html
+
+ /reference/dsadmin.log.html
+
/reference/dsadmin.package_description.html
@@ -231,6 +240,12 @@
/reference/index.html
+
+ /reference/oadmin.activity.html
+
+
+ /reference/oadmin.activity_summary.html
+
/reference/oadmin.install_bioconductor_package.html
@@ -258,6 +273,15 @@
/reference/oadmin.installed_packages.html
+
+ /reference/oadmin.log.html
+
+
+ /reference/oadmin.log_rest.html
+
+
+ /reference/oadmin.log_sql.html
+
/reference/oadmin.package_description.html
@@ -426,6 +450,9 @@
/reference/opal.logout.html
+
+ /reference/opal.perms.html
+
/reference/opal.post.html
.url(opal, ...).url(opal, ...)Verbose flag
-
+
@@ -85,7 +85,7 @@ .verbose().verbose()Verbose flag
diff --git a/docs/reference/dsadmin.activity.html b/docs/reference/dsadmin.activity.html new file mode 100644 index 00000000..a0d1cc75 --- /dev/null +++ b/docs/reference/dsadmin.activity.html @@ -0,0 +1,146 @@ + +
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.activity_summary.html b/docs/reference/dsadmin.activity_summary.html
new file mode 100644
index 00000000..c291b9fe
--- /dev/null
+++ b/docs/reference/dsadmin.activity_summary.html
@@ -0,0 +1,146 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded DataSHIELD session metrics.
+
+
+
+
+ dsadmin.activity(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+ Arguments
+- opal +
Opal connection object.
+
+
+- user +
Optional user name.
+
+
+- profile +
Optional profile name.
+
+
+- from +
Optional start date.
+
+
+- to +
Optional end date.
+
+
+- df +
Return a data.frame (default is TRUE)
+
+
+
+
+ Examples
+if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+dsadmin.activity(o)
+# user and profile specific session metrics
+dsadmin.activity(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+dsadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.get_method.html b/docs/reference/dsadmin.get_method.html
index 35d8bada..7e0286ab 100644
--- a/docs/reference/dsadmin.get_method.html
+++ b/docs/reference/dsadmin.get_method.html
@@ -69,7 +69,7 @@
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded DataSHIELD session metrics, grouped by profile and user.
+
+
+
+
+ dsadmin.activity_summary(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+ Arguments
+- opal +
Opal connection object.
+
+
+- user +
Optional user name.
+
+
+- profile +
Optional profile name.
+
+
+- from +
Optional start date.
+
+
+- to +
Optional end date.
+
+
+- df +
Return a data.frame (default is TRUE)
+
+
+
+
+ Examples
+if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+dsadmin.activity_summary(o)
+# user and profile specific session metrics
+dsadmin.activity_summary(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+dsadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+Get a DataSHIELD method
-
+
dsadmin.get_method(opal, name, type = "aggregate", profile = NULL)dsadmin.get_method(opal, name, type = "aggregate", profile = NULL)
@@ -116,11 +116,11 @@
@@ -135,7 +135,7 @@
diff --git a/docs/reference/dsadmin.get_methods.html b/docs/reference/dsadmin.get_methods.html
index eb9d116f..332bd2e6 100644
--- a/docs/reference/dsadmin.get_methods.html
+++ b/docs/reference/dsadmin.get_methods.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_method(o, 'class')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_method(o, 'class')
+opal.logout(o)
+}
Examples
Get DataSHIELD methods
-
+
dsadmin.get_methods(opal, type = "aggregate", profile = NULL)dsadmin.get_methods(opal, type = "aggregate", profile = NULL)
@@ -112,11 +112,11 @@
@@ -131,7 +131,7 @@
diff --git a/docs/reference/dsadmin.get_options.html b/docs/reference/dsadmin.get_options.html
index 41b6d38f..936afd9a 100644
--- a/docs/reference/dsadmin.get_options.html
+++ b/docs/reference/dsadmin.get_options.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_methods(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_methods(o)
+opal.logout(o)
+}
Examples
Get the DataSHIELD options
-
+
dsadmin.get_options(opal, profile = NULL)dsadmin.get_options(opal, profile = NULL)
@@ -108,11 +108,11 @@
@@ -127,7 +127,7 @@
diff --git a/docs/reference/dsadmin.install_github_package.html b/docs/reference/dsadmin.install_github_package.html
index 3cd61327..9cac06c4 100644
--- a/docs/reference/dsadmin.install_github_package.html
+++ b/docs/reference/dsadmin.install_github_package.html
@@ -69,13 +69,13 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.get_options(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.get_options(o)
+opal.logout(o)
+}
Examples
Install a DataSHIELD package from GitHub
-
+
dsadmin.install_github_package(
- opal,
- pkg,
- username = "datashield",
- ref = "master",
- profile = NULL
-)dsadmin.install_github_package(
+ opal,
+ pkg,
+ username = "datashield",
+ ref = "master",
+ profile = NULL
+)
@@ -132,11 +132,11 @@
@@ -151,7 +151,7 @@
diff --git a/docs/reference/dsadmin.install_local_package.html b/docs/reference/dsadmin.install_local_package.html
index a1a1c76d..d1a6d9a2 100644
--- a/docs/reference/dsadmin.install_local_package.html
+++ b/docs/reference/dsadmin.install_local_package.html
@@ -71,7 +71,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.install_github_package(o, 'dsOmics', username='isglobal-brge')
+opal.logout(o)
+}
Examples
Install a DataSHIELD package from a local archive file
-
+
dsadmin.install_local_package(opal, path, profile = NULL)dsadmin.install_local_package(opal, path, profile = NULL)
@@ -114,14 +114,14 @@
@@ -136,7 +136,7 @@
diff --git a/docs/reference/dsadmin.install_package.html b/docs/reference/dsadmin.install_package.html
index 5a0c9ad1..904d1231 100644
--- a/docs/reference/dsadmin.install_package.html
+++ b/docs/reference/dsadmin.install_package.html
@@ -69,13 +69,13 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# install a pre-built local archive file
-dsadmin.install_local_package(o, '~/dsExposome_1.0.0.tar.gz')
-# or build archive file from local package source (in current working folder)
-dsadmin.install_local_package(o, devtools::build())
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# install a pre-built local archive file
+dsadmin.install_local_package(o, '~/dsExposome_1.0.0.tar.gz')
+# or build archive file from local package source (in current working folder)
+dsadmin.install_local_package(o, devtools::build())
+opal.logout(o)
+}
Examples
Install a DataSHIELD package
-
+
dsadmin.install_package(
- opal,
- pkg,
- githubusername = NULL,
- ref = NULL,
- profile = NULL
-)dsadmin.install_package(
+ opal,
+ pkg,
+ githubusername = NULL,
+ ref = NULL,
+ profile = NULL
+)
@@ -132,11 +132,11 @@
@@ -151,7 +151,7 @@
diff --git a/docs/reference/dsadmin.installed_package.html b/docs/reference/dsadmin.installed_package.html
index 65240b16..d4e1e5f8 100644
--- a/docs/reference/dsadmin.installed_package.html
+++ b/docs/reference/dsadmin.installed_package.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.install_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.install_package(o, 'dsBase')
+opal.logout(o)
+}
Examples
Check DataSHIELD package
-
+
dsadmin.installed_package(opal, pkg, profile = NULL)dsadmin.installed_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@
@@ -137,7 +137,7 @@
diff --git a/docs/reference/dsadmin.log.html b/docs/reference/dsadmin.log.html
new file mode 100644
index 00000000..76fcc36d
--- /dev/null
+++ b/docs/reference/dsadmin.log.html
@@ -0,0 +1,155 @@
+
+See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.installed_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.installed_package(o, 'dsBase')
+opal.logout(o)
+}
Examples
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/dsadmin.package_description.html b/docs/reference/dsadmin.package_description.html
index 3351e46a..29694b5b 100644
--- a/docs/reference/dsadmin.package_description.html
+++ b/docs/reference/dsadmin.package_description.html
@@ -69,7 +69,7 @@
+
+
+
+
+
+
+
+
+
+
+
+ The DataSHIELD log is structured as follows:
+
+
+
+
+ dsadmin.log(opal, all = TRUE)
+
+ Arguments
+- opal +
Opal connection object.
+
+
+- all +
Get all or only latest log messages.
+
+
+
+
+ Details
+Common fields
timestamp: when action is logged
+version: not used
+message: human readable message
+logger_name: name of the log channel
+thread_name: java thread name
+level: log level (TRACE, DEBUG, INFO, WARN, ERROR)
+level_value: log level numeric value
+ip: ip origin of the request, when available
+ds_id: unique DS session ID
+ds_profile: DS profile name (available after the R server session is created, can be after authentication)
+username: DS user name
+r_duration: time spent by the remote R server action (all except PARSE)
+r_size: R result serialized object size in bytes
+ds_action: DS operation (OPEN, CLOSE, PARSE, ASSIGN, AGGREGATE, LS, RM, WS_SAVE, WS_RESTORE)
+
DS operations fields
OPEN: DS session opened (note: happens after successful authentication as R server session creation is deferred)
+CLOSE: DS session closed
+PARSE: R expression parsed
ds_map: DS function mappings used in the R parser, separated by semicolons when several functions are called
+ds_script_in: R script as sent by DS user
+ds_script_out: R script rewritten by opal, to be evaluated
+
+ASSIGN:
ds_symbol: assigned symbol name
+ds_table: table name that is assigned
+ds_resource: resource name that is assigned
+ds_eval: assign R expression that is evaluated
+
+AGGREGATE:
ds_eval: aggregate R expression that is evaluated
+
+LS: R symbols listed
+RM: R symbol removed
ds_symbol: symbol name to remove
+
+WS_SAVE:
ds_ws: workspace name
+
+WS_RESTORE:
ds_ws: workspace name
+
+
+
+
+ Examples
+if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.log(o)
+opal.logout(o)
+}
+Get DataSHIELD package description
-
+
dsadmin.package_description(opal, pkg, fields = NULL, profile = NULL)dsadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
@@ -117,11 +117,11 @@
@@ -136,7 +136,7 @@
diff --git a/docs/reference/dsadmin.package_descriptions.html b/docs/reference/dsadmin.package_descriptions.html
index 5fb8ebc9..7707a023 100644
--- a/docs/reference/dsadmin.package_descriptions.html
+++ b/docs/reference/dsadmin.package_descriptions.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_description(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_description(o, 'dsBase')
+opal.logout(o)
+}
Examples
Get DataSHIELD package descriptions
-
+
dsadmin.package_descriptions(opal, fields = NULL, df = TRUE, profile = NULL)dsadmin.package_descriptions(opal, fields = NULL, df = TRUE, profile = NULL)
@@ -123,11 +123,11 @@
@@ -142,7 +142,7 @@
diff --git a/docs/reference/dsadmin.perm.html b/docs/reference/dsadmin.perm.html
index c397d495..50f5957c 100644
--- a/docs/reference/dsadmin.perm.html
+++ b/docs/reference/dsadmin.perm.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_descriptions(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_descriptions(o)
+opal.logout(o)
+}
Examples
Get the DataSHIELD permissions
-
+
dsadmin.perm(opal)dsadmin.perm(opal)
@@ -87,13 +87,13 @@
@@ -108,7 +108,7 @@
diff --git a/docs/reference/dsadmin.perm_add.html b/docs/reference/dsadmin.perm_add.html
index 832ce0ce..e17b5796 100644
--- a/docs/reference/dsadmin.perm_add.html
+++ b/docs/reference/dsadmin.perm_add.html
@@ -69,7 +69,7 @@ Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
Add or update a DataSHIELD permission
-
+
dsadmin.perm_add(opal, subject, type = "user", permission)dsadmin.perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@
@@ -114,7 +114,7 @@
diff --git a/docs/reference/dsadmin.perm_delete.html b/docs/reference/dsadmin.perm_delete.html
index 91a12ac8..a5ce771c 100644
--- a/docs/reference/dsadmin.perm_delete.html
+++ b/docs/reference/dsadmin.perm_delete.html
@@ -69,7 +69,7 @@ Arguments
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
Delete a DataSHIELD permission
-
+
dsadmin.perm_delete(opal, subject, type = "user")dsadmin.perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@
@@ -110,7 +110,7 @@
diff --git a/docs/reference/dsadmin.profile.html b/docs/reference/dsadmin.profile.html
index d16b82ac..d8859752 100644
--- a/docs/reference/dsadmin.profile.html
+++ b/docs/reference/dsadmin.profile.html
@@ -73,7 +73,7 @@ Arguments
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-dsadmin.perm(o)
-dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+dsadmin.perm(o)
+dsadmin.perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
Get a DataSHIELD profile
-
+
dsadmin.profile(opal, name)dsadmin.profile(opal, name)
@@ -104,11 +104,11 @@
@@ -123,7 +123,7 @@
diff --git a/docs/reference/dsadmin.profile_access.html b/docs/reference/dsadmin.profile_access.html
index b23f41c7..64ad8674 100644
--- a/docs/reference/dsadmin.profile_access.html
+++ b/docs/reference/dsadmin.profile_access.html
@@ -73,7 +73,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile(o, name = 'default')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile(o, name = 'default')
+opal.logout(o)
+}
Examples
Restrict or open access to a DataSHIELD profile
-
+
dsadmin.profile_access(opal, name, restricted = TRUE)dsadmin.profile_access(opal, name, restricted = TRUE)
@@ -108,12 +108,12 @@
@@ -128,7 +128,7 @@
diff --git a/docs/reference/dsadmin.profile_create.html b/docs/reference/dsadmin.profile_create.html
index 5f5fb762..e377a2b7 100644
--- a/docs/reference/dsadmin.profile_create.html
+++ b/docs/reference/dsadmin.profile_create.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_access(o, name = 'survival', restricted = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_access(o, name = 'survival', restricted = TRUE)
+opal.logout(o)
+}
Examples
Create a DataSHIELD profile
-
+
dsadmin.profile_create(opal, name, cluster = "default", rParser = NULL)dsadmin.profile_create(opal, name, cluster = "default", rParser = NULL)
@@ -109,11 +109,11 @@
@@ -128,7 +128,7 @@
diff --git a/docs/reference/dsadmin.profile_delete.html b/docs/reference/dsadmin.profile_delete.html
index 8bb60e74..de86336c 100644
--- a/docs/reference/dsadmin.profile_delete.html
+++ b/docs/reference/dsadmin.profile_delete.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+opal.logout(o)
+}
Examples
Delete a DataSHIELD profile
-
+
dsadmin.profile_delete(opal, name)dsadmin.profile_delete(opal, name)
@@ -100,12 +100,12 @@
@@ -120,7 +120,7 @@
diff --git a/docs/reference/dsadmin.profile_enable.html b/docs/reference/dsadmin.profile_enable.html
index 8901ed93..36ba9503 100644
--- a/docs/reference/dsadmin.profile_enable.html
+++ b/docs/reference/dsadmin.profile_enable.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_delete(o, name = 'survival')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_delete(o, name = 'survival')
+opal.logout(o)
+}
Examples
Enable or disable a DataSHIELD profile
-
+
dsadmin.profile_enable(opal, name, enabled = TRUE)dsadmin.profile_enable(opal, name, enabled = TRUE)
@@ -104,12 +104,12 @@
@@ -124,7 +124,7 @@
diff --git a/docs/reference/dsadmin.profile_exists.html b/docs/reference/dsadmin.profile_exists.html
index e5c19c97..5ea51e86 100644
--- a/docs/reference/dsadmin.profile_exists.html
+++ b/docs/reference/dsadmin.profile_exists.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_enable(o, name = 'survival', enabled = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_enable(o, name = 'survival', enabled = TRUE)
+opal.logout(o)
+}
Examples
Check a DataSHIELD profile exists
-
+
dsadmin.profile_exists(opal, name)dsadmin.profile_exists(opal, name)
@@ -100,12 +100,12 @@
@@ -120,7 +120,7 @@
diff --git a/docs/reference/dsadmin.profile_init.html b/docs/reference/dsadmin.profile_init.html
index 1d117fad..ad4fc311 100644
--- a/docs/reference/dsadmin.profile_init.html
+++ b/docs/reference/dsadmin.profile_init.html
@@ -73,7 +73,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-if (!dsadmin.profile_exists(o, name = 'survival'))
- dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+if (!dsadmin.profile_exists(o, name = 'survival'))
+ dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+opal.logout(o)
+}
Examples
Initialize a DataSHIELD profile
-
+
dsadmin.profile_init(opal, name, packages = NULL)dsadmin.profile_init(opal, name, packages = NULL)
@@ -108,12 +108,12 @@
@@ -128,7 +128,7 @@
diff --git a/docs/reference/dsadmin.profile_perm.html b/docs/reference/dsadmin.profile_perm.html
index ea1913ac..3f90f5de 100644
--- a/docs/reference/dsadmin.profile_perm.html
+++ b/docs/reference/dsadmin.profile_perm.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-dsadmin.profile_init(o, name = 'survival', packages = c('dsSurvival'))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+dsadmin.profile_init(o, name = 'survival', packages = c('dsSurvival'))
+opal.logout(o)
+}
Examples
Get the permissions of a DataSHIELD profile
-
+
dsadmin.profile_perm(opal, name)dsadmin.profile_perm(opal, name)
@@ -106,13 +106,13 @@
@@ -127,7 +127,7 @@
diff --git a/docs/reference/dsadmin.profile_perm_add.html b/docs/reference/dsadmin.profile_perm_add.html
index 5aa4f324..e9b60807 100644
--- a/docs/reference/dsadmin.profile_perm_add.html
+++ b/docs/reference/dsadmin.profile_perm_add.html
@@ -71,13 +71,13 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
Add or update a permission on a DataSHIELD profile
-
+
dsadmin.profile_perm_add(
- opal,
- name,
- subject,
- type = "user",
- permission = "use"
-)dsadmin.profile_perm_add(
+ opal,
+ name,
+ subject,
+ type = "user",
+ permission = "use"
+)
@@ -120,13 +120,13 @@
@@ -141,7 +141,7 @@
diff --git a/docs/reference/dsadmin.profile_perm_delete.html b/docs/reference/dsadmin.profile_perm_delete.html
index 5b218b2b..8d2fa69a 100644
--- a/docs/reference/dsadmin.profile_perm_delete.html
+++ b/docs/reference/dsadmin.profile_perm_delete.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
Delete a permission from a DataSHIELD profile
-
+
dsadmin.profile_perm_delete(opal, name, subject, type = "user")dsadmin.profile_perm_delete(opal, name, subject, type = "user")
@@ -108,13 +108,13 @@
@@ -129,7 +129,7 @@
diff --git a/docs/reference/dsadmin.profile_rparser.html b/docs/reference/dsadmin.profile_rparser.html
index f24c5242..bf9617df 100644
--- a/docs/reference/dsadmin.profile_rparser.html
+++ b/docs/reference/dsadmin.profile_rparser.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
-dsadmin.profile_perm(o, 'default')
-dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_perm_add(o, 'default', c('andrei', 'valentina'), 'user', 'use')
+dsadmin.profile_perm(o, 'default')
+dsadmin.profile_perm_delete(o, 'default', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
Set or remove the R parser version of a DataSHIELD profile
-
+
dsadmin.profile_rparser(opal, name, rParser = NULL)dsadmin.profile_rparser(opal, name, rParser = NULL)
@@ -105,15 +105,15 @@
@@ -128,7 +128,7 @@
diff --git a/docs/reference/dsadmin.profiles.html b/docs/reference/dsadmin.profiles.html
index 7f97e3ad..2ab7201f 100644
--- a/docs/reference/dsadmin.profiles.html
+++ b/docs/reference/dsadmin.profiles.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
-# apply R parser version v2
-dsadmin.profile_rparser(o, name = 'survival', rParser = 'v2')
-# apply system's default R parser version
-dsadmin.profile_rparser(o, name = 'survival')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.profile_create(o, name = 'survival', cluster = 'demo')
+# apply R parser version v2
+dsadmin.profile_rparser(o, name = 'survival', rParser = 'v2')
+# apply system's default R parser version
+dsadmin.profile_rparser(o, name = 'survival')
+opal.logout(o)
+}
Examples
Get DataSHIELD profiles
-
+
dsadmin.profiles(opal, df = TRUE)dsadmin.profiles(opal, df = TRUE)
@@ -106,11 +106,11 @@
@@ -125,7 +125,7 @@
diff --git a/docs/reference/dsadmin.publish_package.html b/docs/reference/dsadmin.publish_package.html
index 1aed7d0b..db0a16e3 100644
--- a/docs/reference/dsadmin.publish_package.html
+++ b/docs/reference/dsadmin.publish_package.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.package_descriptions(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.package_descriptions(o)
+opal.logout(o)
+}
Examples
Publish DataSHIELD package settings
-
+
dsadmin.publish_package(opal, pkg, profile = NULL)dsadmin.publish_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@
@@ -137,7 +137,7 @@
diff --git a/docs/reference/dsadmin.remove_package.html b/docs/reference/dsadmin.remove_package.html
index a696d968..11d7e1d3 100644
--- a/docs/reference/dsadmin.remove_package.html
+++ b/docs/reference/dsadmin.remove_package.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.publish_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.publish_package(o, 'dsBase')
+opal.logout(o)
+}
Examples
Remove DataSHIELD package
-
+
dsadmin.remove_package(opal, pkg, profile = NULL)dsadmin.remove_package(opal, pkg, profile = NULL)
@@ -112,11 +112,11 @@
@@ -131,7 +131,7 @@
diff --git a/docs/reference/dsadmin.rm_method.html b/docs/reference/dsadmin.rm_method.html
index cca7bb9e..b2d596b8 100644
--- a/docs/reference/dsadmin.rm_method.html
+++ b/docs/reference/dsadmin.rm_method.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.remove_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.remove_package(o, 'dsBase')
+opal.logout(o)
+}
Examples
Remove DataSHIELD method
-
+
dsadmin.rm_method(opal, name, type = "aggregate", profile = NULL)dsadmin.rm_method(opal, name, type = "aggregate", profile = NULL)
@@ -116,11 +116,11 @@
@@ -135,7 +135,7 @@
diff --git a/docs/reference/dsadmin.rm_methods.html b/docs/reference/dsadmin.rm_methods.html
index 2532751f..470d8498 100644
--- a/docs/reference/dsadmin.rm_methods.html
+++ b/docs/reference/dsadmin.rm_methods.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_method(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_method(o, 'foo')
+opal.logout(o)
+}
Examples
Remove DataSHIELD methods.
-
+
dsadmin.rm_methods(opal, type = NULL, profile = NULL)dsadmin.rm_methods(opal, type = NULL, profile = NULL)
@@ -112,11 +112,11 @@
@@ -131,7 +131,7 @@
diff --git a/docs/reference/dsadmin.rm_option.html b/docs/reference/dsadmin.rm_option.html
index 64995c5f..1b4ed85b 100644
--- a/docs/reference/dsadmin.rm_option.html
+++ b/docs/reference/dsadmin.rm_option.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_methods(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_methods(o)
+opal.logout(o)
+}
Examples
Remove a DataSHIELD option
-
+
dsadmin.rm_option(opal, name, profile = NULL)dsadmin.rm_option(opal, name, profile = NULL)
@@ -112,11 +112,11 @@
@@ -131,7 +131,7 @@
diff --git a/docs/reference/dsadmin.rm_options.html b/docs/reference/dsadmin.rm_options.html
index 80414f34..2e4e1b38 100644
--- a/docs/reference/dsadmin.rm_options.html
+++ b/docs/reference/dsadmin.rm_options.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_option(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_option(o, 'foo')
+opal.logout(o)
+}
Examples
Remove all DataSHIELD options
-
+
dsadmin.rm_options(opal, profile = NULL)dsadmin.rm_options(opal, profile = NULL)
@@ -108,11 +108,11 @@
@@ -127,7 +127,7 @@
diff --git a/docs/reference/dsadmin.rm_package_methods.html b/docs/reference/dsadmin.rm_package_methods.html
index 26a699ef..f86188d4 100644
--- a/docs/reference/dsadmin.rm_package_methods.html
+++ b/docs/reference/dsadmin.rm_package_methods.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_options(o, 'foo')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_options(o, 'foo')
+opal.logout(o)
+}
Examples
Remove DataSHIELD package methods
-
+
dsadmin.rm_package_methods(opal, pkg, type = NULL, profile = NULL)dsadmin.rm_package_methods(opal, pkg, type = NULL, profile = NULL)
@@ -116,11 +116,11 @@
@@ -135,7 +135,7 @@
diff --git a/docs/reference/dsadmin.set_method.html b/docs/reference/dsadmin.set_method.html
index ab7bc9ff..a1287cc2 100644
--- a/docs/reference/dsadmin.set_method.html
+++ b/docs/reference/dsadmin.set_method.html
@@ -69,14 +69,14 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.rm_package_methods(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.rm_package_methods(o, 'dsBase')
+opal.logout(o)
+}
Examples
Set DataSHIELD method
-
+
dsadmin.set_method(
- opal,
- name,
- func = NULL,
- path = NULL,
- type = "aggregate",
- profile = NULL
-)dsadmin.set_method(
+ opal,
+ name,
+ func = NULL,
+ path = NULL,
+ type = "aggregate",
+ profile = NULL
+)
@@ -131,14 +131,14 @@
@@ -153,7 +153,7 @@
diff --git a/docs/reference/dsadmin.set_option.html b/docs/reference/dsadmin.set_option.html
index fa661b5b..af2b415b 100644
--- a/docs/reference/dsadmin.set_option.html
+++ b/docs/reference/dsadmin.set_option.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# as a package's function
-dsadmin.set_method(o, 'foo', func = 'base::mean')
-# as a custom function
-dsadmin.set_method(o, 'foo', func = function(x) { base::mean(x) })
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# as a package's function
+dsadmin.set_method(o, 'foo', func = 'base::mean')
+# as a custom function
+dsadmin.set_method(o, 'foo', func = function(x) { base::mean(x) })
+opal.logout(o)
+}
Examples
Set DataSHIELD option
-
+
dsadmin.set_option(opal, name, value, profile = NULL)dsadmin.set_option(opal, name, value, profile = NULL)
@@ -116,11 +116,11 @@
@@ -135,7 +135,7 @@
diff --git a/docs/reference/dsadmin.set_package_methods.html b/docs/reference/dsadmin.set_package_methods.html
index 663ff9fd..91a0f0e5 100644
--- a/docs/reference/dsadmin.set_package_methods.html
+++ b/docs/reference/dsadmin.set_package_methods.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.set_option(o, 'foo', 'bar')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.set_option(o, 'foo', 'bar')
+opal.logout(o)
+}
Examples
Set DataSHIELD package methods
-
+
dsadmin.set_package_methods(opal, pkg, type = NULL, profile = NULL)dsadmin.set_package_methods(opal, pkg, type = NULL, profile = NULL)
@@ -122,11 +122,11 @@
@@ -141,7 +141,7 @@
diff --git a/docs/reference/dsadmin.unpublish_package.html b/docs/reference/dsadmin.unpublish_package.html
index 59177cb6..2f4cb561 100644
--- a/docs/reference/dsadmin.unpublish_package.html
+++ b/docs/reference/dsadmin.unpublish_package.html
@@ -69,7 +69,7 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.set_package_methods(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.set_package_methods(o, 'dsBase')
+opal.logout(o)
+}
Examples
Unpublish DataSHIELD package settings
-
+
dsadmin.unpublish_package(opal, pkg, profile = NULL)dsadmin.unpublish_package(opal, pkg, profile = NULL)
@@ -118,11 +118,11 @@
@@ -137,7 +137,7 @@
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 7b8fa952..1410bfd7 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -86,6 +86,14 @@ See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dsadmin.unpublish_package(o, 'dsBase')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dsadmin.unpublish_package(o, 'dsBase')
+opal.logout(o)
+}
Examples
All functions dictionary.inspect()
Inspect the dictionary of a tibble
+
+
+ Get DataSHIELD activity
+
+
+ Get DataSHIELD activity summary
@@ -114,6 +122,10 @@ All functions dsadmin.installed_package()
Check DataSHIELD package
+
+
+ Get DataSHIELD logs
@@ -226,6 +238,14 @@ All functions dsadmin.unpublish_package()
Unpublish DataSHIELD package settings
+
+
+ Get R activity
+
+
+ Get R activity summary
@@ -262,6 +282,18 @@ All functions oadmin.installed_packages()
List installed packages
+
+
+ Get Opal main logs
+
+
+ Get Opal REST API logs
+
+
+ Get Opal SQL API logs
@@ -486,6 +518,10 @@ All functions opal.logout()
Logout from Opal(s)
+
+
+ Get the permissions of a subject
@@ -847,7 +883,7 @@ All functions
diff --git a/docs/reference/oadmin.activity.html b/docs/reference/oadmin.activity.html
new file mode 100644
index 00000000..a11491b6
--- /dev/null
+++ b/docs/reference/oadmin.activity.html
@@ -0,0 +1,146 @@
+
+Get R activity — oadmin.activity • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics.
+
+
+
+ oadmin.activity(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity(o)
+# user and profile specific session metrics
+oadmin.activity(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.activity_summary.html b/docs/reference/oadmin.activity_summary.html
new file mode 100644
index 00000000..a8159421
--- /dev/null
+++ b/docs/reference/oadmin.activity_summary.html
@@ -0,0 +1,146 @@
+
+Get R activity summary — oadmin.activity_summary • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics, grouped by profile and user.
+
+
+
+ oadmin.activity_summary(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity_summary(o)
+# user and profile specific session metrics
+oadmin.activity_summary(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.install_bioconductor_package.html b/docs/reference/oadmin.install_bioconductor_package.html
index adde90ec..2c0551ed 100644
--- a/docs/reference/oadmin.install_bioconductor_package.html
+++ b/docs/reference/oadmin.install_bioconductor_package.html
@@ -69,7 +69,7 @@ Install a package from Bioconductor
- oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
+ oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_bioconductor_package(o, 'GWASTools')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_bioconductor_package(o, 'GWASTools')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.install_cran_package.html b/docs/reference/oadmin.install_cran_package.html
index 3e7e3a18..d229933e 100644
--- a/docs/reference/oadmin.install_cran_package.html
+++ b/docs/reference/oadmin.install_cran_package.html
@@ -69,7 +69,7 @@ Install a package from CRAN
- oadmin.install_cran_package(opal, pkg, profile = NULL)
+ oadmin.install_cran_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_cran_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_cran_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.install_devtools.html b/docs/reference/oadmin.install_devtools.html
index 3f2bc53c..79b175d3 100644
--- a/docs/reference/oadmin.install_devtools.html
+++ b/docs/reference/oadmin.install_devtools.html
@@ -69,7 +69,7 @@ Install devtools package
- oadmin.install_devtools(opal, profile = NULL)
+ oadmin.install_devtools(opal, profile = NULL)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_devtools(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.install_github_package.html b/docs/reference/oadmin.install_github_package.html
index 496f0075..ae130887 100644
--- a/docs/reference/oadmin.install_github_package.html
+++ b/docs/reference/oadmin.install_github_package.html
@@ -69,13 +69,13 @@ Install a package from GitHub
- oadmin.install_github_package(
- opal,
- pkg,
- username = getOption("github.user"),
- ref = "master",
- profile = NULL
-)
+ oadmin.install_github_package(
+ opal,
+ pkg,
+ username = getOption("github.user"),
+ ref = "master",
+ profile = NULL
+)
@@ -117,11 +117,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_github_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_github_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/oadmin.install_local_package.html b/docs/reference/oadmin.install_local_package.html
index 17ddc429..9ddb56c3 100644
--- a/docs/reference/oadmin.install_local_package.html
+++ b/docs/reference/oadmin.install_local_package.html
@@ -71,7 +71,7 @@ Install a package from a local archive file
- oadmin.install_local_package(opal, path, profile = NULL)
+ oadmin.install_local_package(opal, path, profile = NULL)
@@ -105,14 +105,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# install a pre-built local archive file
-oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
-# or build archive file from local package source (in current working folder)
-oadmin.install_local_package(o, devtools::build())
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# install a pre-built local archive file
+oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
+# or build archive file from local package source (in current working folder)
+oadmin.install_local_package(o, devtools::build())
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/oadmin.install_package.html b/docs/reference/oadmin.install_package.html
index 0b2c26c5..7539e7fc 100644
--- a/docs/reference/oadmin.install_package.html
+++ b/docs/reference/oadmin.install_package.html
@@ -69,7 +69,7 @@ Install CRAN package
- oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
+ oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
@@ -113,11 +113,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_package(o, 'xxx')
+opal.logout(o)
+}
@@ -132,7 +132,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_devtools.html b/docs/reference/oadmin.installed_devtools.html
index eaf1b900..a90063c1 100644
--- a/docs/reference/oadmin.installed_devtools.html
+++ b/docs/reference/oadmin.installed_devtools.html
@@ -69,7 +69,7 @@ Check devtools package
- oadmin.installed_devtools(opal, profile = NULL)
+ oadmin.installed_devtools(opal, profile = NULL)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_devtools(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_package.html b/docs/reference/oadmin.installed_package.html
index 604bd8ef..aa802b54 100644
--- a/docs/reference/oadmin.installed_package.html
+++ b/docs/reference/oadmin.installed_package.html
@@ -69,7 +69,7 @@ Check package is installed
- oadmin.installed_package(opal, pkg, profile = NULL)
+ oadmin.installed_package(opal, pkg, profile = NULL)
@@ -109,12 +109,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_package(o, 'xxx')
-oadmin.installed_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_package(o, 'xxx')
+oadmin.installed_package(o, 'stats')
+opal.logout(o)
+}
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_packages.html b/docs/reference/oadmin.installed_packages.html
index 2bc6bfc8..2034f299 100644
--- a/docs/reference/oadmin.installed_packages.html
+++ b/docs/reference/oadmin.installed_packages.html
@@ -69,7 +69,7 @@ List installed packages
- oadmin.installed_packages(opal, profile = NULL)
+ oadmin.installed_packages(opal, profile = NULL)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_packages(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_packages(o)
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/oadmin.log.html b/docs/reference/oadmin.log.html
new file mode 100644
index 00000000..2204fa48
--- /dev/null
+++ b/docs/reference/oadmin.log.html
@@ -0,0 +1,118 @@
+
+Get Opal main logs — oadmin.log • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal main logs
+
+
+
+ oadmin.log(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.log_rest.html b/docs/reference/oadmin.log_rest.html
new file mode 100644
index 00000000..fd2f9ef2
--- /dev/null
+++ b/docs/reference/oadmin.log_rest.html
@@ -0,0 +1,118 @@
+
+Get Opal REST API logs — oadmin.log_rest • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal REST API logs
+
+
+
+ oadmin.log_rest(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_rest(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.log_sql.html b/docs/reference/oadmin.log_sql.html
new file mode 100644
index 00000000..0dc4fae5
--- /dev/null
+++ b/docs/reference/oadmin.log_sql.html
@@ -0,0 +1,118 @@
+
+Get Opal SQL API logs — oadmin.log_sql • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal SQL API logs
+
+
+
+ oadmin.log_sql(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_sql(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.package_description.html b/docs/reference/oadmin.package_description.html
index d07d871e..d402b336 100644
--- a/docs/reference/oadmin.package_description.html
+++ b/docs/reference/oadmin.package_description.html
@@ -69,7 +69,7 @@ Get package description
- oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
+ oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.package_description(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.package_description(o, 'stats')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/oadmin.perm.html b/docs/reference/oadmin.perm.html
index b61d3e13..20a30ecc 100644
--- a/docs/reference/oadmin.perm.html
+++ b/docs/reference/oadmin.perm.html
@@ -69,7 +69,7 @@ Get the R permissions (deprecated)
- oadmin.perm(opal)
+ oadmin.perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.perm_add.html b/docs/reference/oadmin.perm_add.html
index b3a39610..df43a7c7 100644
--- a/docs/reference/oadmin.perm_add.html
+++ b/docs/reference/oadmin.perm_add.html
@@ -69,7 +69,7 @@ Add or update a R permission (deprecated)
- oadmin.perm_add(opal, subject, type = "user", permission)
+ oadmin.perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.perm_delete.html b/docs/reference/oadmin.perm_delete.html
index f629e6fc..fa8fa4de 100644
--- a/docs/reference/oadmin.perm_delete.html
+++ b/docs/reference/oadmin.perm_delete.html
@@ -69,7 +69,7 @@ Delete a R permission (deprecated)
- oadmin.perm_delete(opal, subject, type = "user")
+ oadmin.perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm.html b/docs/reference/oadmin.r_perm.html
index 4bae064d..12b32d20 100644
--- a/docs/reference/oadmin.r_perm.html
+++ b/docs/reference/oadmin.r_perm.html
@@ -69,7 +69,7 @@ Get the R permissions
- oadmin.r_perm(opal)
+ oadmin.r_perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm_add.html b/docs/reference/oadmin.r_perm_add.html
index 06ec844e..fc74abf1 100644
--- a/docs/reference/oadmin.r_perm_add.html
+++ b/docs/reference/oadmin.r_perm_add.html
@@ -69,7 +69,7 @@ Add or update a R permission
- oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
+ oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm_delete.html b/docs/reference/oadmin.r_perm_delete.html
index c68d1ff5..01177602 100644
--- a/docs/reference/oadmin.r_perm_delete.html
+++ b/docs/reference/oadmin.r_perm_delete.html
@@ -69,7 +69,7 @@ Delete a R permission
- oadmin.r_perm_delete(opal, subject, type = "user")
+ oadmin.r_perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.remove_package.html b/docs/reference/oadmin.remove_package.html
index 7d9fd447..0953b827 100644
--- a/docs/reference/oadmin.remove_package.html
+++ b/docs/reference/oadmin.remove_package.html
@@ -69,7 +69,7 @@ Remove package
- oadmin.remove_package(opal, pkg, profile = NULL)
+ oadmin.remove_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.remove_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.remove_package(o, 'xxx')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.system_metrics.html b/docs/reference/oadmin.system_metrics.html
index 4e5ba20e..9eb7d54a 100644
--- a/docs/reference/oadmin.system_metrics.html
+++ b/docs/reference/oadmin.system_metrics.html
@@ -81,7 +81,7 @@ Get system metrics
- oadmin.system_metrics(opal)
+ oadmin.system_metrics(opal)
@@ -93,11 +93,11 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_metrics(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_metrics(o)
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm.html b/docs/reference/oadmin.system_perm.html
index a858025b..5cc5a542 100644
--- a/docs/reference/oadmin.system_perm.html
+++ b/docs/reference/oadmin.system_perm.html
@@ -69,7 +69,7 @@ Get the System permissions
- oadmin.system_perm(opal)
+ oadmin.system_perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm_add.html b/docs/reference/oadmin.system_perm_add.html
index 8b06fd5e..ecc56a90 100644
--- a/docs/reference/oadmin.system_perm_add.html
+++ b/docs/reference/oadmin.system_perm_add.html
@@ -69,7 +69,7 @@ Add or update a System permission
- oadmin.system_perm_add(opal, subject, type = "user", permission)
+ oadmin.system_perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm_delete.html b/docs/reference/oadmin.system_perm_delete.html
index c78fc7d4..5268feec 100644
--- a/docs/reference/oadmin.system_perm_delete.html
+++ b/docs/reference/oadmin.system_perm_delete.html
@@ -69,7 +69,7 @@ Delete a System permission
- oadmin.system_perm_delete(opal, subject, type = "user")
+ oadmin.system_perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.user_add.html b/docs/reference/oadmin.user_add.html
index e5a58e5b..1b82c9b6 100644
--- a/docs/reference/oadmin.user_add.html
+++ b/docs/reference/oadmin.user_add.html
@@ -69,7 +69,7 @@ Add a user
- oadmin.user_add(opal, name, groups = NULL, password = NULL)
+ oadmin.user_add(opal, name, groups = NULL, password = NULL)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/oadmin.user_delete.html b/docs/reference/oadmin.user_delete.html
index 123be6e5..1ae1cb20 100644
--- a/docs/reference/oadmin.user_delete.html
+++ b/docs/reference/oadmin.user_delete.html
@@ -69,7 +69,7 @@ Delete a user
- oadmin.user_delete(opal, name)
+ oadmin.user_delete(opal, name)
@@ -96,12 +96,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_delete(o, "foo")
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/oadmin.user_enable.html b/docs/reference/oadmin.user_enable.html
index 1b531f3a..5b480d04 100644
--- a/docs/reference/oadmin.user_enable.html
+++ b/docs/reference/oadmin.user_enable.html
@@ -69,7 +69,7 @@ Enable a user
- oadmin.user_enable(opal, name, enabled = TRUE)
+ oadmin.user_enable(opal, name, enabled = TRUE)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_enable(o, "foo", enabled = FALSE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_enable(o, "foo", enabled = FALSE)
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/oadmin.user_exists.html b/docs/reference/oadmin.user_exists.html
index e05a1f79..fad76e33 100644
--- a/docs/reference/oadmin.user_exists.html
+++ b/docs/reference/oadmin.user_exists.html
@@ -71,7 +71,7 @@ Check user exists
- oadmin.user_exists(opal, name)
+ oadmin.user_exists(opal, name)
@@ -98,12 +98,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-if (!oadmin.user_exists(o, "foo"))
- oadmin.user_add(o, "foo", password = "bar123")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+if (!oadmin.user_exists(o, "foo"))
+ oadmin.user_add(o, "foo", password = "bar123")
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.user_profile_delete.html b/docs/reference/oadmin.user_profile_delete.html
index e1aab115..2e585266 100644
--- a/docs/reference/oadmin.user_profile_delete.html
+++ b/docs/reference/oadmin.user_profile_delete.html
@@ -75,7 +75,7 @@ Delete a user profile
- oadmin.user_profile_delete(opal, name)
+ oadmin.user_profile_delete(opal, name)
@@ -102,12 +102,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_profile_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_profile_delete(o, "foo")
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.user_profiles.html b/docs/reference/oadmin.user_profiles.html
index 2c1e5a94..f23f1669 100644
--- a/docs/reference/oadmin.user_profiles.html
+++ b/docs/reference/oadmin.user_profiles.html
@@ -71,7 +71,7 @@ Get user profiles
- oadmin.user_profiles(opal, df = TRUE)
+ oadmin.user_profiles(opal, df = TRUE)
@@ -98,11 +98,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.user_profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.user_profiles(o)
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/oadmin.user_reset_password.html b/docs/reference/oadmin.user_reset_password.html
index 7bc446ae..75e27675 100644
--- a/docs/reference/oadmin.user_reset_password.html
+++ b/docs/reference/oadmin.user_reset_password.html
@@ -69,7 +69,7 @@ Reset user password
- oadmin.user_reset_password(opal, name, password = NULL)
+ oadmin.user_reset_password(opal, name, password = NULL)
@@ -100,13 +100,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_reset_password(o, "foo", password = "password1234")
-oadmin.user_rm(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_reset_password(o, "foo", password = "password1234")
+oadmin.user_rm(o, "foo")
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/oadmin.users.html b/docs/reference/oadmin.users.html
index e16383d7..f7a3388e 100644
--- a/docs/reference/oadmin.users.html
+++ b/docs/reference/oadmin.users.html
@@ -69,7 +69,7 @@ Get the users
- oadmin.users(opal, df = TRUE)
+ oadmin.users(opal, df = TRUE)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.users(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.users(o)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.annotate.html b/docs/reference/opal.annotate.html
index f8b0529c..d0970046 100644
--- a/docs/reference/opal.annotate.html
+++ b/docs/reference/opal.annotate.html
@@ -71,7 +71,7 @@ Apply the annotations to a Opal table
- opal.annotate(opal, datasource, table, annotations)
+ opal.annotate(opal, datasource, table, annotations)
@@ -111,12 +111,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/opal.annotations.html b/docs/reference/opal.annotations.html
index 54727239..9f6b17eb 100644
--- a/docs/reference/opal.annotations.html
+++ b/docs/reference/opal.annotations.html
@@ -69,7 +69,7 @@ Get the annotations of a Opal table
- opal.annotations(opal, datasource, table)
+ opal.annotations(opal, datasource, table)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.as_md_table.html b/docs/reference/opal.as_md_table.html
index e37dd66e..b6b4c121 100644
--- a/docs/reference/opal.as_md_table.html
+++ b/docs/reference/opal.as_md_table.html
@@ -69,14 +69,14 @@ Array to Markdown
-
+
@@ -108,11 +108,11 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/opal.assign.data.html b/docs/reference/opal.assign.data.html
index e7b39e90..2be27522 100644
--- a/docs/reference/opal.assign.data.html
+++ b/docs/reference/opal.assign.data.html
@@ -69,7 +69,7 @@ Data assignment
- opal.assign.data(opal, symbol, value, async = FALSE)
+ opal.assign.data(opal, symbol, value, async = FALSE)
@@ -102,16 +102,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# push an arbitrary data frame to the R server
-opal.assign.data(o, "D", mtcars)
-# push an arbitrary vector to the R server
-opal.assign.data(o, "C", mtcars$cyl)
-# push a string
-opal.assign.data(o, "S", "Hello!")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# push an arbitrary data frame to the R server
+opal.assign.data(o, "D", mtcars)
+# push an arbitrary vector to the R server
+opal.assign.data(o, "C", mtcars$cyl)
+# push a string
+opal.assign.data(o, "S", "Hello!")
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.assign.html b/docs/reference/opal.assign.html
index c0c14727..83bab276 100644
--- a/docs/reference/opal.assign.html
+++ b/docs/reference/opal.assign.html
@@ -69,17 +69,17 @@ Data or expression assignment
- opal.assign(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- async = FALSE
-)
+ opal.assign(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ async = FALSE
+)
@@ -132,21 +132,21 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-# push an arbitrary data frame to the R server
-#opal.assign(o, "D", mtcars)
-# push an arbitrary vector to the R server
-#opal.assign(o, "C", mtcars$cyl)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+# push an arbitrary data frame to the R server
+#opal.assign(o, "D", mtcars)
+# push an arbitrary vector to the R server
+#opal.assign(o, "C", mtcars$cyl)
+opal.logout(o)
+}
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/opal.assign.resource.html b/docs/reference/opal.assign.resource.html
index 649d475e..b06c3fee 100644
--- a/docs/reference/opal.assign.resource.html
+++ b/docs/reference/opal.assign.resource.html
@@ -69,7 +69,7 @@ Resource assignment
- opal.assign.resource(opal, symbol, value, async = FALSE)
+ opal.assign.resource(opal, symbol, value, async = FALSE)
@@ -102,13 +102,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a resource and make some operation on it
-opal.assign.resource(o, "D", "datashield.cram1")
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a resource and make some operation on it
+opal.assign.resource(o, "D", "datashield.cram1")
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.assign.script.html b/docs/reference/opal.assign.script.html
index ce2ee8a8..4826146e 100644
--- a/docs/reference/opal.assign.script.html
+++ b/docs/reference/opal.assign.script.html
@@ -69,7 +69,7 @@ R script assignment
- opal.assign.script(opal, symbol, value, async = FALSE)
+ opal.assign.script(opal, symbol, value, async = FALSE)
@@ -102,13 +102,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.assign.table.html b/docs/reference/opal.assign.table.html
index f23b63b9..b853219b 100644
--- a/docs/reference/opal.assign.table.html
+++ b/docs/reference/opal.assign.table.html
@@ -69,18 +69,18 @@ Data assignment to a data.frame
- opal.assign.table(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- class = "data.frame",
- async = FALSE
-)
+ opal.assign.table(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ class = "data.frame",
+ async = FALSE
+)
@@ -137,19 +137,19 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-opal.execute(o, "colnames(D)")
-# assign a table CNSIM1 with a identifiers column
-opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
-opal.execute(o, "colnames(H)")
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-opal.execute(o, "colnames(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+opal.execute(o, "colnames(D)")
+# assign a table CNSIM1 with a identifiers column
+opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
+opal.execute(o, "colnames(H)")
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+opal.execute(o, "colnames(D)")
+opal.logout(o)
+}
@@ -164,7 +164,7 @@ Examples
diff --git a/docs/reference/opal.assign.table.tibble.html b/docs/reference/opal.assign.table.tibble.html
index 95dc04a3..e508e729 100644
--- a/docs/reference/opal.assign.table.tibble.html
+++ b/docs/reference/opal.assign.table.tibble.html
@@ -69,18 +69,18 @@ Data assignment to a tibble
- opal.assign.table.tibble(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = "id",
- with.factors = FALSE,
- updated.name = NULL,
- async = FALSE
-)
+ opal.assign.table.tibble(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = "id",
+ with.factors = FALSE,
+ updated.name = NULL,
+ async = FALSE
+)
@@ -137,13 +137,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a table and make some operation on it
-opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a table and make some operation on it
+opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
@@ -158,7 +158,7 @@ Examples
diff --git a/docs/reference/opal.attribute_values.html b/docs/reference/opal.attribute_values.html
index dd1b1537..98a94106 100644
--- a/docs/reference/opal.attribute_values.html
+++ b/docs/reference/opal.attribute_values.html
@@ -69,7 +69,7 @@ Get a vector of attribute values
- opal.attribute_values(attributes, namespace = NULL, name = "label")
+ opal.attribute_values(attributes, namespace = NULL, name = "label")
@@ -103,12 +103,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.attribute_values(var$attributes)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.attribute_values(var$attributes)
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.command.html b/docs/reference/opal.command.html
index 0f88509d..4f419a6e 100644
--- a/docs/reference/opal.command.html
+++ b/docs/reference/opal.command.html
@@ -69,7 +69,7 @@ Get an asynchronous command
- opal.command(opal, id, wait = FALSE)
+ opal.command(opal, id, wait = FALSE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command(o, '1234')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.command_result.html b/docs/reference/opal.command_result.html
index 5289b55a..35bc7964 100644
--- a/docs/reference/opal.command_result.html
+++ b/docs/reference/opal.command_result.html
@@ -71,7 +71,7 @@ Get result of an asynchronous command
- opal.command_result(opal, id, wait = FALSE)
+ opal.command_result(opal, id, wait = FALSE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_result(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_result(o, '1234')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.command_rm.html b/docs/reference/opal.command_rm.html
index c43351fa..e7fea6bb 100644
--- a/docs/reference/opal.command_rm.html
+++ b/docs/reference/opal.command_rm.html
@@ -69,7 +69,7 @@ Remove an asynchronous command
- opal.command_rm(opal, id)
+ opal.command_rm(opal, id)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_rm(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_rm(o, '1234')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.commands.html b/docs/reference/opal.commands.html
index f184c2a2..e5067c0f 100644
--- a/docs/reference/opal.commands.html
+++ b/docs/reference/opal.commands.html
@@ -69,7 +69,7 @@ List the asynchronous commands
- opal.commands(opal, df = TRUE)
+ opal.commands(opal, df = TRUE)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands(o)
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.commands_rm.html b/docs/reference/opal.commands_rm.html
index a79be20b..dad19270 100644
--- a/docs/reference/opal.commands_rm.html
+++ b/docs/reference/opal.commands_rm.html
@@ -69,7 +69,7 @@ Remove all asynchronous commands
- opal.commands_rm(opal)
+ opal.commands_rm(opal)
@@ -89,11 +89,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands_rm(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands_rm(o)
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/opal.datasource.html b/docs/reference/opal.datasource.html
index db4e3140..18ec94fc 100644
--- a/docs/reference/opal.datasource.html
+++ b/docs/reference/opal.datasource.html
@@ -69,7 +69,7 @@ Get a datasource
- opal.datasource(opal, datasource)
+ opal.datasource(opal, datasource)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasource(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasource(o, 'CNSIM')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.datasources.html b/docs/reference/opal.datasources.html
index 2c0c3136..b541b556 100644
--- a/docs/reference/opal.datasources.html
+++ b/docs/reference/opal.datasources.html
@@ -69,7 +69,7 @@ Get datasources
- opal.datasources(opal, df = TRUE)
+ opal.datasources(opal, df = TRUE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasources(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasources(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.delete.html b/docs/reference/opal.delete.html
index 9acf1da1..97b75ae3 100644
--- a/docs/reference/opal.delete.html
+++ b/docs/reference/opal.delete.html
@@ -69,7 +69,7 @@ Generic REST resource deletion.
- opal.delete(opal, ..., query = list(), callback = NULL)
+ opal.delete(opal, ..., query = list(), callback = NULL)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.delete(o, 'some', 'resource')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.delete(o, 'some', 'resource')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.execute.html b/docs/reference/opal.execute.html
index 244ade02..f91dcca6 100644
--- a/docs/reference/opal.execute.html
+++ b/docs/reference/opal.execute.html
@@ -69,7 +69,7 @@ Execute a R script
- opal.execute(opal, script, async = FALSE)
+ opal.execute(opal, script, async = FALSE)
@@ -97,12 +97,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute(o, "x <- 'foo'")
-opal.execute(o, "ls()")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute(o, "x <- 'foo'")
+opal.execute(o, "ls()")
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/opal.execute.source.html b/docs/reference/opal.execute.source.html
index 9ad4eef0..f512ffb2 100644
--- a/docs/reference/opal.execute.source.html
+++ b/docs/reference/opal.execute.source.html
@@ -69,7 +69,7 @@ Execute a R file script
- opal.execute.source(opal, path, async = FALSE)
+ opal.execute.source(opal, path, async = FALSE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute.source(o, "myscript.R")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute.source(o, "myscript.R")
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.file.html b/docs/reference/opal.file.html
index 074023d1..72a13d97 100644
--- a/docs/reference/opal.file.html
+++ b/docs/reference/opal.file.html
@@ -69,7 +69,7 @@ Get file content
- opal.file(opal, path, key = NULL)
+ opal.file(opal, path, key = NULL)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.file(o, '/home/administrator/joins/join-src-3.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.file(o, '/home/administrator/joins/join-src-3.csv')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.file_cp.html b/docs/reference/opal.file_cp.html
index c895e41c..33bb18fd 100644
--- a/docs/reference/opal.file_cp.html
+++ b/docs/reference/opal.file_cp.html
@@ -69,7 +69,7 @@ Copy a file
- opal.file_cp(opal, source, destination)
+ opal.file_cp(opal, source, destination)
@@ -104,14 +104,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# copy a file to another folder
-opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# copy recursively a folder to another folder
-opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# copy a file to another folder
+opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# copy recursively a folder to another folder
+opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.file_download.html b/docs/reference/opal.file_download.html
index dde0cba7..e6770678 100644
--- a/docs/reference/opal.file_download.html
+++ b/docs/reference/opal.file_download.html
@@ -69,7 +69,7 @@ Download a file
- opal.file_download(opal, source, destination = NULL, key = NULL)
+ opal.file_download(opal, source, destination = NULL, key = NULL)
@@ -108,19 +108,19 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# download a file
-opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
-# download a file encrypted by a key: resulting file is a zip with an encrypted content
-opal.file_download(o, '/home/administrator/export/some-data.csv',
- destination='some-data.zip', key='AZF57893FBDE')
-# download, create destination folder and rename file
-opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
-# download a folder
-opal.file_download(o, '/home/administrator/export', 'export.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# download a file
+opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
+# download a file encrypted by a key: resulting file is a zip with an encrypted content
+opal.file_download(o, '/home/administrator/export/some-data.csv',
+ destination='some-data.zip', key='AZF57893FBDE')
+# download, create destination folder and rename file
+opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
+# download a folder
+opal.file_download(o, '/home/administrator/export', 'export.zip')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.file_ls.html b/docs/reference/opal.file_ls.html
index c57e02da..8664df11 100644
--- a/docs/reference/opal.file_ls.html
+++ b/docs/reference/opal.file_ls.html
@@ -69,7 +69,7 @@ List content of a folder
- opal.file_ls(opal, path)
+ opal.file_ls(opal, path)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# list content of a folder
-opal.file_ls(o, '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# list content of a folder
+opal.file_ls(o, '/home/administrator')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.file_mkdir.html b/docs/reference/opal.file_mkdir.html
index 0ed72ad7..d15743df 100644
--- a/docs/reference/opal.file_mkdir.html
+++ b/docs/reference/opal.file_mkdir.html
@@ -71,7 +71,7 @@ Make a folder
- opal.file_mkdir(opal, path, parents = FALSE)
+ opal.file_mkdir(opal, path, parents = FALSE)
@@ -106,12 +106,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.file_mkdir_tmp.html b/docs/reference/opal.file_mkdir_tmp.html
index 396c04ff..8e187fcb 100644
--- a/docs/reference/opal.file_mkdir_tmp.html
+++ b/docs/reference/opal.file_mkdir_tmp.html
@@ -69,7 +69,7 @@ Make a temporary folder
- opal.file_mkdir_tmp(opal)
+ opal.file_mkdir_tmp(opal)
@@ -102,12 +102,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-path <- opal.file_mkdir_tmp(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+path <- opal.file_mkdir_tmp(o)
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/opal.file_mv.html b/docs/reference/opal.file_mv.html
index fc322297..1d6874df 100644
--- a/docs/reference/opal.file_mv.html
+++ b/docs/reference/opal.file_mv.html
@@ -69,7 +69,7 @@ Move and/or rename a file
- opal.file_mv(opal, source, destination)
+ opal.file_mv(opal, source, destination)
@@ -104,18 +104,18 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# move a file to another folder
-opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/administrator/export/some-data.csv')
-# move and rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/userx/deliverables/some-data.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# move a file to another folder
+opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/administrator/export/some-data.csv')
+# move and rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/userx/deliverables/some-data.csv')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.file_read.html b/docs/reference/opal.file_read.html
index 64f4982d..1807b28c 100644
--- a/docs/reference/opal.file_read.html
+++ b/docs/reference/opal.file_read.html
@@ -69,7 +69,7 @@ Read a file
- opal.file_read(opal, source, destination)
+ opal.file_read(opal, source, destination)
@@ -104,16 +104,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# read into folder
-opal.file_read(o,"DatabaseTest.sav", "/tmp")
-# read and rename
-opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
-# user home expansion
-opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# read into folder
+opal.file_read(o,"DatabaseTest.sav", "/tmp")
+# read and rename
+opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
+# user home expansion
+opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.file_rm.html b/docs/reference/opal.file_rm.html
index a23dee2e..5d79795c 100644
--- a/docs/reference/opal.file_rm.html
+++ b/docs/reference/opal.file_rm.html
@@ -69,7 +69,7 @@ Remove a file
- opal.file_rm(opal, path)
+ opal.file_rm(opal, path)
@@ -100,14 +100,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# remove a file
-opal.file_rm(o, '/home/administrator/export/some-data.csv')
-# remove recursively a folder
-opal.file_rm(o, '/home/administrator/export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# remove a file
+opal.file_rm(o, '/home/administrator/export/some-data.csv')
+# remove recursively a folder
+opal.file_rm(o, '/home/administrator/export')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/opal.file_unzip.html b/docs/reference/opal.file_unzip.html
index 66eaea32..a695dfec 100644
--- a/docs/reference/opal.file_unzip.html
+++ b/docs/reference/opal.file_unzip.html
@@ -69,7 +69,7 @@ Unzip a zip archive file
- opal.file_unzip(opal, source, destination, key = NULL)
+ opal.file_unzip(opal, source, destination, key = NULL)
@@ -114,12 +114,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# unzip
-path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# unzip
+path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.file_upload.html b/docs/reference/opal.file_upload.html
index 83a6426c..70c2faea 100644
--- a/docs/reference/opal.file_upload.html
+++ b/docs/reference/opal.file_upload.html
@@ -71,7 +71,7 @@ Upload a file or a folder
- opal.file_upload(opal, source, destination, all.files = TRUE)
+ opal.file_upload(opal, source, destination, all.files = TRUE)
@@ -111,14 +111,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# upload a file
-opal.file_upload(o, 'some_data.csv', '/home/administrator')
-# upload a folder
-opal.file_upload(o, 'some_data', '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# upload a file
+opal.file_upload(o, 'some_data.csv', '/home/administrator')
+# upload a folder
+opal.file_upload(o, 'some_data', '/home/administrator')
+opal.logout(o)
+}
@@ -133,7 +133,7 @@ Examples
diff --git a/docs/reference/opal.file_write.html b/docs/reference/opal.file_write.html
index a1bfb19d..f0835d11 100644
--- a/docs/reference/opal.file_write.html
+++ b/docs/reference/opal.file_write.html
@@ -69,7 +69,7 @@ Write a file
- opal.file_write(opal, source, destination = NULL)
+ opal.file_write(opal, source, destination = NULL)
@@ -104,16 +104,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# user home expansion
-opal.file_write(o, "~/spss/DatabaseTest.sav")
-# rename file
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
-# create sub-folder
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# user home expansion
+opal.file_write(o, "~/spss/DatabaseTest.sav")
+# rename file
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
+# create sub-folder
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.get.html b/docs/reference/opal.get.html
index 19e0f260..f83d5cb9 100644
--- a/docs/reference/opal.get.html
+++ b/docs/reference/opal.get.html
@@ -69,14 +69,14 @@ Generic REST resource getter.
- opal.get(
- opal,
- ...,
- query = list(),
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)
+ opal.get(
+ opal,
+ ...,
+ query = list(),
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)
@@ -115,11 +115,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.get(o, 'project', 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.get(o, 'project', 'CNSIM')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.load_package.html b/docs/reference/opal.load_package.html
index 15e9967f..cba05243 100644
--- a/docs/reference/opal.load_package.html
+++ b/docs/reference/opal.load_package.html
@@ -69,7 +69,7 @@ Load package
- opal.load_package(opal, pkg)
+ opal.load_package(opal, pkg)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.load_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.load_package(o, 'stats')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.login.html b/docs/reference/opal.login.html
index f9523698..549cdc71 100644
--- a/docs/reference/opal.login.html
+++ b/docs/reference/opal.login.html
@@ -73,15 +73,15 @@ Opal login
-
+
@@ -132,44 +132,44 @@ See also
Examples
- if (FALSE) {
-#### The below examples illustrate the different ways to login in opal ####
-
-# explicite username/password login
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
- # explicite personal access token login
-o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login using options and user credentials
-options(opal.username = 'administrator',
- opal.password = 'password',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using options and personal access token
-options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using ssl key pair
-options(opal.opts = list(
- sslcert = 'my-publickey.pem',
- sslkey = 'my-privatekey.pem'))
-o <- opal.login(url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login with a R server profile
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org', profile = 'default')
-opal.logout(o)
-}
+ if (FALSE) {
+#### The below examples illustrate the different ways to login in opal ####
+
+# explicite username/password login
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+ # explicite personal access token login
+o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login using options and user credentials
+options(opal.username = 'administrator',
+ opal.password = 'password',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using options and personal access token
+options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using ssl key pair
+options(opal.opts = list(
+ sslcert = 'my-publickey.pem',
+ sslkey = 'my-privatekey.pem'))
+o <- opal.login(url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login with a R server profile
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org', profile = 'default')
+opal.logout(o)
+}
@@ -184,7 +184,7 @@ Examples
diff --git a/docs/reference/opal.logout.html b/docs/reference/opal.logout.html
index e64f3e86..b91868aa 100644
--- a/docs/reference/opal.logout.html
+++ b/docs/reference/opal.logout.html
@@ -69,7 +69,7 @@ Logout from Opal(s)
- opal.logout(opal, save = FALSE)
+ opal.logout(opal, save = FALSE)
@@ -91,10 +91,10 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+}
@@ -109,7 +109,7 @@ Examples
diff --git a/docs/reference/opal.perms.html b/docs/reference/opal.perms.html
new file mode 100644
index 00000000..aab233ff
--- /dev/null
+++ b/docs/reference/opal.perms.html
@@ -0,0 +1,154 @@
+
+Get the permissions of a subject — opal.perms • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the permissions of a subject. If the subject is a user, the permissions of
+the groups to which the user belongs are also added to the result.
+
+
+
+ opal.perms(opal, subject, type = "user")
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- subject
+A subject identifier: user or group name.
- type
+The type of subject: user (default) or group.
+
+ Value
+
+
+A data.frame with columns: subject, type, target (path to the opal object to which
+the permission applies), target_type and perm (the permission name)
+
+
+ See also
+ Other table functions:
+opal.resource_view_create(),
+opal.resource_view_reconnect(),
+opal.table_create(),
+opal.table_delete(),
+opal.table_dictionary_get(),
+opal.table_dictionary_update(),
+opal.table_exists(),
+opal.table_export(),
+opal.table_get(),
+opal.table_import(),
+opal.table_perm_add(),
+opal.table_perm_delete(),
+opal.table_perm(),
+opal.table_save(),
+opal.table_truncate(),
+opal.table_view_create(),
+opal.table_view_update()
+
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.perms(o, 'andrei')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/opal.post.html b/docs/reference/opal.post.html
index d93bb6bf..f7d80068 100644
--- a/docs/reference/opal.post.html
+++ b/docs/reference/opal.post.html
@@ -69,16 +69,16 @@ Generic REST resource creation.
- opal.post(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)
+ opal.post(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)
@@ -125,11 +125,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.post(o, 'some', 'resources', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.post(o, 'some', 'resources', body = '{"some":"value"}')
+opal.logout(o)
+}
@@ -144,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.profiles.html b/docs/reference/opal.profiles.html
index 067273c2..1e96f85c 100644
--- a/docs/reference/opal.profiles.html
+++ b/docs/reference/opal.profiles.html
@@ -71,7 +71,7 @@ List R profiles
- opal.profiles(opal, df = TRUE)
+ opal.profiles(opal, df = TRUE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.profiles(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.project.html b/docs/reference/opal.project.html
index cd3a4f68..3e6b4a16 100644
--- a/docs/reference/opal.project.html
+++ b/docs/reference/opal.project.html
@@ -69,7 +69,7 @@ Get a project
- opal.project(opal, project)
+ opal.project(opal, project)
@@ -94,11 +94,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project(o, 'datashield')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project(o, 'datashield')
+opal.logout(o)
+}
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/opal.project_backup.html b/docs/reference/opal.project_backup.html
index 9fe7543f..58bf4b6e 100644
--- a/docs/reference/opal.project_backup.html
+++ b/docs/reference/opal.project_backup.html
@@ -75,14 +75,14 @@ Backup a project
- opal.project_backup(
- opal,
- project,
- archive,
- viewsAsTables = FALSE,
- override = TRUE,
- wait = TRUE
-)
+ opal.project_backup(
+ opal,
+ project,
+ archive,
+ viewsAsTables = FALSE,
+ override = TRUE,
+ wait = TRUE
+)
@@ -120,12 +120,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
-opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
+opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
+opal.logout(o)
+}
@@ -140,7 +140,7 @@ Examples
diff --git a/docs/reference/opal.project_command.html b/docs/reference/opal.project_command.html
index 13740837..9e6c5e62 100644
--- a/docs/reference/opal.project_command.html
+++ b/docs/reference/opal.project_command.html
@@ -69,7 +69,7 @@ Get project task
- opal.project_command(opal, project, id)
+ opal.project_command(opal, project, id)
@@ -95,12 +95,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
-opal.project_command(opal, 'GREENSPACE', id)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
+opal.project_command(opal, 'GREENSPACE', id)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.project_create.html b/docs/reference/opal.project_create.html
index 2524037d..d1eb8488 100644
--- a/docs/reference/opal.project_create.html
+++ b/docs/reference/opal.project_create.html
@@ -69,15 +69,15 @@ Create a project
- opal.project_create(
- opal,
- project,
- database = NULL,
- title = NULL,
- description = NULL,
- tags = NULL,
- exportFolder = NULL
-)
+ opal.project_create(
+ opal,
+ project,
+ database = NULL,
+ title = NULL,
+ description = NULL,
+ tags = NULL,
+ exportFolder = NULL
+)
@@ -124,16 +124,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with named database
-opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
-# with default database
-opal.project_create(o, 'test_default_db', database = TRUE)
-# no database, for views and resources only
-opal.project_create(o, 'test_no_db')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with named database
+opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
+# with default database
+opal.project_create(o, 'test_default_db', database = TRUE)
+# no database, for views and resources only
+opal.project_create(o, 'test_no_db')
+opal.logout(o)
+}
@@ -148,7 +148,7 @@ Examples
diff --git a/docs/reference/opal.project_delete.html b/docs/reference/opal.project_delete.html
index 0975b5d4..249dfdd3 100644
--- a/docs/reference/opal.project_delete.html
+++ b/docs/reference/opal.project_delete.html
@@ -69,7 +69,7 @@ Delete a project
- opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
+ opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
@@ -102,11 +102,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_delete(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_delete(o, 'test')
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/opal.project_exists.html b/docs/reference/opal.project_exists.html
index 2d217cab..10266208 100644
--- a/docs/reference/opal.project_exists.html
+++ b/docs/reference/opal.project_exists.html
@@ -69,7 +69,7 @@ Check a project exists
- opal.project_exists(opal, project)
+ opal.project_exists(opal, project)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_exists(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_exists(o, 'test')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.project_perm.html b/docs/reference/opal.project_perm.html
index 07a974c3..abba6946 100644
--- a/docs/reference/opal.project_perm.html
+++ b/docs/reference/opal.project_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a project
- opal.project_perm(opal, project)
+ opal.project_perm(opal, project)
@@ -91,13 +91,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.project_perm_add.html b/docs/reference/opal.project_perm_add.html
index 1fd19072..e134d7b0 100644
--- a/docs/reference/opal.project_perm_add.html
+++ b/docs/reference/opal.project_perm_add.html
@@ -69,13 +69,13 @@ Add or update a permission on a project
- opal.project_perm_add(
- opal,
- project,
- subject,
- type = "user",
- permission = "administrate"
-)
+ opal.project_perm_add(
+ opal,
+ project,
+ subject,
+ type = "user",
+ permission = "administrate"
+)
@@ -103,13 +103,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.project_perm_delete.html b/docs/reference/opal.project_perm_delete.html
index 8a290c35..885e9c53 100644
--- a/docs/reference/opal.project_perm_delete.html
+++ b/docs/reference/opal.project_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a project
- opal.project_perm_delete(opal, project, subject, type = "user")
+ opal.project_perm_delete(opal, project, subject, type = "user")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/opal.project_restore.html b/docs/reference/opal.project_restore.html
index 76c5f138..8f4c0d05 100644
--- a/docs/reference/opal.project_restore.html
+++ b/docs/reference/opal.project_restore.html
@@ -75,14 +75,14 @@ Restore a project
- opal.project_restore(
- opal,
- project,
- archive,
- key = NULL,
- override = TRUE,
- wait = TRUE
-)
+ opal.project_restore(
+ opal,
+ project,
+ archive,
+ key = NULL,
+ override = TRUE,
+ wait = TRUE
+)
@@ -120,15 +120,15 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# create the project to restore, with the default database (to store tables)
-opal.project_create(o, 'GREENSPACE2', database = TRUE)
-# upload backup zip and launch restore task
-opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
-opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# create the project to restore, with the default database (to store tables)
+opal.project_create(o, 'GREENSPACE2', database = TRUE)
+# upload backup zip and launch restore task
+opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
+opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
+opal.logout(o)
+}
@@ -143,7 +143,7 @@ Examples
diff --git a/docs/reference/opal.projects.html b/docs/reference/opal.projects.html
index e8d51a41..73e9e973 100644
--- a/docs/reference/opal.projects.html
+++ b/docs/reference/opal.projects.html
@@ -69,7 +69,7 @@ Get projects
- opal.projects(opal, df = TRUE)
+ opal.projects(opal, df = TRUE)
@@ -94,11 +94,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects(o)
+opal.logout(o)
+}
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/opal.projects_databases.html b/docs/reference/opal.projects_databases.html
index 45f818b3..2a9dc9f0 100644
--- a/docs/reference/opal.projects_databases.html
+++ b/docs/reference/opal.projects_databases.html
@@ -69,7 +69,7 @@ Get projects databases
- opal.projects_databases(opal)
+ opal.projects_databases(opal)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects_databases(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects_databases(o)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.put.html b/docs/reference/opal.put.html
index de59ef78..1622010c 100644
--- a/docs/reference/opal.put.html
+++ b/docs/reference/opal.put.html
@@ -69,14 +69,14 @@ Generic REST resource update.
- opal.put(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- callback = NULL
-)
+ opal.put(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ callback = NULL
+)
@@ -115,11 +115,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.report.html b/docs/reference/opal.report.html
index eaf6c399..efc8d7c1 100644
--- a/docs/reference/opal.report.html
+++ b/docs/reference/opal.report.html
@@ -69,13 +69,13 @@ Opal report
- opal.report(
- input,
- output = NULL,
- progress = FALSE,
- verbose = FALSE,
- boot_style = NULL
-)
+ opal.report(
+ input,
+ output = NULL,
+ progress = FALSE,
+ verbose = FALSE,
+ boot_style = NULL
+)
@@ -103,9 +103,9 @@ Arguments
Examples
- if (FALSE) {
-opal.report('input.Rmd', 'report', progress=TRUE)
-}
+ if (FALSE) {
+opal.report('input.Rmd', 'report', progress=TRUE)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.report_md.html b/docs/reference/opal.report_md.html
index ad0cadd5..50a44df1 100644
--- a/docs/reference/opal.report_md.html
+++ b/docs/reference/opal.report_md.html
@@ -69,7 +69,7 @@ Turn a R markdown file to html.
- opal.report_md(inputFile, progress, verbose)
+ opal.report_md(inputFile, progress, verbose)
@@ -85,7 +85,7 @@ Turn a R markdown file to html.
diff --git a/docs/reference/opal.resource.html b/docs/reference/opal.resource.html
index 8040add0..128ece62 100644
--- a/docs/reference/opal.resource.html
+++ b/docs/reference/opal.resource.html
@@ -69,7 +69,7 @@ Get a resource reference of a project
- opal.resource(opal, project, resource)
+ opal.resource(opal, project, resource)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.resource_create.html b/docs/reference/opal.resource_create.html
index a7f47634..9ed343f2 100644
--- a/docs/reference/opal.resource_create.html
+++ b/docs/reference/opal.resource_create.html
@@ -69,17 +69,17 @@ Create a resource reference in a project
- opal.resource_create(
- opal,
- project,
- name,
- url,
- description = NULL,
- format = NULL,
- package = NULL,
- identity = NULL,
- secret = NULL
-)
+ opal.resource_create(
+ opal,
+ project,
+ name,
+ url,
+ description = NULL,
+ format = NULL,
+ package = NULL,
+ identity = NULL,
+ secret = NULL
+)
@@ -139,13 +139,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_create(o, 'RSRC', 'CNSIM4',
- url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
- format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_create(o, 'RSRC', 'CNSIM4',
+ url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
+ format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
+opal.logout(o)
+}
@@ -160,7 +160,7 @@ Examples
diff --git a/docs/reference/opal.resource_delete.html b/docs/reference/opal.resource_delete.html
index 41eee541..a3e48fb8 100644
--- a/docs/reference/opal.resource_delete.html
+++ b/docs/reference/opal.resource_delete.html
@@ -69,7 +69,7 @@ Delete a resource reference
- opal.resource_delete(opal, project, resource, silent = TRUE)
+ opal.resource_delete(opal, project, resource, silent = TRUE)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_delete(o, "RSRC", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_delete(o, "RSRC", "CNSIM4")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.resource_exists.html b/docs/reference/opal.resource_exists.html
index 7a5852e1..700fd693 100644
--- a/docs/reference/opal.resource_exists.html
+++ b/docs/reference/opal.resource_exists.html
@@ -69,7 +69,7 @@ Check a resource reference exists
- opal.resource_exists(opal, project, resource)
+ opal.resource_exists(opal, project, resource)
@@ -111,11 +111,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_exists(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_exists(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.resource_extension_create.html b/docs/reference/opal.resource_extension_create.html
index c0a045fe..1c8013c4 100644
--- a/docs/reference/opal.resource_extension_create.html
+++ b/docs/reference/opal.resource_extension_create.html
@@ -69,16 +69,16 @@ Create an extended resource reference in a project
- opal.resource_extension_create(
- opal,
- project,
- name,
- provider,
- factory,
- parameters,
- description = NULL,
- credentials = NULL
-)
+ opal.resource_extension_create(
+ opal,
+ project,
+ name,
+ provider,
+ factory,
+ parameters,
+ description = NULL,
+ credentials = NULL
+)
@@ -134,21 +134,21 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
- provider = 'dsOmics', factory = 'ga4gh-htsget',
- parameters = list(
- host = 'https://htsget.ga4gh.org',
- sample = '1000genomes.phase1.chr1',
- reference = '1',
- start = '1',
- end = '100000',
- format = 'GA4GHVCF'
- )
-)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
+ provider = 'dsOmics', factory = 'ga4gh-htsget',
+ parameters = list(
+ host = 'https://htsget.ga4gh.org',
+ sample = '1000genomes.phase1.chr1',
+ reference = '1',
+ start = '1',
+ end = '100000',
+ format = 'GA4GHVCF'
+ )
+)
+opal.logout(o)
+}
@@ -163,7 +163,7 @@ Examples
diff --git a/docs/reference/opal.resource_get.html b/docs/reference/opal.resource_get.html
index ae00707a..80a02871 100644
--- a/docs/reference/opal.resource_get.html
+++ b/docs/reference/opal.resource_get.html
@@ -69,7 +69,7 @@ Get the resource object of a project
- opal.resource_get(opal, project, resource)
+ opal.resource_get(opal, project, resource)
@@ -105,17 +105,17 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
-# then interpret locally the resource object (load the appropriate R packages)
-library(resourcer)
-# coerce to a data.frame
-as.data.frame(res)
-# or get the resource client object for low-level interactions
-rescli <- resourcer::newResourceClient(res)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
+# then interpret locally the resource object (load the appropriate R packages)
+library(resourcer)
+# coerce to a data.frame
+as.data.frame(res)
+# or get the resource client object for low-level interactions
+rescli <- resourcer::newResourceClient(res)
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm.html b/docs/reference/opal.resource_perm.html
index e6856cab..d97e7fef 100644
--- a/docs/reference/opal.resource_perm.html
+++ b/docs/reference/opal.resource_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a resource
- opal.resource_perm(opal, project, resource)
+ opal.resource_perm(opal, project, resource)
@@ -111,13 +111,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -132,7 +132,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm_add.html b/docs/reference/opal.resource_perm_add.html
index 9c3d1438..6ad84919 100644
--- a/docs/reference/opal.resource_perm_add.html
+++ b/docs/reference/opal.resource_perm_add.html
@@ -69,14 +69,14 @@ Add or update a permission on a resource
- opal.resource_perm_add(
- opal,
- project,
- resource,
- subject,
- type = "user",
- permission
-)
+ opal.resource_perm_add(
+ opal,
+ project,
+ resource,
+ subject,
+ type = "user",
+ permission
+)
@@ -125,13 +125,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -146,7 +146,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm_delete.html b/docs/reference/opal.resource_perm_delete.html
index df299ed2..541396ce 100644
--- a/docs/reference/opal.resource_perm_delete.html
+++ b/docs/reference/opal.resource_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a resource
- opal.resource_perm_delete(opal, project, resource, subject, type = "user")
+ opal.resource_perm_delete(opal, project, resource, subject, type = "user")
@@ -113,13 +113,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.resource_view_create.html b/docs/reference/opal.resource_view_create.html
index d653a1cf..f3a7a1f2 100644
--- a/docs/reference/opal.resource_view_create.html
+++ b/docs/reference/opal.resource_view_create.html
@@ -73,15 +73,15 @@ Create an Opal view over a resource reference
- opal.resource_view_create(
- opal,
- project,
- table,
- resource,
- type = "Participant",
- idColumn = NULL,
- profile = NULL
-)
+ opal.resource_view_create(
+ opal,
+ project,
+ table,
+ resource,
+ type = "Participant",
+ idColumn = NULL,
+ profile = NULL
+)
@@ -119,6 +119,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
@@ -139,14 +140,14 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
- resource = "RSRC.FEMALE_2439", idColumn = "Name")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
+ resource = "RSRC.FEMALE_2439", idColumn = "Name")
+opal.logout(o)
+}
@@ -161,7 +162,7 @@ Examples
diff --git a/docs/reference/opal.resource_view_reconnect.html b/docs/reference/opal.resource_view_reconnect.html
index e8650b92..06f03a44 100644
--- a/docs/reference/opal.resource_view_reconnect.html
+++ b/docs/reference/opal.resource_view_reconnect.html
@@ -73,7 +73,7 @@ Reconnect an Opal view to its underlying resource
- opal.resource_view_reconnect(opal, project, table)
+ opal.resource_view_reconnect(opal, project, table)
@@ -93,6 +93,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.table_create(),
opal.table_delete(),
@@ -113,14 +114,14 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-# re-initialize the view's connection to the resource
-opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+# re-initialize the view's connection to the resource
+opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
+opal.logout(o)
+}
@@ -135,7 +136,7 @@ Examples
diff --git a/docs/reference/opal.resources.html b/docs/reference/opal.resources.html
index 305236d9..1219e1b9 100644
--- a/docs/reference/opal.resources.html
+++ b/docs/reference/opal.resources.html
@@ -69,7 +69,7 @@ Get the resource references of a project
- opal.resources(opal, project, df = TRUE)
+ opal.resources(opal, project, df = TRUE)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources(o, 'RSRC')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources(o, 'RSRC')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm.html b/docs/reference/opal.resources_perm.html
index ba3302b2..c53289ba 100644
--- a/docs/reference/opal.resources_perm.html
+++ b/docs/reference/opal.resources_perm.html
@@ -69,7 +69,7 @@ Get the permissions on any resource
- opal.resources_perm(opal, project)
+ opal.resources_perm(opal, project)
@@ -107,13 +107,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm_add.html b/docs/reference/opal.resources_perm_add.html
index 1a4a38e2..f1c870b4 100644
--- a/docs/reference/opal.resources_perm_add.html
+++ b/docs/reference/opal.resources_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on any resource
- opal.resources_perm_add(opal, project, subject, type = "user", permission)
+ opal.resources_perm_add(opal, project, subject, type = "user", permission)
@@ -114,13 +114,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm_delete.html b/docs/reference/opal.resources_perm_delete.html
index e7c09535..5c093566 100644
--- a/docs/reference/opal.resources_perm_delete.html
+++ b/docs/reference/opal.resources_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from any resource
- opal.resources_perm_delete(opal, project, subject, type = "user")
+ opal.resources_perm_delete(opal, project, subject, type = "user")
@@ -109,13 +109,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM', 'CNSIM1')
-opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM', 'CNSIM1')
+opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.rm.html b/docs/reference/opal.rm.html
index f444e41c..728ec6d4 100644
--- a/docs/reference/opal.rm.html
+++ b/docs/reference/opal.rm.html
@@ -69,7 +69,7 @@ Remove a R symbol (deprecated)
- opal.rm(opal, symbol)
+ opal.rm(opal, symbol)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.rm(o, 'D')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.sql.html b/docs/reference/opal.sql.html
index 41f13417..5fa1f9b8 100644
--- a/docs/reference/opal.sql.html
+++ b/docs/reference/opal.sql.html
@@ -75,7 +75,7 @@ Execute a SQL query on tables
- opal.sql(opal, query, project = NULL, id.name = "_id")
+ opal.sql(opal, query, project = NULL, id.name = "_id")
@@ -106,23 +106,23 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from CNSIM1
- where LAB_HDL is not null
- group by GENDER',
- 'CNSIM')
-# without project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from `CNSIM.CNSIM1`
- where LAB_HDL is not null
- group by GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from CNSIM1
+ where LAB_HDL is not null
+ group by GENDER',
+ 'CNSIM')
+# without project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from `CNSIM.CNSIM1`
+ where LAB_HDL is not null
+ group by GENDER')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/opal.sql_history.html b/docs/reference/opal.sql_history.html
index ff53d0db..1bd338f2 100644
--- a/docs/reference/opal.sql_history.html
+++ b/docs/reference/opal.sql_history.html
@@ -71,14 +71,14 @@ SQL query execution history
- opal.sql_history(
- opal,
- project = NULL,
- offset = 0,
- limit = 100,
- user = NULL,
- df = TRUE
-)
+ opal.sql_history(
+ opal,
+ project = NULL,
+ offset = 0,
+ limit = 100,
+ user = NULL,
+ df = TRUE
+)
@@ -118,16 +118,16 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql_history(o, 'CNSIM')
-# without project context
-opal.sql_history(o, NA)
-# with or without project context
-opal.sql_history(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql_history(o, 'CNSIM')
+# without project context
+opal.sql_history(o, NA)
+# with or without project context
+opal.sql_history(o)
+opal.logout(o)
+}
@@ -142,7 +142,7 @@ Examples
diff --git a/docs/reference/opal.symbol_import.html b/docs/reference/opal.symbol_import.html
index ae50bd82..5ee219a5 100644
--- a/docs/reference/opal.symbol_import.html
+++ b/docs/reference/opal.symbol_import.html
@@ -71,16 +71,16 @@ Import a tibble
- opal.symbol_import(
- opal,
- symbol,
- project,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)
+ opal.symbol_import(
+ opal,
+ symbol,
+ project,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)
@@ -128,11 +128,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_import(o, 'D', 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_import(o, 'D', 'test')
+opal.logout(o)
+}
@@ -147,7 +147,7 @@ Examples
diff --git a/docs/reference/opal.symbol_rm.html b/docs/reference/opal.symbol_rm.html
index d0cfd696..6d16a689 100644
--- a/docs/reference/opal.symbol_rm.html
+++ b/docs/reference/opal.symbol_rm.html
@@ -69,7 +69,7 @@ Remove a R symbol
- opal.symbol_rm(opal, symbol)
+ opal.symbol_rm(opal, symbol)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_rm(o, 'D')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.symbol_save.html b/docs/reference/opal.symbol_save.html
index f2a900f1..79035aa9 100644
--- a/docs/reference/opal.symbol_save.html
+++ b/docs/reference/opal.symbol_save.html
@@ -69,7 +69,7 @@ Save a tibble
- opal.symbol_save(opal, symbol, destination)
+ opal.symbol_save(opal, symbol, destination)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_save(o, 'D', 'test.sav')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_save(o, 'D', 'test.sav')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.symbols.html b/docs/reference/opal.symbols.html
index bb88de70..1b7894c4 100644
--- a/docs/reference/opal.symbols.html
+++ b/docs/reference/opal.symbols.html
@@ -69,7 +69,7 @@ List R symbols
- opal.symbols(opal)
+ opal.symbols(opal)
@@ -89,11 +89,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbols(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbols(o)
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/opal.table.html b/docs/reference/opal.table.html
index b4d05790..be03e321 100644
--- a/docs/reference/opal.table.html
+++ b/docs/reference/opal.table.html
@@ -69,7 +69,7 @@ Get a table of a datasource
- opal.table(opal, datasource, table, counts = FALSE)
+ opal.table(opal, datasource, table, counts = FALSE)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.table_create.html b/docs/reference/opal.table_create.html
index 44e433ba..46cf045b 100644
--- a/docs/reference/opal.table_create.html
+++ b/docs/reference/opal.table_create.html
@@ -73,7 +73,7 @@ Create an Opal table or view
- opal.table_create(opal, project, table, type = "Participant", tables = NULL)
+ opal.table_create(opal, project, table, type = "Participant", tables = NULL)
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_delete(),
@@ -122,15 +123,15 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a raw table
-opal.table_create(o, "CNSIM", "CNSIM4")
-# make a view
-opal.table_create(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a raw table
+opal.table_create(o, "CNSIM", "CNSIM4")
+# make a view
+opal.table_create(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
@@ -145,7 +146,7 @@ Examples
diff --git a/docs/reference/opal.table_delete.html b/docs/reference/opal.table_delete.html
index 778f2343..cba12a39 100644
--- a/docs/reference/opal.table_delete.html
+++ b/docs/reference/opal.table_delete.html
@@ -71,7 +71,7 @@ Delete a Opal table
- opal.table_delete(opal, project, table, silent = TRUE)
+ opal.table_delete(opal, project, table, silent = TRUE)
@@ -95,6 +95,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,11 +116,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_delete(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_delete(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -134,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.table_dictionary_get.html b/docs/reference/opal.table_dictionary_get.html
index 95a5c21a..59126cc2 100644
--- a/docs/reference/opal.table_dictionary_get.html
+++ b/docs/reference/opal.table_dictionary_get.html
@@ -69,7 +69,7 @@ Get the dictionary of a Opal table
- opal.table_dictionary_get(opal, project, table)
+ opal.table_dictionary_get(opal, project, table)
@@ -89,6 +89,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -109,11 +110,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -128,7 +129,7 @@ Examples
diff --git a/docs/reference/opal.table_dictionary_update.html b/docs/reference/opal.table_dictionary_update.html
index c2e5bfc5..090a7d91 100644
--- a/docs/reference/opal.table_dictionary_update.html
+++ b/docs/reference/opal.table_dictionary_update.html
@@ -69,13 +69,13 @@ Update the dictionary of a Opal table
- opal.table_dictionary_update(
- opal,
- project,
- table,
- variables,
- categories = NULL
-)
+ opal.table_dictionary_update(
+ opal,
+ project,
+ table,
+ variables,
+ categories = NULL
+)
@@ -104,6 +104,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -124,23 +125,23 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-variables <- tibble::tribble(
- ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
- "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
- "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
- "disp", "decimal", "Disp label", NA, NA, 1, 3
-)
-categories <- tibble::tribble(
- ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
- "cyl", "4", 0, "Four", "Quatre",
- "cyl", "6", 0, "Six", "Six",
- "cyl", "8", 1, "Height", "Huit"
-)
-opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+variables <- tibble::tribble(
+ ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
+ "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
+ "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
+ "disp", "decimal", "Disp label", NA, NA, 1, 3
+)
+categories <- tibble::tribble(
+ ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
+ "cyl", "4", 0, "Four", "Quatre",
+ "cyl", "6", 0, "Six", "Six",
+ "cyl", "8", 1, "Height", "Huit"
+)
+opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
+opal.logout(o)
+}
@@ -155,7 +156,7 @@ Examples
diff --git a/docs/reference/opal.table_exists.html b/docs/reference/opal.table_exists.html
index 10649da8..e4ac20bb 100644
--- a/docs/reference/opal.table_exists.html
+++ b/docs/reference/opal.table_exists.html
@@ -71,7 +71,7 @@ Check a Opal table exists
- opal.table_exists(opal, project, table, view = NA)
+ opal.table_exists(opal, project, table, view = NA)
@@ -96,6 +96,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -116,16 +117,16 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# check table exists
-opal.table_exists(o, "CNSIM", "CNSIM1")
-# check table exists AND is a NOT a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
-# check table exists AND is a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# check table exists
+opal.table_exists(o, "CNSIM", "CNSIM1")
+# check table exists AND is a NOT a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
+# check table exists AND is a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
+opal.logout(o)
+}
@@ -140,7 +141,7 @@ Examples
diff --git a/docs/reference/opal.table_export.html b/docs/reference/opal.table_export.html
index f5eb8c76..5110bb07 100644
--- a/docs/reference/opal.table_export.html
+++ b/docs/reference/opal.table_export.html
@@ -73,15 +73,15 @@ Export a table as a file
- opal.table_export(
- opal,
- project,
- table,
- file,
- identifiers = NULL,
- id.name = "id",
- wait = TRUE
-)
+ opal.table_export(
+ opal,
+ project,
+ table,
+ file,
+ identifiers = NULL,
+ id.name = "id",
+ wait = TRUE
+)
@@ -120,6 +120,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -140,12 +141,12 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
- file = "/home/administrator/cnsim1.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
+ file = "/home/administrator/cnsim1.sav")
+opal.logout(o)
+}
@@ -160,7 +161,7 @@ Examples
diff --git a/docs/reference/opal.table_get.html b/docs/reference/opal.table_get.html
index 8a695e18..50b31621 100644
--- a/docs/reference/opal.table_get.html
+++ b/docs/reference/opal.table_get.html
@@ -73,14 +73,14 @@ Get a Opal table as a tibble
- opal.table_get(
- opal,
- project,
- table,
- id.name = "id",
- variables = NULL,
- missings = TRUE
-)
+ opal.table_get(
+ opal,
+ project,
+ table,
+ id.name = "id",
+ variables = NULL,
+ missings = TRUE
+)
@@ -112,6 +112,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -132,11 +133,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+opal.logout(o)
+}
@@ -151,7 +152,7 @@ Examples
diff --git a/docs/reference/opal.table_import.html b/docs/reference/opal.table_import.html
index e7a050a5..587ba457 100644
--- a/docs/reference/opal.table_import.html
+++ b/docs/reference/opal.table_import.html
@@ -77,17 +77,17 @@ Import a file as table
- opal.table_import(
- opal,
- file,
- project,
- table,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)
+ opal.table_import(
+ opal,
+ file,
+ project,
+ table,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)
@@ -131,6 +131,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -151,11 +152,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
+opal.logout(o)
+}
@@ -170,7 +171,7 @@ Examples
diff --git a/docs/reference/opal.table_perm.html b/docs/reference/opal.table_perm.html
index d6ebf2a3..b007ebba 100644
--- a/docs/reference/opal.table_perm.html
+++ b/docs/reference/opal.table_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a table
- opal.table_perm(opal, project, table)
+ opal.table_perm(opal, project, table)
@@ -95,6 +95,7 @@ Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,13 +116,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -136,7 +137,7 @@ Examples
diff --git a/docs/reference/opal.table_perm_add.html b/docs/reference/opal.table_perm_add.html
index dcd7c7bc..0a6d3975 100644
--- a/docs/reference/opal.table_perm_add.html
+++ b/docs/reference/opal.table_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on a table
- opal.table_perm_add(opal, project, table, subject, type = "user", permission)
+ opal.table_perm_add(opal, project, table, subject, type = "user", permission)
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -143,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.table_perm_delete.html b/docs/reference/opal.table_perm_delete.html
index 8b9b72de..940dd6c6 100644
--- a/docs/reference/opal.table_perm_delete.html
+++ b/docs/reference/opal.table_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a table
- opal.table_perm_delete(opal, project, table, subject, type = "user")
+ opal.table_perm_delete(opal, project, table, subject, type = "user")
@@ -97,6 +97,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -117,13 +118,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -138,7 +139,7 @@ Examples
diff --git a/docs/reference/opal.table_save.html b/docs/reference/opal.table_save.html
index 99d85274..b60ae4ab 100644
--- a/docs/reference/opal.table_save.html
+++ b/docs/reference/opal.table_save.html
@@ -71,18 +71,18 @@ Save a local tibble as a Opal table
- opal.table_save(
- opal,
- tibble,
- project,
- table,
- overwrite = TRUE,
- force = FALSE,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant"
-)
+ opal.table_save(
+ opal,
+ tibble,
+ project,
+ table,
+ overwrite = TRUE,
+ force = FALSE,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant"
+)
@@ -142,6 +142,7 @@ Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -162,15 +163,15 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-# do some (meta)data transformations, then save in opal's database
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
-# or overwrite data only (keep original data dictionary)
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+# do some (meta)data transformations, then save in opal's database
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
+# or overwrite data only (keep original data dictionary)
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
+opal.logout(o)
+}
@@ -185,7 +186,7 @@ Examples
diff --git a/docs/reference/opal.table_truncate.html b/docs/reference/opal.table_truncate.html
index 13487c0d..41394336 100644
--- a/docs/reference/opal.table_truncate.html
+++ b/docs/reference/opal.table_truncate.html
@@ -71,7 +71,7 @@ Truncate a Opal table
- opal.table_truncate(opal, project, table)
+ opal.table_truncate(opal, project, table)
@@ -91,6 +91,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -111,11 +112,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_truncate(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_truncate(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -130,7 +131,7 @@ Examples
diff --git a/docs/reference/opal.table_view_create.html b/docs/reference/opal.table_view_create.html
index 9b40db41..704d8e1c 100644
--- a/docs/reference/opal.table_view_create.html
+++ b/docs/reference/opal.table_view_create.html
@@ -73,7 +73,7 @@ Create an Opal view over tables
- opal.table_view_create(opal, project, table, tables, type = "Participant")
+ opal.table_view_create(opal, project, table, tables, type = "Participant")
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
@@ -143,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.table_view_update.html b/docs/reference/opal.table_view_update.html
index c4892e57..edf8750f 100644
--- a/docs/reference/opal.table_view_update.html
+++ b/docs/reference/opal.table_view_update.html
@@ -73,7 +73,7 @@ Update the table references and the entity filter of an Opal view
- opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
+ opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
@@ -101,6 +101,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -121,28 +122,28 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1"))
-
-# update the table references
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-
-# update the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
-
-# remove the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
-
-# update both the table references and the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
- where = "$('LAB_TSC').ge(5)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1"))
+
+# update the table references
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+
+# update the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
+
+# remove the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
+
+# update both the table references and the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
+ where = "$('LAB_TSC').ge(5)")
+opal.logout(o)
+}
@@ -157,7 +158,7 @@ Examples
diff --git a/docs/reference/opal.tables.html b/docs/reference/opal.tables.html
index da771ccc..3523f1ce 100644
--- a/docs/reference/opal.tables.html
+++ b/docs/reference/opal.tables.html
@@ -69,7 +69,7 @@ Get tables of a datasource
- opal.tables(opal, datasource, counts = FALSE, df = TRUE)
+ opal.tables(opal, datasource, counts = FALSE, df = TRUE)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables(o, 'CNSIM')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm.html b/docs/reference/opal.tables_perm.html
index e401969e..eaf76e27 100644
--- a/docs/reference/opal.tables_perm.html
+++ b/docs/reference/opal.tables_perm.html
@@ -69,7 +69,7 @@ Get the permissions on any table of a project
- opal.tables_perm(opal, project)
+ opal.tables_perm(opal, project)
@@ -91,13 +91,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm_add.html b/docs/reference/opal.tables_perm_add.html
index f9f318fe..34f1092b 100644
--- a/docs/reference/opal.tables_perm_add.html
+++ b/docs/reference/opal.tables_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on any table of a project
- opal.tables_perm_add(opal, project, subject, type = "user", permission)
+ opal.tables_perm_add(opal, project, subject, type = "user", permission)
@@ -97,13 +97,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm_delete.html b/docs/reference/opal.tables_perm_delete.html
index 58317fa1..c6c2bbb4 100644
--- a/docs/reference/opal.tables_perm_delete.html
+++ b/docs/reference/opal.tables_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from any table of a project
- opal.tables_perm_delete(opal, project, subject, type = "user")
+ opal.tables_perm_delete(opal, project, subject, type = "user")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/opal.task.html b/docs/reference/opal.task.html
index 5f63c0bb..9f2abe58 100644
--- a/docs/reference/opal.task.html
+++ b/docs/reference/opal.task.html
@@ -69,7 +69,7 @@ Get a task
- opal.task(opal, id)
+ opal.task(opal, id)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task(o, '1')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.task_cancel.html b/docs/reference/opal.task_cancel.html
index 4d2f68ff..a6d3af66 100644
--- a/docs/reference/opal.task_cancel.html
+++ b/docs/reference/opal.task_cancel.html
@@ -69,7 +69,7 @@ Cancel a task
- opal.task_cancel(opal, id)
+ opal.task_cancel(opal, id)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_cancel(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_cancel(o, '1')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.task_wait.html b/docs/reference/opal.task_wait.html
index e46c9ad1..c75baf8d 100644
--- a/docs/reference/opal.task_wait.html
+++ b/docs/reference/opal.task_wait.html
@@ -69,7 +69,7 @@ Wait for a task to complete.
- opal.task_wait(opal, id, max = NULL)
+ opal.task_wait(opal, id, max = NULL)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_wait(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_wait(o, '1')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.tasks.html b/docs/reference/opal.tasks.html
index b03cca25..bbc1909c 100644
--- a/docs/reference/opal.tasks.html
+++ b/docs/reference/opal.tasks.html
@@ -69,7 +69,7 @@ Get the tasks
- opal.tasks(opal, df = TRUE)
+ opal.tasks(opal, df = TRUE)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tasks(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tasks(o)
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.taxonomies.html b/docs/reference/opal.taxonomies.html
index 6eb7c9fc..7fdeb65c 100644
--- a/docs/reference/opal.taxonomies.html
+++ b/docs/reference/opal.taxonomies.html
@@ -71,7 +71,7 @@ Get taxonomies
- opal.taxonomies(opal, locale = "en", df = TRUE)
+ opal.taxonomies(opal, locale = "en", df = TRUE)
@@ -102,11 +102,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomies(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomies(o)
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy.html b/docs/reference/opal.taxonomy.html
index 588356cb..830f2f20 100644
--- a/docs/reference/opal.taxonomy.html
+++ b/docs/reference/opal.taxonomy.html
@@ -69,7 +69,7 @@ Get a taxonomy
- opal.taxonomy(opal, taxonomy)
+ opal.taxonomy(opal, taxonomy)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_delete.html b/docs/reference/opal.taxonomy_delete.html
index 56a28d51..16c5fe75 100644
--- a/docs/reference/opal.taxonomy_delete.html
+++ b/docs/reference/opal.taxonomy_delete.html
@@ -69,7 +69,7 @@ Delete a taxonomy
- opal.taxonomy_delete(opal, taxonomy)
+ opal.taxonomy_delete(opal, taxonomy)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_delete(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_delete(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_download.html b/docs/reference/opal.taxonomy_download.html
index bde9b7cc..72ddba73 100644
--- a/docs/reference/opal.taxonomy_download.html
+++ b/docs/reference/opal.taxonomy_download.html
@@ -69,7 +69,7 @@ Download a taxonomy file
- opal.taxonomy_download(opal, taxonomy, destination = NULL)
+ opal.taxonomy_download(opal, taxonomy, destination = NULL)
@@ -101,11 +101,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_upload.html b/docs/reference/opal.taxonomy_upload.html
index f64a1c9c..33aa2918 100644
--- a/docs/reference/opal.taxonomy_upload.html
+++ b/docs/reference/opal.taxonomy_upload.html
@@ -71,7 +71,7 @@ Upload a taxonomy file
- opal.taxonomy_upload(opal, path)
+ opal.taxonomy_upload(opal, path)
@@ -98,11 +98,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/opal.terms.html b/docs/reference/opal.terms.html
index 42d3ba1c..4514444d 100644
--- a/docs/reference/opal.terms.html
+++ b/docs/reference/opal.terms.html
@@ -69,7 +69,7 @@ Get the terms of a vocabulary
- opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
+ opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/opal.token.html b/docs/reference/opal.token.html
index 139cfb7f..2b23254c 100644
--- a/docs/reference/opal.token.html
+++ b/docs/reference/opal.token.html
@@ -71,7 +71,7 @@ Get a personal access token
- opal.token(opal, name)
+ opal.token(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_datashield_create.html b/docs/reference/opal.token_datashield_create.html
index 3eb7cd13..2f127a6b 100644
--- a/docs/reference/opal.token_datashield_create.html
+++ b/docs/reference/opal.token_datashield_create.html
@@ -71,7 +71,7 @@ Create a personal access token for Datashield usage
- opal.token_datashield_create(opal, name, projects = NULL)
+ opal.token_datashield_create(opal, name, projects = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_datashield_create(o, 'ds-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_datashield_create(o, 'ds-1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.token_delete.html b/docs/reference/opal.token_delete.html
index 780eb5ed..402a3d26 100644
--- a/docs/reference/opal.token_delete.html
+++ b/docs/reference/opal.token_delete.html
@@ -71,7 +71,7 @@ Delete a personal access token
- opal.token_delete(opal, name)
+ opal.token_delete(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_delete(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_delete(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_r_create.html b/docs/reference/opal.token_r_create.html
index b0b36787..c8222189 100644
--- a/docs/reference/opal.token_r_create.html
+++ b/docs/reference/opal.token_r_create.html
@@ -71,13 +71,13 @@ Create a personal access token for R usage
- opal.token_r_create(
- opal,
- name,
- projects = NULL,
- access = NULL,
- commands = c("export")
-)
+ opal.token_r_create(
+ opal,
+ name,
+ projects = NULL,
+ access = NULL,
+ commands = c("export")
+)
@@ -121,11 +121,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
+opal.logout(o)
+}
@@ -140,7 +140,7 @@ Examples
diff --git a/docs/reference/opal.token_renew.html b/docs/reference/opal.token_renew.html
index 72208339..e11a4f33 100644
--- a/docs/reference/opal.token_renew.html
+++ b/docs/reference/opal.token_renew.html
@@ -71,7 +71,7 @@ Renew an inactive personal access token
- opal.token_renew(opal, name)
+ opal.token_renew(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_renew(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_renew(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_sql_create.html b/docs/reference/opal.token_sql_create.html
index b618980e..d65e177c 100644
--- a/docs/reference/opal.token_sql_create.html
+++ b/docs/reference/opal.token_sql_create.html
@@ -71,7 +71,7 @@ Create a personal access token for SQL usage
- opal.token_sql_create(opal, name, projects = NULL)
+ opal.token_sql_create(opal, name, projects = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_sql_create(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_sql_create(o, 'sql-1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.tokens.html b/docs/reference/opal.tokens.html
index 59d4edfa..703771e5 100644
--- a/docs/reference/opal.tokens.html
+++ b/docs/reference/opal.tokens.html
@@ -71,7 +71,7 @@ Get the personal access tokens
- opal.tokens(opal, df = TRUE)
+ opal.tokens(opal, df = TRUE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tokens(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tokens(o)
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.unload_package.html b/docs/reference/opal.unload_package.html
index cb7ded42..6b5ebac0 100644
--- a/docs/reference/opal.unload_package.html
+++ b/docs/reference/opal.unload_package.html
@@ -69,7 +69,7 @@ Unload package
- opal.unload_package(opal, pkg)
+ opal.unload_package(opal, pkg)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.unload_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.unload_package(o, 'stats')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.valueset.html b/docs/reference/opal.valueset.html
index 7bbd50a4..d0c5c00a 100644
--- a/docs/reference/opal.valueset.html
+++ b/docs/reference/opal.valueset.html
@@ -69,7 +69,7 @@ Get the values of an entity
- opal.valueset(opal, datasource, table, identifier)
+ opal.valueset(opal, datasource, table, identifier)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.variable.html b/docs/reference/opal.variable.html
index 3e2e9155..2269ea5d 100644
--- a/docs/reference/opal.variable.html
+++ b/docs/reference/opal.variable.html
@@ -69,7 +69,7 @@ Get a variable of a table
- opal.variable(opal, datasource, table, variable)
+ opal.variable(opal, datasource, table, variable)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.variable_summary.html b/docs/reference/opal.variable_summary.html
index 75fda252..5686692d 100644
--- a/docs/reference/opal.variable_summary.html
+++ b/docs/reference/opal.variable_summary.html
@@ -69,14 +69,14 @@ Get summary statistics of a variable of a table
- opal.variable_summary(
- opal,
- datasource,
- table,
- variable,
- cached = TRUE,
- nature = NULL
-)
+ opal.variable_summary(
+ opal,
+ datasource,
+ table,
+ variable,
+ cached = TRUE,
+ nature = NULL
+)
@@ -124,11 +124,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
@@ -143,7 +143,7 @@ Examples
diff --git a/docs/reference/opal.variables.html b/docs/reference/opal.variables.html
index e1072df8..3ea90c87 100644
--- a/docs/reference/opal.variables.html
+++ b/docs/reference/opal.variables.html
@@ -69,7 +69,7 @@ Get variables of a table
- opal.variables(opal, datasource, table, locale = "en", df = TRUE)
+ opal.variables(opal, datasource, table, locale = "en", df = TRUE)
@@ -111,11 +111,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variables(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variables(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.version_compare.html b/docs/reference/opal.version_compare.html
index f9a8bc44..b8a11b96 100644
--- a/docs/reference/opal.version_compare.html
+++ b/docs/reference/opal.version_compare.html
@@ -71,7 +71,7 @@ Compare
- opal.version_compare(opal, version)
+ opal.version_compare(opal, version)
@@ -93,11 +93,11 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.version_compare(o, "2.6.0")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.version_compare(o, "2.6.0")
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.vocabularies.html b/docs/reference/opal.vocabularies.html
index 2a4ae4ac..edaf165e 100644
--- a/docs/reference/opal.vocabularies.html
+++ b/docs/reference/opal.vocabularies.html
@@ -69,7 +69,7 @@ Get the vocabularies of a taxonomy
- opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
+ opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabularies(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabularies(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.vocabulary.html b/docs/reference/opal.vocabulary.html
index 8dd847d4..18c471f7 100644
--- a/docs/reference/opal.vocabulary.html
+++ b/docs/reference/opal.vocabulary.html
@@ -69,7 +69,7 @@ Get a taxonomy vocabulary
- opal.vocabulary(opal, taxonomy, vocabulary)
+ opal.vocabulary(opal, taxonomy, vocabulary)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.workspace_restore.html b/docs/reference/opal.workspace_restore.html
index 192c945b..705b823a 100644
--- a/docs/reference/opal.workspace_restore.html
+++ b/docs/reference/opal.workspace_restore.html
@@ -69,7 +69,7 @@ Restore a R workspace from a opal.
- opal.workspace_restore(opal, ws)
+ opal.workspace_restore(opal, ws)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_restore(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_restore(o, 'test')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.workspace_rm.html b/docs/reference/opal.workspace_rm.html
index e33cf1d2..4bce81f9 100644
--- a/docs/reference/opal.workspace_rm.html
+++ b/docs/reference/opal.workspace_rm.html
@@ -69,7 +69,7 @@ Remove a R workspace from a opal.
- opal.workspace_rm(opal, ws, user = NULL)
+ opal.workspace_rm(opal, ws, user = NULL)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_rm(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_rm(o, 'test')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.workspace_save.html b/docs/reference/opal.workspace_save.html
index 074274e0..aa974933 100644
--- a/docs/reference/opal.workspace_save.html
+++ b/docs/reference/opal.workspace_save.html
@@ -69,7 +69,7 @@ Save the current session in a opal R workspace.
- opal.workspace_save(opal, save = TRUE)
+ opal.workspace_save(opal, save = TRUE)
@@ -98,14 +98,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# provide a workspace ID
-opal.workspace_save(o, 'test')
-# or use default one
-id <- opal.workspace_save(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# provide a workspace ID
+opal.workspace_save(o, 'test')
+# or use default one
+id <- opal.workspace_save(o)
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.workspaces.html b/docs/reference/opal.workspaces.html
index 83f92fdc..f4b0c155 100644
--- a/docs/reference/opal.workspaces.html
+++ b/docs/reference/opal.workspaces.html
@@ -69,7 +69,7 @@ Get the R workspaces from a opal.
- opal.workspaces(opal)
+ opal.workspaces(opal)
@@ -88,11 +88,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspaces(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspaces(o)
+opal.logout(o)
+}
@@ -107,7 +107,7 @@ Examples
diff --git a/docs/reference/opalr-package.html b/docs/reference/opalr-package.html
index acf0539c..7a3957ef 100644
--- a/docs/reference/opalr-package.html
+++ b/docs/reference/opalr-package.html
@@ -99,7 +99,7 @@ Author
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index db0185af..5d5b6ce2 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -123,6 +123,12 @@
/reference/dot-verbose.html
+
+ /reference/dsadmin.activity.html
+
+
+ /reference/dsadmin.activity_summary.html
+
/reference/dsadmin.get_method.html
@@ -144,6 +150,9 @@
/reference/dsadmin.installed_package.html
+
+ /reference/dsadmin.log.html
+
/reference/dsadmin.package_description.html
@@ -231,6 +240,12 @@
/reference/index.html
+
+ /reference/oadmin.activity.html
+
+
+ /reference/oadmin.activity_summary.html
+
/reference/oadmin.install_bioconductor_package.html
@@ -258,6 +273,15 @@
/reference/oadmin.installed_packages.html
+
+ /reference/oadmin.log.html
+
+
+ /reference/oadmin.log_rest.html
+
+
+ /reference/oadmin.log_sql.html
+
/reference/oadmin.package_description.html
@@ -426,6 +450,9 @@
/reference/opal.logout.html
+
+ /reference/opal.perms.html
+
/reference/opal.post.html
Inspect the dictionary of a tibble
Get DataSHIELD activity
Get DataSHIELD activity summary
All functions dsadmin.installed_package()
Check DataSHIELD package
Check DataSHIELD package
Get DataSHIELD logs
All functions dsadmin.unpublish_package()
Unpublish DataSHIELD package settings
Unpublish DataSHIELD package settings
Get R activity
Get R activity summary
All functions oadmin.installed_packages()
List installed packages
List installed packages
Get Opal main logs
Get Opal REST API logs
Get Opal SQL API logs
All functions opal.logout()
Logout from Opal(s)
Logout from Opal(s)
Get the permissions of a subject
All functions
diff --git a/docs/reference/oadmin.activity.html b/docs/reference/oadmin.activity.html
new file mode 100644
index 00000000..a11491b6
--- /dev/null
+++ b/docs/reference/oadmin.activity.html
@@ -0,0 +1,146 @@
+
+Get R activity — oadmin.activity • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics.
+
+
+
+ oadmin.activity(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity(o)
+# user and profile specific session metrics
+oadmin.activity(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.activity_summary.html b/docs/reference/oadmin.activity_summary.html
new file mode 100644
index 00000000..a8159421
--- /dev/null
+++ b/docs/reference/oadmin.activity_summary.html
@@ -0,0 +1,146 @@
+
+Get R activity summary — oadmin.activity_summary • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics, grouped by profile and user.
+
+
+
+ oadmin.activity_summary(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- user
+Optional user name.
- profile
+Optional profile name.
- from
+Optional start date.
- to
+Optional end date.
- df
+Return a data.frame (default is TRUE)
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity_summary(o)
+# user and profile specific session metrics
+oadmin.activity_summary(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.install_bioconductor_package.html b/docs/reference/oadmin.install_bioconductor_package.html
index adde90ec..2c0551ed 100644
--- a/docs/reference/oadmin.install_bioconductor_package.html
+++ b/docs/reference/oadmin.install_bioconductor_package.html
@@ -69,7 +69,7 @@ Install a package from Bioconductor
- oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
+ oadmin.install_bioconductor_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_bioconductor_package(o, 'GWASTools')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_bioconductor_package(o, 'GWASTools')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.install_cran_package.html b/docs/reference/oadmin.install_cran_package.html
index 3e7e3a18..d229933e 100644
--- a/docs/reference/oadmin.install_cran_package.html
+++ b/docs/reference/oadmin.install_cran_package.html
@@ -69,7 +69,7 @@ Install a package from CRAN
- oadmin.install_cran_package(opal, pkg, profile = NULL)
+ oadmin.install_cran_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_cran_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_cran_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.install_devtools.html b/docs/reference/oadmin.install_devtools.html
index 3f2bc53c..79b175d3 100644
--- a/docs/reference/oadmin.install_devtools.html
+++ b/docs/reference/oadmin.install_devtools.html
@@ -69,7 +69,7 @@ Install devtools package
- oadmin.install_devtools(opal, profile = NULL)
+ oadmin.install_devtools(opal, profile = NULL)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_devtools(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.install_github_package.html b/docs/reference/oadmin.install_github_package.html
index 496f0075..ae130887 100644
--- a/docs/reference/oadmin.install_github_package.html
+++ b/docs/reference/oadmin.install_github_package.html
@@ -69,13 +69,13 @@ Install a package from GitHub
- oadmin.install_github_package(
- opal,
- pkg,
- username = getOption("github.user"),
- ref = "master",
- profile = NULL
-)
+ oadmin.install_github_package(
+ opal,
+ pkg,
+ username = getOption("github.user"),
+ ref = "master",
+ profile = NULL
+)
@@ -117,11 +117,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_github_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_github_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
@@ -136,7 +136,7 @@ Examples
diff --git a/docs/reference/oadmin.install_local_package.html b/docs/reference/oadmin.install_local_package.html
index 17ddc429..9ddb56c3 100644
--- a/docs/reference/oadmin.install_local_package.html
+++ b/docs/reference/oadmin.install_local_package.html
@@ -71,7 +71,7 @@ Install a package from a local archive file
- oadmin.install_local_package(opal, path, profile = NULL)
+ oadmin.install_local_package(opal, path, profile = NULL)
@@ -105,14 +105,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# install a pre-built local archive file
-oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
-# or build archive file from local package source (in current working folder)
-oadmin.install_local_package(o, devtools::build())
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# install a pre-built local archive file
+oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
+# or build archive file from local package source (in current working folder)
+oadmin.install_local_package(o, devtools::build())
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/oadmin.install_package.html b/docs/reference/oadmin.install_package.html
index 0b2c26c5..7539e7fc 100644
--- a/docs/reference/oadmin.install_package.html
+++ b/docs/reference/oadmin.install_package.html
@@ -69,7 +69,7 @@ Install CRAN package
- oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
+ oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)
@@ -113,11 +113,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_package(o, 'xxx')
+opal.logout(o)
+}
@@ -132,7 +132,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_devtools.html b/docs/reference/oadmin.installed_devtools.html
index eaf1b900..a90063c1 100644
--- a/docs/reference/oadmin.installed_devtools.html
+++ b/docs/reference/oadmin.installed_devtools.html
@@ -69,7 +69,7 @@ Check devtools package
- oadmin.installed_devtools(opal, profile = NULL)
+ oadmin.installed_devtools(opal, profile = NULL)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_devtools(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_package.html b/docs/reference/oadmin.installed_package.html
index 604bd8ef..aa802b54 100644
--- a/docs/reference/oadmin.installed_package.html
+++ b/docs/reference/oadmin.installed_package.html
@@ -69,7 +69,7 @@ Check package is installed
- oadmin.installed_package(opal, pkg, profile = NULL)
+ oadmin.installed_package(opal, pkg, profile = NULL)
@@ -109,12 +109,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_package(o, 'xxx')
-oadmin.installed_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_package(o, 'xxx')
+oadmin.installed_package(o, 'stats')
+opal.logout(o)
+}
@@ -129,7 +129,7 @@ Examples
diff --git a/docs/reference/oadmin.installed_packages.html b/docs/reference/oadmin.installed_packages.html
index 2bc6bfc8..2034f299 100644
--- a/docs/reference/oadmin.installed_packages.html
+++ b/docs/reference/oadmin.installed_packages.html
@@ -69,7 +69,7 @@ List installed packages
- oadmin.installed_packages(opal, profile = NULL)
+ oadmin.installed_packages(opal, profile = NULL)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_packages(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_packages(o)
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/oadmin.log.html b/docs/reference/oadmin.log.html
new file mode 100644
index 00000000..2204fa48
--- /dev/null
+++ b/docs/reference/oadmin.log.html
@@ -0,0 +1,118 @@
+
+Get Opal main logs — oadmin.log • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal main logs
+
+
+
+ oadmin.log(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.log_rest.html b/docs/reference/oadmin.log_rest.html
new file mode 100644
index 00000000..fd2f9ef2
--- /dev/null
+++ b/docs/reference/oadmin.log_rest.html
@@ -0,0 +1,118 @@
+
+Get Opal REST API logs — oadmin.log_rest • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal REST API logs
+
+
+
+ oadmin.log_rest(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_rest(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.log_sql.html b/docs/reference/oadmin.log_sql.html
new file mode 100644
index 00000000..0dc4fae5
--- /dev/null
+++ b/docs/reference/oadmin.log_sql.html
@@ -0,0 +1,118 @@
+
+Get Opal SQL API logs — oadmin.log_sql • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal SQL API logs
+
+
+
+ oadmin.log_sql(opal, all = TRUE)
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- all
+Get all or only latest log messages.
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_sql(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/oadmin.package_description.html b/docs/reference/oadmin.package_description.html
index d07d871e..d402b336 100644
--- a/docs/reference/oadmin.package_description.html
+++ b/docs/reference/oadmin.package_description.html
@@ -69,7 +69,7 @@ Get package description
- oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
+ oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.package_description(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.package_description(o, 'stats')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/oadmin.perm.html b/docs/reference/oadmin.perm.html
index b61d3e13..20a30ecc 100644
--- a/docs/reference/oadmin.perm.html
+++ b/docs/reference/oadmin.perm.html
@@ -69,7 +69,7 @@ Get the R permissions (deprecated)
- oadmin.perm(opal)
+ oadmin.perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.perm_add.html b/docs/reference/oadmin.perm_add.html
index b3a39610..df43a7c7 100644
--- a/docs/reference/oadmin.perm_add.html
+++ b/docs/reference/oadmin.perm_add.html
@@ -69,7 +69,7 @@ Add or update a R permission (deprecated)
- oadmin.perm_add(opal, subject, type = "user", permission)
+ oadmin.perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.perm_delete.html b/docs/reference/oadmin.perm_delete.html
index f629e6fc..fa8fa4de 100644
--- a/docs/reference/oadmin.perm_delete.html
+++ b/docs/reference/oadmin.perm_delete.html
@@ -69,7 +69,7 @@ Delete a R permission (deprecated)
- oadmin.perm_delete(opal, subject, type = "user")
+ oadmin.perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm.html b/docs/reference/oadmin.r_perm.html
index 4bae064d..12b32d20 100644
--- a/docs/reference/oadmin.r_perm.html
+++ b/docs/reference/oadmin.r_perm.html
@@ -69,7 +69,7 @@ Get the R permissions
- oadmin.r_perm(opal)
+ oadmin.r_perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm_add.html b/docs/reference/oadmin.r_perm_add.html
index 06ec844e..fc74abf1 100644
--- a/docs/reference/oadmin.r_perm_add.html
+++ b/docs/reference/oadmin.r_perm_add.html
@@ -69,7 +69,7 @@ Add or update a R permission
- oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
+ oadmin.r_perm_add(opal, subject, type = "user", permission = "use")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.r_perm_delete.html b/docs/reference/oadmin.r_perm_delete.html
index c68d1ff5..01177602 100644
--- a/docs/reference/oadmin.r_perm_delete.html
+++ b/docs/reference/oadmin.r_perm_delete.html
@@ -69,7 +69,7 @@ Delete a R permission
- oadmin.r_perm_delete(opal, subject, type = "user")
+ oadmin.r_perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.remove_package.html b/docs/reference/oadmin.remove_package.html
index 7d9fd447..0953b827 100644
--- a/docs/reference/oadmin.remove_package.html
+++ b/docs/reference/oadmin.remove_package.html
@@ -69,7 +69,7 @@ Remove package
- oadmin.remove_package(opal, pkg, profile = NULL)
+ oadmin.remove_package(opal, pkg, profile = NULL)
@@ -103,11 +103,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.remove_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.remove_package(o, 'xxx')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.system_metrics.html b/docs/reference/oadmin.system_metrics.html
index 4e5ba20e..9eb7d54a 100644
--- a/docs/reference/oadmin.system_metrics.html
+++ b/docs/reference/oadmin.system_metrics.html
@@ -81,7 +81,7 @@ Get system metrics
- oadmin.system_metrics(opal)
+ oadmin.system_metrics(opal)
@@ -93,11 +93,11 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_metrics(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_metrics(o)
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm.html b/docs/reference/oadmin.system_perm.html
index a858025b..5cc5a542 100644
--- a/docs/reference/oadmin.system_perm.html
+++ b/docs/reference/oadmin.system_perm.html
@@ -69,7 +69,7 @@ Get the System permissions
- oadmin.system_perm(opal)
+ oadmin.system_perm(opal)
@@ -87,13 +87,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm_add.html b/docs/reference/oadmin.system_perm_add.html
index 8b06fd5e..ecc56a90 100644
--- a/docs/reference/oadmin.system_perm_add.html
+++ b/docs/reference/oadmin.system_perm_add.html
@@ -69,7 +69,7 @@ Add or update a System permission
- oadmin.system_perm_add(opal, subject, type = "user", permission)
+ oadmin.system_perm_add(opal, subject, type = "user", permission)
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/oadmin.system_perm_delete.html b/docs/reference/oadmin.system_perm_delete.html
index c78fc7d4..5268feec 100644
--- a/docs/reference/oadmin.system_perm_delete.html
+++ b/docs/reference/oadmin.system_perm_delete.html
@@ -69,7 +69,7 @@ Delete a System permission
- oadmin.system_perm_delete(opal, subject, type = "user")
+ oadmin.system_perm_delete(opal, subject, type = "user")
@@ -89,13 +89,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -110,7 +110,7 @@ Examples
diff --git a/docs/reference/oadmin.user_add.html b/docs/reference/oadmin.user_add.html
index e5a58e5b..1b82c9b6 100644
--- a/docs/reference/oadmin.user_add.html
+++ b/docs/reference/oadmin.user_add.html
@@ -69,7 +69,7 @@ Add a user
- oadmin.user_add(opal, name, groups = NULL, password = NULL)
+ oadmin.user_add(opal, name, groups = NULL, password = NULL)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/oadmin.user_delete.html b/docs/reference/oadmin.user_delete.html
index 123be6e5..1ae1cb20 100644
--- a/docs/reference/oadmin.user_delete.html
+++ b/docs/reference/oadmin.user_delete.html
@@ -69,7 +69,7 @@ Delete a user
- oadmin.user_delete(opal, name)
+ oadmin.user_delete(opal, name)
@@ -96,12 +96,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_delete(o, "foo")
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/oadmin.user_enable.html b/docs/reference/oadmin.user_enable.html
index 1b531f3a..5b480d04 100644
--- a/docs/reference/oadmin.user_enable.html
+++ b/docs/reference/oadmin.user_enable.html
@@ -69,7 +69,7 @@ Enable a user
- oadmin.user_enable(opal, name, enabled = TRUE)
+ oadmin.user_enable(opal, name, enabled = TRUE)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_enable(o, "foo", enabled = FALSE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_enable(o, "foo", enabled = FALSE)
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/oadmin.user_exists.html b/docs/reference/oadmin.user_exists.html
index e05a1f79..fad76e33 100644
--- a/docs/reference/oadmin.user_exists.html
+++ b/docs/reference/oadmin.user_exists.html
@@ -71,7 +71,7 @@ Check user exists
- oadmin.user_exists(opal, name)
+ oadmin.user_exists(opal, name)
@@ -98,12 +98,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-if (!oadmin.user_exists(o, "foo"))
- oadmin.user_add(o, "foo", password = "bar123")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+if (!oadmin.user_exists(o, "foo"))
+ oadmin.user_add(o, "foo", password = "bar123")
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/oadmin.user_profile_delete.html b/docs/reference/oadmin.user_profile_delete.html
index e1aab115..2e585266 100644
--- a/docs/reference/oadmin.user_profile_delete.html
+++ b/docs/reference/oadmin.user_profile_delete.html
@@ -75,7 +75,7 @@ Delete a user profile
- oadmin.user_profile_delete(opal, name)
+ oadmin.user_profile_delete(opal, name)
@@ -102,12 +102,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_profile_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_profile_delete(o, "foo")
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/oadmin.user_profiles.html b/docs/reference/oadmin.user_profiles.html
index 2c1e5a94..f23f1669 100644
--- a/docs/reference/oadmin.user_profiles.html
+++ b/docs/reference/oadmin.user_profiles.html
@@ -71,7 +71,7 @@ Get user profiles
- oadmin.user_profiles(opal, df = TRUE)
+ oadmin.user_profiles(opal, df = TRUE)
@@ -98,11 +98,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.user_profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.user_profiles(o)
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/oadmin.user_reset_password.html b/docs/reference/oadmin.user_reset_password.html
index 7bc446ae..75e27675 100644
--- a/docs/reference/oadmin.user_reset_password.html
+++ b/docs/reference/oadmin.user_reset_password.html
@@ -69,7 +69,7 @@ Reset user password
- oadmin.user_reset_password(opal, name, password = NULL)
+ oadmin.user_reset_password(opal, name, password = NULL)
@@ -100,13 +100,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_reset_password(o, "foo", password = "password1234")
-oadmin.user_rm(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_reset_password(o, "foo", password = "password1234")
+oadmin.user_rm(o, "foo")
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/oadmin.users.html b/docs/reference/oadmin.users.html
index e16383d7..f7a3388e 100644
--- a/docs/reference/oadmin.users.html
+++ b/docs/reference/oadmin.users.html
@@ -69,7 +69,7 @@ Get the users
- oadmin.users(opal, df = TRUE)
+ oadmin.users(opal, df = TRUE)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.users(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.users(o)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.annotate.html b/docs/reference/opal.annotate.html
index f8b0529c..d0970046 100644
--- a/docs/reference/opal.annotate.html
+++ b/docs/reference/opal.annotate.html
@@ -71,7 +71,7 @@ Apply the annotations to a Opal table
- opal.annotate(opal, datasource, table, annotations)
+ opal.annotate(opal, datasource, table, annotations)
@@ -111,12 +111,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
+opal.logout(o)
+}
@@ -131,7 +131,7 @@ Examples
diff --git a/docs/reference/opal.annotations.html b/docs/reference/opal.annotations.html
index 54727239..9f6b17eb 100644
--- a/docs/reference/opal.annotations.html
+++ b/docs/reference/opal.annotations.html
@@ -69,7 +69,7 @@ Get the annotations of a Opal table
- opal.annotations(opal, datasource, table)
+ opal.annotations(opal, datasource, table)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.as_md_table.html b/docs/reference/opal.as_md_table.html
index e37dd66e..b6b4c121 100644
--- a/docs/reference/opal.as_md_table.html
+++ b/docs/reference/opal.as_md_table.html
@@ -69,14 +69,14 @@ Array to Markdown
-
+
@@ -108,11 +108,11 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/opal.assign.data.html b/docs/reference/opal.assign.data.html
index e7b39e90..2be27522 100644
--- a/docs/reference/opal.assign.data.html
+++ b/docs/reference/opal.assign.data.html
@@ -69,7 +69,7 @@ Data assignment
- opal.assign.data(opal, symbol, value, async = FALSE)
+ opal.assign.data(opal, symbol, value, async = FALSE)
@@ -102,16 +102,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# push an arbitrary data frame to the R server
-opal.assign.data(o, "D", mtcars)
-# push an arbitrary vector to the R server
-opal.assign.data(o, "C", mtcars$cyl)
-# push a string
-opal.assign.data(o, "S", "Hello!")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# push an arbitrary data frame to the R server
+opal.assign.data(o, "D", mtcars)
+# push an arbitrary vector to the R server
+opal.assign.data(o, "C", mtcars$cyl)
+# push a string
+opal.assign.data(o, "S", "Hello!")
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.assign.html b/docs/reference/opal.assign.html
index c0c14727..83bab276 100644
--- a/docs/reference/opal.assign.html
+++ b/docs/reference/opal.assign.html
@@ -69,17 +69,17 @@ Data or expression assignment
- opal.assign(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- async = FALSE
-)
+ opal.assign(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ async = FALSE
+)
@@ -132,21 +132,21 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-# push an arbitrary data frame to the R server
-#opal.assign(o, "D", mtcars)
-# push an arbitrary vector to the R server
-#opal.assign(o, "C", mtcars$cyl)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+# push an arbitrary data frame to the R server
+#opal.assign(o, "D", mtcars)
+# push an arbitrary vector to the R server
+#opal.assign(o, "C", mtcars$cyl)
+opal.logout(o)
+}
@@ -161,7 +161,7 @@ Examples
diff --git a/docs/reference/opal.assign.resource.html b/docs/reference/opal.assign.resource.html
index 649d475e..b06c3fee 100644
--- a/docs/reference/opal.assign.resource.html
+++ b/docs/reference/opal.assign.resource.html
@@ -69,7 +69,7 @@ Resource assignment
- opal.assign.resource(opal, symbol, value, async = FALSE)
+ opal.assign.resource(opal, symbol, value, async = FALSE)
@@ -102,13 +102,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a resource and make some operation on it
-opal.assign.resource(o, "D", "datashield.cram1")
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a resource and make some operation on it
+opal.assign.resource(o, "D", "datashield.cram1")
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.assign.script.html b/docs/reference/opal.assign.script.html
index ce2ee8a8..4826146e 100644
--- a/docs/reference/opal.assign.script.html
+++ b/docs/reference/opal.assign.script.html
@@ -69,7 +69,7 @@ R script assignment
- opal.assign.script(opal, symbol, value, async = FALSE)
+ opal.assign.script(opal, symbol, value, async = FALSE)
@@ -102,13 +102,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.assign.table.html b/docs/reference/opal.assign.table.html
index f23b63b9..b853219b 100644
--- a/docs/reference/opal.assign.table.html
+++ b/docs/reference/opal.assign.table.html
@@ -69,18 +69,18 @@ Data assignment to a data.frame
- opal.assign.table(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- class = "data.frame",
- async = FALSE
-)
+ opal.assign.table(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ class = "data.frame",
+ async = FALSE
+)
@@ -137,19 +137,19 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-opal.execute(o, "colnames(D)")
-# assign a table CNSIM1 with a identifiers column
-opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
-opal.execute(o, "colnames(H)")
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-opal.execute(o, "colnames(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+opal.execute(o, "colnames(D)")
+# assign a table CNSIM1 with a identifiers column
+opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
+opal.execute(o, "colnames(H)")
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+opal.execute(o, "colnames(D)")
+opal.logout(o)
+}
@@ -164,7 +164,7 @@ Examples
diff --git a/docs/reference/opal.assign.table.tibble.html b/docs/reference/opal.assign.table.tibble.html
index 95dc04a3..e508e729 100644
--- a/docs/reference/opal.assign.table.tibble.html
+++ b/docs/reference/opal.assign.table.tibble.html
@@ -69,18 +69,18 @@ Data assignment to a tibble
- opal.assign.table.tibble(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = "id",
- with.factors = FALSE,
- updated.name = NULL,
- async = FALSE
-)
+ opal.assign.table.tibble(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = "id",
+ with.factors = FALSE,
+ updated.name = NULL,
+ async = FALSE
+)
@@ -137,13 +137,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a table and make some operation on it
-opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a table and make some operation on it
+opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
@@ -158,7 +158,7 @@ Examples
diff --git a/docs/reference/opal.attribute_values.html b/docs/reference/opal.attribute_values.html
index dd1b1537..98a94106 100644
--- a/docs/reference/opal.attribute_values.html
+++ b/docs/reference/opal.attribute_values.html
@@ -69,7 +69,7 @@ Get a vector of attribute values
- opal.attribute_values(attributes, namespace = NULL, name = "label")
+ opal.attribute_values(attributes, namespace = NULL, name = "label")
@@ -103,12 +103,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.attribute_values(var$attributes)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.attribute_values(var$attributes)
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.command.html b/docs/reference/opal.command.html
index 0f88509d..4f419a6e 100644
--- a/docs/reference/opal.command.html
+++ b/docs/reference/opal.command.html
@@ -69,7 +69,7 @@ Get an asynchronous command
- opal.command(opal, id, wait = FALSE)
+ opal.command(opal, id, wait = FALSE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command(o, '1234')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.command_result.html b/docs/reference/opal.command_result.html
index 5289b55a..35bc7964 100644
--- a/docs/reference/opal.command_result.html
+++ b/docs/reference/opal.command_result.html
@@ -71,7 +71,7 @@ Get result of an asynchronous command
- opal.command_result(opal, id, wait = FALSE)
+ opal.command_result(opal, id, wait = FALSE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_result(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_result(o, '1234')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.command_rm.html b/docs/reference/opal.command_rm.html
index c43351fa..e7fea6bb 100644
--- a/docs/reference/opal.command_rm.html
+++ b/docs/reference/opal.command_rm.html
@@ -69,7 +69,7 @@ Remove an asynchronous command
- opal.command_rm(opal, id)
+ opal.command_rm(opal, id)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_rm(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_rm(o, '1234')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.commands.html b/docs/reference/opal.commands.html
index f184c2a2..e5067c0f 100644
--- a/docs/reference/opal.commands.html
+++ b/docs/reference/opal.commands.html
@@ -69,7 +69,7 @@ List the asynchronous commands
- opal.commands(opal, df = TRUE)
+ opal.commands(opal, df = TRUE)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands(o)
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.commands_rm.html b/docs/reference/opal.commands_rm.html
index a79be20b..dad19270 100644
--- a/docs/reference/opal.commands_rm.html
+++ b/docs/reference/opal.commands_rm.html
@@ -69,7 +69,7 @@ Remove all asynchronous commands
- opal.commands_rm(opal)
+ opal.commands_rm(opal)
@@ -89,11 +89,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands_rm(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands_rm(o)
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/opal.datasource.html b/docs/reference/opal.datasource.html
index db4e3140..18ec94fc 100644
--- a/docs/reference/opal.datasource.html
+++ b/docs/reference/opal.datasource.html
@@ -69,7 +69,7 @@ Get a datasource
- opal.datasource(opal, datasource)
+ opal.datasource(opal, datasource)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasource(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasource(o, 'CNSIM')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.datasources.html b/docs/reference/opal.datasources.html
index 2c0c3136..b541b556 100644
--- a/docs/reference/opal.datasources.html
+++ b/docs/reference/opal.datasources.html
@@ -69,7 +69,7 @@ Get datasources
- opal.datasources(opal, df = TRUE)
+ opal.datasources(opal, df = TRUE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasources(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasources(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.delete.html b/docs/reference/opal.delete.html
index 9acf1da1..97b75ae3 100644
--- a/docs/reference/opal.delete.html
+++ b/docs/reference/opal.delete.html
@@ -69,7 +69,7 @@ Generic REST resource deletion.
- opal.delete(opal, ..., query = list(), callback = NULL)
+ opal.delete(opal, ..., query = list(), callback = NULL)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.delete(o, 'some', 'resource')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.delete(o, 'some', 'resource')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.execute.html b/docs/reference/opal.execute.html
index 244ade02..f91dcca6 100644
--- a/docs/reference/opal.execute.html
+++ b/docs/reference/opal.execute.html
@@ -69,7 +69,7 @@ Execute a R script
- opal.execute(opal, script, async = FALSE)
+ opal.execute(opal, script, async = FALSE)
@@ -97,12 +97,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute(o, "x <- 'foo'")
-opal.execute(o, "ls()")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute(o, "x <- 'foo'")
+opal.execute(o, "ls()")
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/opal.execute.source.html b/docs/reference/opal.execute.source.html
index 9ad4eef0..f512ffb2 100644
--- a/docs/reference/opal.execute.source.html
+++ b/docs/reference/opal.execute.source.html
@@ -69,7 +69,7 @@ Execute a R file script
- opal.execute.source(opal, path, async = FALSE)
+ opal.execute.source(opal, path, async = FALSE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute.source(o, "myscript.R")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute.source(o, "myscript.R")
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.file.html b/docs/reference/opal.file.html
index 074023d1..72a13d97 100644
--- a/docs/reference/opal.file.html
+++ b/docs/reference/opal.file.html
@@ -69,7 +69,7 @@ Get file content
- opal.file(opal, path, key = NULL)
+ opal.file(opal, path, key = NULL)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.file(o, '/home/administrator/joins/join-src-3.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.file(o, '/home/administrator/joins/join-src-3.csv')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.file_cp.html b/docs/reference/opal.file_cp.html
index c895e41c..33bb18fd 100644
--- a/docs/reference/opal.file_cp.html
+++ b/docs/reference/opal.file_cp.html
@@ -69,7 +69,7 @@ Copy a file
- opal.file_cp(opal, source, destination)
+ opal.file_cp(opal, source, destination)
@@ -104,14 +104,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# copy a file to another folder
-opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# copy recursively a folder to another folder
-opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# copy a file to another folder
+opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# copy recursively a folder to another folder
+opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.file_download.html b/docs/reference/opal.file_download.html
index dde0cba7..e6770678 100644
--- a/docs/reference/opal.file_download.html
+++ b/docs/reference/opal.file_download.html
@@ -69,7 +69,7 @@ Download a file
- opal.file_download(opal, source, destination = NULL, key = NULL)
+ opal.file_download(opal, source, destination = NULL, key = NULL)
@@ -108,19 +108,19 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# download a file
-opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
-# download a file encrypted by a key: resulting file is a zip with an encrypted content
-opal.file_download(o, '/home/administrator/export/some-data.csv',
- destination='some-data.zip', key='AZF57893FBDE')
-# download, create destination folder and rename file
-opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
-# download a folder
-opal.file_download(o, '/home/administrator/export', 'export.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# download a file
+opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
+# download a file encrypted by a key: resulting file is a zip with an encrypted content
+opal.file_download(o, '/home/administrator/export/some-data.csv',
+ destination='some-data.zip', key='AZF57893FBDE')
+# download, create destination folder and rename file
+opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
+# download a folder
+opal.file_download(o, '/home/administrator/export', 'export.zip')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.file_ls.html b/docs/reference/opal.file_ls.html
index c57e02da..8664df11 100644
--- a/docs/reference/opal.file_ls.html
+++ b/docs/reference/opal.file_ls.html
@@ -69,7 +69,7 @@ List content of a folder
- opal.file_ls(opal, path)
+ opal.file_ls(opal, path)
@@ -100,12 +100,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# list content of a folder
-opal.file_ls(o, '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# list content of a folder
+opal.file_ls(o, '/home/administrator')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.file_mkdir.html b/docs/reference/opal.file_mkdir.html
index 0ed72ad7..d15743df 100644
--- a/docs/reference/opal.file_mkdir.html
+++ b/docs/reference/opal.file_mkdir.html
@@ -71,7 +71,7 @@ Make a folder
- opal.file_mkdir(opal, path, parents = FALSE)
+ opal.file_mkdir(opal, path, parents = FALSE)
@@ -106,12 +106,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.file_mkdir_tmp.html b/docs/reference/opal.file_mkdir_tmp.html
index 396c04ff..8e187fcb 100644
--- a/docs/reference/opal.file_mkdir_tmp.html
+++ b/docs/reference/opal.file_mkdir_tmp.html
@@ -69,7 +69,7 @@ Make a temporary folder
- opal.file_mkdir_tmp(opal)
+ opal.file_mkdir_tmp(opal)
@@ -102,12 +102,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-path <- opal.file_mkdir_tmp(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+path <- opal.file_mkdir_tmp(o)
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/opal.file_mv.html b/docs/reference/opal.file_mv.html
index fc322297..1d6874df 100644
--- a/docs/reference/opal.file_mv.html
+++ b/docs/reference/opal.file_mv.html
@@ -69,7 +69,7 @@ Move and/or rename a file
- opal.file_mv(opal, source, destination)
+ opal.file_mv(opal, source, destination)
@@ -104,18 +104,18 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# move a file to another folder
-opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/administrator/export/some-data.csv')
-# move and rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/userx/deliverables/some-data.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# move a file to another folder
+opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/administrator/export/some-data.csv')
+# move and rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/userx/deliverables/some-data.csv')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.file_read.html b/docs/reference/opal.file_read.html
index 64f4982d..1807b28c 100644
--- a/docs/reference/opal.file_read.html
+++ b/docs/reference/opal.file_read.html
@@ -69,7 +69,7 @@ Read a file
- opal.file_read(opal, source, destination)
+ opal.file_read(opal, source, destination)
@@ -104,16 +104,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# read into folder
-opal.file_read(o,"DatabaseTest.sav", "/tmp")
-# read and rename
-opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
-# user home expansion
-opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# read into folder
+opal.file_read(o,"DatabaseTest.sav", "/tmp")
+# read and rename
+opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
+# user home expansion
+opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.file_rm.html b/docs/reference/opal.file_rm.html
index a23dee2e..5d79795c 100644
--- a/docs/reference/opal.file_rm.html
+++ b/docs/reference/opal.file_rm.html
@@ -69,7 +69,7 @@ Remove a file
- opal.file_rm(opal, path)
+ opal.file_rm(opal, path)
@@ -100,14 +100,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# remove a file
-opal.file_rm(o, '/home/administrator/export/some-data.csv')
-# remove recursively a folder
-opal.file_rm(o, '/home/administrator/export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# remove a file
+opal.file_rm(o, '/home/administrator/export/some-data.csv')
+# remove recursively a folder
+opal.file_rm(o, '/home/administrator/export')
+opal.logout(o)
+}
@@ -122,7 +122,7 @@ Examples
diff --git a/docs/reference/opal.file_unzip.html b/docs/reference/opal.file_unzip.html
index 66eaea32..a695dfec 100644
--- a/docs/reference/opal.file_unzip.html
+++ b/docs/reference/opal.file_unzip.html
@@ -69,7 +69,7 @@ Unzip a zip archive file
- opal.file_unzip(opal, source, destination, key = NULL)
+ opal.file_unzip(opal, source, destination, key = NULL)
@@ -114,12 +114,12 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# unzip
-path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# unzip
+path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.file_upload.html b/docs/reference/opal.file_upload.html
index 83a6426c..70c2faea 100644
--- a/docs/reference/opal.file_upload.html
+++ b/docs/reference/opal.file_upload.html
@@ -71,7 +71,7 @@ Upload a file or a folder
- opal.file_upload(opal, source, destination, all.files = TRUE)
+ opal.file_upload(opal, source, destination, all.files = TRUE)
@@ -111,14 +111,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# upload a file
-opal.file_upload(o, 'some_data.csv', '/home/administrator')
-# upload a folder
-opal.file_upload(o, 'some_data', '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# upload a file
+opal.file_upload(o, 'some_data.csv', '/home/administrator')
+# upload a folder
+opal.file_upload(o, 'some_data', '/home/administrator')
+opal.logout(o)
+}
@@ -133,7 +133,7 @@ Examples
diff --git a/docs/reference/opal.file_write.html b/docs/reference/opal.file_write.html
index a1bfb19d..f0835d11 100644
--- a/docs/reference/opal.file_write.html
+++ b/docs/reference/opal.file_write.html
@@ -69,7 +69,7 @@ Write a file
- opal.file_write(opal, source, destination = NULL)
+ opal.file_write(opal, source, destination = NULL)
@@ -104,16 +104,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# user home expansion
-opal.file_write(o, "~/spss/DatabaseTest.sav")
-# rename file
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
-# create sub-folder
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# user home expansion
+opal.file_write(o, "~/spss/DatabaseTest.sav")
+# rename file
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
+# create sub-folder
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.get.html b/docs/reference/opal.get.html
index 19e0f260..f83d5cb9 100644
--- a/docs/reference/opal.get.html
+++ b/docs/reference/opal.get.html
@@ -69,14 +69,14 @@ Generic REST resource getter.
- opal.get(
- opal,
- ...,
- query = list(),
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)
+ opal.get(
+ opal,
+ ...,
+ query = list(),
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)
@@ -115,11 +115,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.get(o, 'project', 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.get(o, 'project', 'CNSIM')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.load_package.html b/docs/reference/opal.load_package.html
index 15e9967f..cba05243 100644
--- a/docs/reference/opal.load_package.html
+++ b/docs/reference/opal.load_package.html
@@ -69,7 +69,7 @@ Load package
- opal.load_package(opal, pkg)
+ opal.load_package(opal, pkg)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.load_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.load_package(o, 'stats')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.login.html b/docs/reference/opal.login.html
index f9523698..549cdc71 100644
--- a/docs/reference/opal.login.html
+++ b/docs/reference/opal.login.html
@@ -73,15 +73,15 @@ Opal login
-
+
@@ -132,44 +132,44 @@ See also
Examples
- if (FALSE) {
-#### The below examples illustrate the different ways to login in opal ####
-
-# explicite username/password login
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
- # explicite personal access token login
-o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login using options and user credentials
-options(opal.username = 'administrator',
- opal.password = 'password',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using options and personal access token
-options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using ssl key pair
-options(opal.opts = list(
- sslcert = 'my-publickey.pem',
- sslkey = 'my-privatekey.pem'))
-o <- opal.login(url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login with a R server profile
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org', profile = 'default')
-opal.logout(o)
-}
+ if (FALSE) {
+#### The below examples illustrate the different ways to login in opal ####
+
+# explicite username/password login
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+ # explicite personal access token login
+o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login using options and user credentials
+options(opal.username = 'administrator',
+ opal.password = 'password',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using options and personal access token
+options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using ssl key pair
+options(opal.opts = list(
+ sslcert = 'my-publickey.pem',
+ sslkey = 'my-privatekey.pem'))
+o <- opal.login(url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login with a R server profile
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org', profile = 'default')
+opal.logout(o)
+}
@@ -184,7 +184,7 @@ Examples
diff --git a/docs/reference/opal.logout.html b/docs/reference/opal.logout.html
index e64f3e86..b91868aa 100644
--- a/docs/reference/opal.logout.html
+++ b/docs/reference/opal.logout.html
@@ -69,7 +69,7 @@ Logout from Opal(s)
- opal.logout(opal, save = FALSE)
+ opal.logout(opal, save = FALSE)
@@ -91,10 +91,10 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+}
@@ -109,7 +109,7 @@ Examples
diff --git a/docs/reference/opal.perms.html b/docs/reference/opal.perms.html
new file mode 100644
index 00000000..aab233ff
--- /dev/null
+++ b/docs/reference/opal.perms.html
@@ -0,0 +1,154 @@
+
+Get the permissions of a subject — opal.perms • opalr
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the permissions of a subject. If the subject is a user, the permissions of
+the groups to which the user belongs are also added to the result.
+
+
+
+ opal.perms(opal, subject, type = "user")
+
+
+
+ Arguments
+ - opal
+Opal connection object.
- subject
+A subject identifier: user or group name.
- type
+The type of subject: user (default) or group.
+
+ Value
+
+
+A data.frame with columns: subject, type, target (path to the opal object to which
+the permission applies), target_type and perm (the permission name)
+
+
+ See also
+ Other table functions:
+opal.resource_view_create(),
+opal.resource_view_reconnect(),
+opal.table_create(),
+opal.table_delete(),
+opal.table_dictionary_get(),
+opal.table_dictionary_update(),
+opal.table_exists(),
+opal.table_export(),
+opal.table_get(),
+opal.table_import(),
+opal.table_perm_add(),
+opal.table_perm_delete(),
+opal.table_perm(),
+opal.table_save(),
+opal.table_truncate(),
+opal.table_view_create(),
+opal.table_view_update()
+
+
+
+ Examples
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.perms(o, 'andrei')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/reference/opal.post.html b/docs/reference/opal.post.html
index d93bb6bf..f7d80068 100644
--- a/docs/reference/opal.post.html
+++ b/docs/reference/opal.post.html
@@ -69,16 +69,16 @@ Generic REST resource creation.
- opal.post(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)
+ opal.post(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)
@@ -125,11 +125,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.post(o, 'some', 'resources', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.post(o, 'some', 'resources', body = '{"some":"value"}')
+opal.logout(o)
+}
@@ -144,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.profiles.html b/docs/reference/opal.profiles.html
index 067273c2..1e96f85c 100644
--- a/docs/reference/opal.profiles.html
+++ b/docs/reference/opal.profiles.html
@@ -71,7 +71,7 @@ List R profiles
- opal.profiles(opal, df = TRUE)
+ opal.profiles(opal, df = TRUE)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.profiles(o)
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.project.html b/docs/reference/opal.project.html
index cd3a4f68..3e6b4a16 100644
--- a/docs/reference/opal.project.html
+++ b/docs/reference/opal.project.html
@@ -69,7 +69,7 @@ Get a project
- opal.project(opal, project)
+ opal.project(opal, project)
@@ -94,11 +94,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project(o, 'datashield')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project(o, 'datashield')
+opal.logout(o)
+}
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/opal.project_backup.html b/docs/reference/opal.project_backup.html
index 9fe7543f..58bf4b6e 100644
--- a/docs/reference/opal.project_backup.html
+++ b/docs/reference/opal.project_backup.html
@@ -75,14 +75,14 @@ Backup a project
- opal.project_backup(
- opal,
- project,
- archive,
- viewsAsTables = FALSE,
- override = TRUE,
- wait = TRUE
-)
+ opal.project_backup(
+ opal,
+ project,
+ archive,
+ viewsAsTables = FALSE,
+ override = TRUE,
+ wait = TRUE
+)
@@ -120,12 +120,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
-opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
+opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
+opal.logout(o)
+}
@@ -140,7 +140,7 @@ Examples
diff --git a/docs/reference/opal.project_command.html b/docs/reference/opal.project_command.html
index 13740837..9e6c5e62 100644
--- a/docs/reference/opal.project_command.html
+++ b/docs/reference/opal.project_command.html
@@ -69,7 +69,7 @@ Get project task
- opal.project_command(opal, project, id)
+ opal.project_command(opal, project, id)
@@ -95,12 +95,12 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
-opal.project_command(opal, 'GREENSPACE', id)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
+opal.project_command(opal, 'GREENSPACE', id)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.project_create.html b/docs/reference/opal.project_create.html
index 2524037d..d1eb8488 100644
--- a/docs/reference/opal.project_create.html
+++ b/docs/reference/opal.project_create.html
@@ -69,15 +69,15 @@ Create a project
- opal.project_create(
- opal,
- project,
- database = NULL,
- title = NULL,
- description = NULL,
- tags = NULL,
- exportFolder = NULL
-)
+ opal.project_create(
+ opal,
+ project,
+ database = NULL,
+ title = NULL,
+ description = NULL,
+ tags = NULL,
+ exportFolder = NULL
+)
@@ -124,16 +124,16 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with named database
-opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
-# with default database
-opal.project_create(o, 'test_default_db', database = TRUE)
-# no database, for views and resources only
-opal.project_create(o, 'test_no_db')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with named database
+opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
+# with default database
+opal.project_create(o, 'test_default_db', database = TRUE)
+# no database, for views and resources only
+opal.project_create(o, 'test_no_db')
+opal.logout(o)
+}
@@ -148,7 +148,7 @@ Examples
diff --git a/docs/reference/opal.project_delete.html b/docs/reference/opal.project_delete.html
index 0975b5d4..249dfdd3 100644
--- a/docs/reference/opal.project_delete.html
+++ b/docs/reference/opal.project_delete.html
@@ -69,7 +69,7 @@ Delete a project
- opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
+ opal.project_delete(opal, project, archive = FALSE, silent = TRUE)
@@ -102,11 +102,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_delete(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_delete(o, 'test')
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/opal.project_exists.html b/docs/reference/opal.project_exists.html
index 2d217cab..10266208 100644
--- a/docs/reference/opal.project_exists.html
+++ b/docs/reference/opal.project_exists.html
@@ -69,7 +69,7 @@ Check a project exists
- opal.project_exists(opal, project)
+ opal.project_exists(opal, project)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_exists(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_exists(o, 'test')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.project_perm.html b/docs/reference/opal.project_perm.html
index 07a974c3..abba6946 100644
--- a/docs/reference/opal.project_perm.html
+++ b/docs/reference/opal.project_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a project
- opal.project_perm(opal, project)
+ opal.project_perm(opal, project)
@@ -91,13 +91,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.project_perm_add.html b/docs/reference/opal.project_perm_add.html
index 1fd19072..e134d7b0 100644
--- a/docs/reference/opal.project_perm_add.html
+++ b/docs/reference/opal.project_perm_add.html
@@ -69,13 +69,13 @@ Add or update a permission on a project
- opal.project_perm_add(
- opal,
- project,
- subject,
- type = "user",
- permission = "administrate"
-)
+ opal.project_perm_add(
+ opal,
+ project,
+ subject,
+ type = "user",
+ permission = "administrate"
+)
@@ -103,13 +103,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.project_perm_delete.html b/docs/reference/opal.project_perm_delete.html
index 8a290c35..885e9c53 100644
--- a/docs/reference/opal.project_perm_delete.html
+++ b/docs/reference/opal.project_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a project
- opal.project_perm_delete(opal, project, subject, type = "user")
+ opal.project_perm_delete(opal, project, subject, type = "user")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/opal.project_restore.html b/docs/reference/opal.project_restore.html
index 76c5f138..8f4c0d05 100644
--- a/docs/reference/opal.project_restore.html
+++ b/docs/reference/opal.project_restore.html
@@ -75,14 +75,14 @@ Restore a project
- opal.project_restore(
- opal,
- project,
- archive,
- key = NULL,
- override = TRUE,
- wait = TRUE
-)
+ opal.project_restore(
+ opal,
+ project,
+ archive,
+ key = NULL,
+ override = TRUE,
+ wait = TRUE
+)
@@ -120,15 +120,15 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# create the project to restore, with the default database (to store tables)
-opal.project_create(o, 'GREENSPACE2', database = TRUE)
-# upload backup zip and launch restore task
-opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
-opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# create the project to restore, with the default database (to store tables)
+opal.project_create(o, 'GREENSPACE2', database = TRUE)
+# upload backup zip and launch restore task
+opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
+opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
+opal.logout(o)
+}
@@ -143,7 +143,7 @@ Examples
diff --git a/docs/reference/opal.projects.html b/docs/reference/opal.projects.html
index e8d51a41..73e9e973 100644
--- a/docs/reference/opal.projects.html
+++ b/docs/reference/opal.projects.html
@@ -69,7 +69,7 @@ Get projects
- opal.projects(opal, df = TRUE)
+ opal.projects(opal, df = TRUE)
@@ -94,11 +94,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects(o)
+opal.logout(o)
+}
@@ -113,7 +113,7 @@ Examples
diff --git a/docs/reference/opal.projects_databases.html b/docs/reference/opal.projects_databases.html
index 45f818b3..2a9dc9f0 100644
--- a/docs/reference/opal.projects_databases.html
+++ b/docs/reference/opal.projects_databases.html
@@ -69,7 +69,7 @@ Get projects databases
- opal.projects_databases(opal)
+ opal.projects_databases(opal)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects_databases(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects_databases(o)
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.put.html b/docs/reference/opal.put.html
index de59ef78..1622010c 100644
--- a/docs/reference/opal.put.html
+++ b/docs/reference/opal.put.html
@@ -69,14 +69,14 @@ Generic REST resource update.
- opal.put(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- callback = NULL
-)
+ opal.put(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ callback = NULL
+)
@@ -115,11 +115,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.report.html b/docs/reference/opal.report.html
index eaf6c399..efc8d7c1 100644
--- a/docs/reference/opal.report.html
+++ b/docs/reference/opal.report.html
@@ -69,13 +69,13 @@ Opal report
- opal.report(
- input,
- output = NULL,
- progress = FALSE,
- verbose = FALSE,
- boot_style = NULL
-)
+ opal.report(
+ input,
+ output = NULL,
+ progress = FALSE,
+ verbose = FALSE,
+ boot_style = NULL
+)
@@ -103,9 +103,9 @@ Arguments
Examples
- if (FALSE) {
-opal.report('input.Rmd', 'report', progress=TRUE)
-}
+ if (FALSE) {
+opal.report('input.Rmd', 'report', progress=TRUE)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.report_md.html b/docs/reference/opal.report_md.html
index ad0cadd5..50a44df1 100644
--- a/docs/reference/opal.report_md.html
+++ b/docs/reference/opal.report_md.html
@@ -69,7 +69,7 @@ Turn a R markdown file to html.
- opal.report_md(inputFile, progress, verbose)
+ opal.report_md(inputFile, progress, verbose)
@@ -85,7 +85,7 @@ Turn a R markdown file to html.
diff --git a/docs/reference/opal.resource.html b/docs/reference/opal.resource.html
index 8040add0..128ece62 100644
--- a/docs/reference/opal.resource.html
+++ b/docs/reference/opal.resource.html
@@ -69,7 +69,7 @@ Get a resource reference of a project
- opal.resource(opal, project, resource)
+ opal.resource(opal, project, resource)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.resource_create.html b/docs/reference/opal.resource_create.html
index a7f47634..9ed343f2 100644
--- a/docs/reference/opal.resource_create.html
+++ b/docs/reference/opal.resource_create.html
@@ -69,17 +69,17 @@ Create a resource reference in a project
- opal.resource_create(
- opal,
- project,
- name,
- url,
- description = NULL,
- format = NULL,
- package = NULL,
- identity = NULL,
- secret = NULL
-)
+ opal.resource_create(
+ opal,
+ project,
+ name,
+ url,
+ description = NULL,
+ format = NULL,
+ package = NULL,
+ identity = NULL,
+ secret = NULL
+)
@@ -139,13 +139,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_create(o, 'RSRC', 'CNSIM4',
- url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
- format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_create(o, 'RSRC', 'CNSIM4',
+ url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
+ format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
+opal.logout(o)
+}
@@ -160,7 +160,7 @@ Examples
diff --git a/docs/reference/opal.resource_delete.html b/docs/reference/opal.resource_delete.html
index 41eee541..a3e48fb8 100644
--- a/docs/reference/opal.resource_delete.html
+++ b/docs/reference/opal.resource_delete.html
@@ -69,7 +69,7 @@ Delete a resource reference
- opal.resource_delete(opal, project, resource, silent = TRUE)
+ opal.resource_delete(opal, project, resource, silent = TRUE)
@@ -109,11 +109,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_delete(o, "RSRC", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_delete(o, "RSRC", "CNSIM4")
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.resource_exists.html b/docs/reference/opal.resource_exists.html
index 7a5852e1..700fd693 100644
--- a/docs/reference/opal.resource_exists.html
+++ b/docs/reference/opal.resource_exists.html
@@ -69,7 +69,7 @@ Check a resource reference exists
- opal.resource_exists(opal, project, resource)
+ opal.resource_exists(opal, project, resource)
@@ -111,11 +111,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_exists(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_exists(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.resource_extension_create.html b/docs/reference/opal.resource_extension_create.html
index c0a045fe..1c8013c4 100644
--- a/docs/reference/opal.resource_extension_create.html
+++ b/docs/reference/opal.resource_extension_create.html
@@ -69,16 +69,16 @@ Create an extended resource reference in a project
- opal.resource_extension_create(
- opal,
- project,
- name,
- provider,
- factory,
- parameters,
- description = NULL,
- credentials = NULL
-)
+ opal.resource_extension_create(
+ opal,
+ project,
+ name,
+ provider,
+ factory,
+ parameters,
+ description = NULL,
+ credentials = NULL
+)
@@ -134,21 +134,21 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
- provider = 'dsOmics', factory = 'ga4gh-htsget',
- parameters = list(
- host = 'https://htsget.ga4gh.org',
- sample = '1000genomes.phase1.chr1',
- reference = '1',
- start = '1',
- end = '100000',
- format = 'GA4GHVCF'
- )
-)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
+ provider = 'dsOmics', factory = 'ga4gh-htsget',
+ parameters = list(
+ host = 'https://htsget.ga4gh.org',
+ sample = '1000genomes.phase1.chr1',
+ reference = '1',
+ start = '1',
+ end = '100000',
+ format = 'GA4GHVCF'
+ )
+)
+opal.logout(o)
+}
@@ -163,7 +163,7 @@ Examples
diff --git a/docs/reference/opal.resource_get.html b/docs/reference/opal.resource_get.html
index ae00707a..80a02871 100644
--- a/docs/reference/opal.resource_get.html
+++ b/docs/reference/opal.resource_get.html
@@ -69,7 +69,7 @@ Get the resource object of a project
- opal.resource_get(opal, project, resource)
+ opal.resource_get(opal, project, resource)
@@ -105,17 +105,17 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
-# then interpret locally the resource object (load the appropriate R packages)
-library(resourcer)
-# coerce to a data.frame
-as.data.frame(res)
-# or get the resource client object for low-level interactions
-rescli <- resourcer::newResourceClient(res)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
+# then interpret locally the resource object (load the appropriate R packages)
+library(resourcer)
+# coerce to a data.frame
+as.data.frame(res)
+# or get the resource client object for low-level interactions
+rescli <- resourcer::newResourceClient(res)
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm.html b/docs/reference/opal.resource_perm.html
index e6856cab..d97e7fef 100644
--- a/docs/reference/opal.resource_perm.html
+++ b/docs/reference/opal.resource_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a resource
- opal.resource_perm(opal, project, resource)
+ opal.resource_perm(opal, project, resource)
@@ -111,13 +111,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -132,7 +132,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm_add.html b/docs/reference/opal.resource_perm_add.html
index 9c3d1438..6ad84919 100644
--- a/docs/reference/opal.resource_perm_add.html
+++ b/docs/reference/opal.resource_perm_add.html
@@ -69,14 +69,14 @@ Add or update a permission on a resource
- opal.resource_perm_add(
- opal,
- project,
- resource,
- subject,
- type = "user",
- permission
-)
+ opal.resource_perm_add(
+ opal,
+ project,
+ resource,
+ subject,
+ type = "user",
+ permission
+)
@@ -125,13 +125,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -146,7 +146,7 @@ Examples
diff --git a/docs/reference/opal.resource_perm_delete.html b/docs/reference/opal.resource_perm_delete.html
index df299ed2..541396ce 100644
--- a/docs/reference/opal.resource_perm_delete.html
+++ b/docs/reference/opal.resource_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a resource
- opal.resource_perm_delete(opal, project, resource, subject, type = "user")
+ opal.resource_perm_delete(opal, project, resource, subject, type = "user")
@@ -113,13 +113,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -134,7 +134,7 @@ Examples
diff --git a/docs/reference/opal.resource_view_create.html b/docs/reference/opal.resource_view_create.html
index d653a1cf..f3a7a1f2 100644
--- a/docs/reference/opal.resource_view_create.html
+++ b/docs/reference/opal.resource_view_create.html
@@ -73,15 +73,15 @@ Create an Opal view over a resource reference
- opal.resource_view_create(
- opal,
- project,
- table,
- resource,
- type = "Participant",
- idColumn = NULL,
- profile = NULL
-)
+ opal.resource_view_create(
+ opal,
+ project,
+ table,
+ resource,
+ type = "Participant",
+ idColumn = NULL,
+ profile = NULL
+)
@@ -119,6 +119,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
@@ -139,14 +140,14 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
- resource = "RSRC.FEMALE_2439", idColumn = "Name")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
+ resource = "RSRC.FEMALE_2439", idColumn = "Name")
+opal.logout(o)
+}
@@ -161,7 +162,7 @@ Examples
diff --git a/docs/reference/opal.resource_view_reconnect.html b/docs/reference/opal.resource_view_reconnect.html
index e8650b92..06f03a44 100644
--- a/docs/reference/opal.resource_view_reconnect.html
+++ b/docs/reference/opal.resource_view_reconnect.html
@@ -73,7 +73,7 @@ Reconnect an Opal view to its underlying resource
- opal.resource_view_reconnect(opal, project, table)
+ opal.resource_view_reconnect(opal, project, table)
@@ -93,6 +93,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.table_create(),
opal.table_delete(),
@@ -113,14 +114,14 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-# re-initialize the view's connection to the resource
-opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+# re-initialize the view's connection to the resource
+opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
+opal.logout(o)
+}
@@ -135,7 +136,7 @@ Examples
diff --git a/docs/reference/opal.resources.html b/docs/reference/opal.resources.html
index 305236d9..1219e1b9 100644
--- a/docs/reference/opal.resources.html
+++ b/docs/reference/opal.resources.html
@@ -69,7 +69,7 @@ Get the resource references of a project
- opal.resources(opal, project, df = TRUE)
+ opal.resources(opal, project, df = TRUE)
@@ -105,11 +105,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources(o, 'RSRC')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources(o, 'RSRC')
+opal.logout(o)
+}
@@ -124,7 +124,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm.html b/docs/reference/opal.resources_perm.html
index ba3302b2..c53289ba 100644
--- a/docs/reference/opal.resources_perm.html
+++ b/docs/reference/opal.resources_perm.html
@@ -69,7 +69,7 @@ Get the permissions on any resource
- opal.resources_perm(opal, project)
+ opal.resources_perm(opal, project)
@@ -107,13 +107,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -128,7 +128,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm_add.html b/docs/reference/opal.resources_perm_add.html
index 1a4a38e2..f1c870b4 100644
--- a/docs/reference/opal.resources_perm_add.html
+++ b/docs/reference/opal.resources_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on any resource
- opal.resources_perm_add(opal, project, subject, type = "user", permission)
+ opal.resources_perm_add(opal, project, subject, type = "user", permission)
@@ -114,13 +114,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -135,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.resources_perm_delete.html b/docs/reference/opal.resources_perm_delete.html
index e7c09535..5c093566 100644
--- a/docs/reference/opal.resources_perm_delete.html
+++ b/docs/reference/opal.resources_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from any resource
- opal.resources_perm_delete(opal, project, subject, type = "user")
+ opal.resources_perm_delete(opal, project, subject, type = "user")
@@ -109,13 +109,13 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM', 'CNSIM1')
-opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM', 'CNSIM1')
+opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.rm.html b/docs/reference/opal.rm.html
index f444e41c..728ec6d4 100644
--- a/docs/reference/opal.rm.html
+++ b/docs/reference/opal.rm.html
@@ -69,7 +69,7 @@ Remove a R symbol (deprecated)
- opal.rm(opal, symbol)
+ opal.rm(opal, symbol)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.rm(o, 'D')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.sql.html b/docs/reference/opal.sql.html
index 41f13417..5fa1f9b8 100644
--- a/docs/reference/opal.sql.html
+++ b/docs/reference/opal.sql.html
@@ -75,7 +75,7 @@ Execute a SQL query on tables
- opal.sql(opal, query, project = NULL, id.name = "_id")
+ opal.sql(opal, query, project = NULL, id.name = "_id")
@@ -106,23 +106,23 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from CNSIM1
- where LAB_HDL is not null
- group by GENDER',
- 'CNSIM')
-# without project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from `CNSIM.CNSIM1`
- where LAB_HDL is not null
- group by GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from CNSIM1
+ where LAB_HDL is not null
+ group by GENDER',
+ 'CNSIM')
+# without project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from `CNSIM.CNSIM1`
+ where LAB_HDL is not null
+ group by GENDER')
+opal.logout(o)
+}
@@ -137,7 +137,7 @@ Examples
diff --git a/docs/reference/opal.sql_history.html b/docs/reference/opal.sql_history.html
index ff53d0db..1bd338f2 100644
--- a/docs/reference/opal.sql_history.html
+++ b/docs/reference/opal.sql_history.html
@@ -71,14 +71,14 @@ SQL query execution history
- opal.sql_history(
- opal,
- project = NULL,
- offset = 0,
- limit = 100,
- user = NULL,
- df = TRUE
-)
+ opal.sql_history(
+ opal,
+ project = NULL,
+ offset = 0,
+ limit = 100,
+ user = NULL,
+ df = TRUE
+)
@@ -118,16 +118,16 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql_history(o, 'CNSIM')
-# without project context
-opal.sql_history(o, NA)
-# with or without project context
-opal.sql_history(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql_history(o, 'CNSIM')
+# without project context
+opal.sql_history(o, NA)
+# with or without project context
+opal.sql_history(o)
+opal.logout(o)
+}
@@ -142,7 +142,7 @@ Examples
diff --git a/docs/reference/opal.symbol_import.html b/docs/reference/opal.symbol_import.html
index ae50bd82..5ee219a5 100644
--- a/docs/reference/opal.symbol_import.html
+++ b/docs/reference/opal.symbol_import.html
@@ -71,16 +71,16 @@ Import a tibble
- opal.symbol_import(
- opal,
- symbol,
- project,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)
+ opal.symbol_import(
+ opal,
+ symbol,
+ project,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)
@@ -128,11 +128,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_import(o, 'D', 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_import(o, 'D', 'test')
+opal.logout(o)
+}
@@ -147,7 +147,7 @@ Examples
diff --git a/docs/reference/opal.symbol_rm.html b/docs/reference/opal.symbol_rm.html
index d0cfd696..6d16a689 100644
--- a/docs/reference/opal.symbol_rm.html
+++ b/docs/reference/opal.symbol_rm.html
@@ -69,7 +69,7 @@ Remove a R symbol
- opal.symbol_rm(opal, symbol)
+ opal.symbol_rm(opal, symbol)
@@ -93,11 +93,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_rm(o, 'D')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.symbol_save.html b/docs/reference/opal.symbol_save.html
index f2a900f1..79035aa9 100644
--- a/docs/reference/opal.symbol_save.html
+++ b/docs/reference/opal.symbol_save.html
@@ -69,7 +69,7 @@ Save a tibble
- opal.symbol_save(opal, symbol, destination)
+ opal.symbol_save(opal, symbol, destination)
@@ -99,11 +99,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_save(o, 'D', 'test.sav')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_save(o, 'D', 'test.sav')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.symbols.html b/docs/reference/opal.symbols.html
index bb88de70..1b7894c4 100644
--- a/docs/reference/opal.symbols.html
+++ b/docs/reference/opal.symbols.html
@@ -69,7 +69,7 @@ List R symbols
- opal.symbols(opal)
+ opal.symbols(opal)
@@ -89,11 +89,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbols(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbols(o)
+opal.logout(o)
+}
@@ -108,7 +108,7 @@ Examples
diff --git a/docs/reference/opal.table.html b/docs/reference/opal.table.html
index b4d05790..be03e321 100644
--- a/docs/reference/opal.table.html
+++ b/docs/reference/opal.table.html
@@ -69,7 +69,7 @@ Get a table of a datasource
- opal.table(opal, datasource, table, counts = FALSE)
+ opal.table(opal, datasource, table, counts = FALSE)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.table_create.html b/docs/reference/opal.table_create.html
index 44e433ba..46cf045b 100644
--- a/docs/reference/opal.table_create.html
+++ b/docs/reference/opal.table_create.html
@@ -73,7 +73,7 @@ Create an Opal table or view
- opal.table_create(opal, project, table, type = "Participant", tables = NULL)
+ opal.table_create(opal, project, table, type = "Participant", tables = NULL)
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_delete(),
@@ -122,15 +123,15 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a raw table
-opal.table_create(o, "CNSIM", "CNSIM4")
-# make a view
-opal.table_create(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a raw table
+opal.table_create(o, "CNSIM", "CNSIM4")
+# make a view
+opal.table_create(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
@@ -145,7 +146,7 @@ Examples
diff --git a/docs/reference/opal.table_delete.html b/docs/reference/opal.table_delete.html
index 778f2343..cba12a39 100644
--- a/docs/reference/opal.table_delete.html
+++ b/docs/reference/opal.table_delete.html
@@ -71,7 +71,7 @@ Delete a Opal table
- opal.table_delete(opal, project, table, silent = TRUE)
+ opal.table_delete(opal, project, table, silent = TRUE)
@@ -95,6 +95,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,11 +116,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_delete(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_delete(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -134,7 +135,7 @@ Examples
diff --git a/docs/reference/opal.table_dictionary_get.html b/docs/reference/opal.table_dictionary_get.html
index 95a5c21a..59126cc2 100644
--- a/docs/reference/opal.table_dictionary_get.html
+++ b/docs/reference/opal.table_dictionary_get.html
@@ -69,7 +69,7 @@ Get the dictionary of a Opal table
- opal.table_dictionary_get(opal, project, table)
+ opal.table_dictionary_get(opal, project, table)
@@ -89,6 +89,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -109,11 +110,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -128,7 +129,7 @@ Examples
diff --git a/docs/reference/opal.table_dictionary_update.html b/docs/reference/opal.table_dictionary_update.html
index c2e5bfc5..090a7d91 100644
--- a/docs/reference/opal.table_dictionary_update.html
+++ b/docs/reference/opal.table_dictionary_update.html
@@ -69,13 +69,13 @@ Update the dictionary of a Opal table
- opal.table_dictionary_update(
- opal,
- project,
- table,
- variables,
- categories = NULL
-)
+ opal.table_dictionary_update(
+ opal,
+ project,
+ table,
+ variables,
+ categories = NULL
+)
@@ -104,6 +104,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -124,23 +125,23 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-variables <- tibble::tribble(
- ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
- "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
- "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
- "disp", "decimal", "Disp label", NA, NA, 1, 3
-)
-categories <- tibble::tribble(
- ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
- "cyl", "4", 0, "Four", "Quatre",
- "cyl", "6", 0, "Six", "Six",
- "cyl", "8", 1, "Height", "Huit"
-)
-opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+variables <- tibble::tribble(
+ ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
+ "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
+ "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
+ "disp", "decimal", "Disp label", NA, NA, 1, 3
+)
+categories <- tibble::tribble(
+ ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
+ "cyl", "4", 0, "Four", "Quatre",
+ "cyl", "6", 0, "Six", "Six",
+ "cyl", "8", 1, "Height", "Huit"
+)
+opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
+opal.logout(o)
+}
@@ -155,7 +156,7 @@ Examples
diff --git a/docs/reference/opal.table_exists.html b/docs/reference/opal.table_exists.html
index 10649da8..e4ac20bb 100644
--- a/docs/reference/opal.table_exists.html
+++ b/docs/reference/opal.table_exists.html
@@ -71,7 +71,7 @@ Check a Opal table exists
- opal.table_exists(opal, project, table, view = NA)
+ opal.table_exists(opal, project, table, view = NA)
@@ -96,6 +96,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -116,16 +117,16 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# check table exists
-opal.table_exists(o, "CNSIM", "CNSIM1")
-# check table exists AND is a NOT a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
-# check table exists AND is a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# check table exists
+opal.table_exists(o, "CNSIM", "CNSIM1")
+# check table exists AND is a NOT a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
+# check table exists AND is a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
+opal.logout(o)
+}
@@ -140,7 +141,7 @@ Examples
diff --git a/docs/reference/opal.table_export.html b/docs/reference/opal.table_export.html
index f5eb8c76..5110bb07 100644
--- a/docs/reference/opal.table_export.html
+++ b/docs/reference/opal.table_export.html
@@ -73,15 +73,15 @@ Export a table as a file
- opal.table_export(
- opal,
- project,
- table,
- file,
- identifiers = NULL,
- id.name = "id",
- wait = TRUE
-)
+ opal.table_export(
+ opal,
+ project,
+ table,
+ file,
+ identifiers = NULL,
+ id.name = "id",
+ wait = TRUE
+)
@@ -120,6 +120,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -140,12 +141,12 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
- file = "/home/administrator/cnsim1.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
+ file = "/home/administrator/cnsim1.sav")
+opal.logout(o)
+}
@@ -160,7 +161,7 @@ Examples
diff --git a/docs/reference/opal.table_get.html b/docs/reference/opal.table_get.html
index 8a695e18..50b31621 100644
--- a/docs/reference/opal.table_get.html
+++ b/docs/reference/opal.table_get.html
@@ -73,14 +73,14 @@ Get a Opal table as a tibble
- opal.table_get(
- opal,
- project,
- table,
- id.name = "id",
- variables = NULL,
- missings = TRUE
-)
+ opal.table_get(
+ opal,
+ project,
+ table,
+ id.name = "id",
+ variables = NULL,
+ missings = TRUE
+)
@@ -112,6 +112,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -132,11 +133,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+opal.logout(o)
+}
@@ -151,7 +152,7 @@ Examples
diff --git a/docs/reference/opal.table_import.html b/docs/reference/opal.table_import.html
index e7a050a5..587ba457 100644
--- a/docs/reference/opal.table_import.html
+++ b/docs/reference/opal.table_import.html
@@ -77,17 +77,17 @@ Import a file as table
- opal.table_import(
- opal,
- file,
- project,
- table,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)
+ opal.table_import(
+ opal,
+ file,
+ project,
+ table,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)
@@ -131,6 +131,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -151,11 +152,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
+opal.logout(o)
+}
@@ -170,7 +171,7 @@ Examples
diff --git a/docs/reference/opal.table_perm.html b/docs/reference/opal.table_perm.html
index d6ebf2a3..b007ebba 100644
--- a/docs/reference/opal.table_perm.html
+++ b/docs/reference/opal.table_perm.html
@@ -69,7 +69,7 @@ Get the permissions on a table
- opal.table_perm(opal, project, table)
+ opal.table_perm(opal, project, table)
@@ -95,6 +95,7 @@ Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,13 +116,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -136,7 +137,7 @@ Examples
diff --git a/docs/reference/opal.table_perm_add.html b/docs/reference/opal.table_perm_add.html
index dcd7c7bc..0a6d3975 100644
--- a/docs/reference/opal.table_perm_add.html
+++ b/docs/reference/opal.table_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on a table
- opal.table_perm_add(opal, project, table, subject, type = "user", permission)
+ opal.table_perm_add(opal, project, table, subject, type = "user", permission)
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -143,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.table_perm_delete.html b/docs/reference/opal.table_perm_delete.html
index 8b9b72de..940dd6c6 100644
--- a/docs/reference/opal.table_perm_delete.html
+++ b/docs/reference/opal.table_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from a table
- opal.table_perm_delete(opal, project, table, subject, type = "user")
+ opal.table_perm_delete(opal, project, table, subject, type = "user")
@@ -97,6 +97,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -117,13 +118,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -138,7 +139,7 @@ Examples
diff --git a/docs/reference/opal.table_save.html b/docs/reference/opal.table_save.html
index 99d85274..b60ae4ab 100644
--- a/docs/reference/opal.table_save.html
+++ b/docs/reference/opal.table_save.html
@@ -71,18 +71,18 @@ Save a local tibble as a Opal table
- opal.table_save(
- opal,
- tibble,
- project,
- table,
- overwrite = TRUE,
- force = FALSE,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant"
-)
+ opal.table_save(
+ opal,
+ tibble,
+ project,
+ table,
+ overwrite = TRUE,
+ force = FALSE,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant"
+)
@@ -142,6 +142,7 @@ Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -162,15 +163,15 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-# do some (meta)data transformations, then save in opal's database
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
-# or overwrite data only (keep original data dictionary)
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+# do some (meta)data transformations, then save in opal's database
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
+# or overwrite data only (keep original data dictionary)
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
+opal.logout(o)
+}
@@ -185,7 +186,7 @@ Examples
diff --git a/docs/reference/opal.table_truncate.html b/docs/reference/opal.table_truncate.html
index 13487c0d..41394336 100644
--- a/docs/reference/opal.table_truncate.html
+++ b/docs/reference/opal.table_truncate.html
@@ -71,7 +71,7 @@ Truncate a Opal table
- opal.table_truncate(opal, project, table)
+ opal.table_truncate(opal, project, table)
@@ -91,6 +91,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -111,11 +112,11 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_truncate(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_truncate(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
@@ -130,7 +131,7 @@ Examples
diff --git a/docs/reference/opal.table_view_create.html b/docs/reference/opal.table_view_create.html
index 9b40db41..704d8e1c 100644
--- a/docs/reference/opal.table_view_create.html
+++ b/docs/reference/opal.table_view_create.html
@@ -73,7 +73,7 @@ Create an Opal view over tables
- opal.table_view_create(opal, project, table, tables, type = "Participant")
+ opal.table_view_create(opal, project, table, tables, type = "Participant")
@@ -102,6 +102,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
@@ -143,7 +144,7 @@ Examples
diff --git a/docs/reference/opal.table_view_update.html b/docs/reference/opal.table_view_update.html
index c4892e57..edf8750f 100644
--- a/docs/reference/opal.table_view_update.html
+++ b/docs/reference/opal.table_view_update.html
@@ -73,7 +73,7 @@ Update the table references and the entity filter of an Opal view
- opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
+ opal.table_view_update(opal, project, table, tables = NULL, where = NULL)
@@ -101,6 +101,7 @@ Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -121,28 +122,28 @@
See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1"))
-
-# update the table references
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-
-# update the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
-
-# remove the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
-
-# update both the table references and the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
- where = "$('LAB_TSC').ge(5)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1"))
+
+# update the table references
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+
+# update the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
+
+# remove the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
+
+# update both the table references and the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
+ where = "$('LAB_TSC').ge(5)")
+opal.logout(o)
+}
@@ -157,7 +158,7 @@ Examples
diff --git a/docs/reference/opal.tables.html b/docs/reference/opal.tables.html
index da771ccc..3523f1ce 100644
--- a/docs/reference/opal.tables.html
+++ b/docs/reference/opal.tables.html
@@ -69,7 +69,7 @@ Get tables of a datasource
- opal.tables(opal, datasource, counts = FALSE, df = TRUE)
+ opal.tables(opal, datasource, counts = FALSE, df = TRUE)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables(o, 'CNSIM')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm.html b/docs/reference/opal.tables_perm.html
index e401969e..eaf76e27 100644
--- a/docs/reference/opal.tables_perm.html
+++ b/docs/reference/opal.tables_perm.html
@@ -69,7 +69,7 @@ Get the permissions on any table of a project
- opal.tables_perm(opal, project)
+ opal.tables_perm(opal, project)
@@ -91,13 +91,13 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm_add.html b/docs/reference/opal.tables_perm_add.html
index f9f318fe..34f1092b 100644
--- a/docs/reference/opal.tables_perm_add.html
+++ b/docs/reference/opal.tables_perm_add.html
@@ -69,7 +69,7 @@ Add or update a permission on any table of a project
- opal.tables_perm_add(opal, project, subject, type = "user", permission)
+ opal.tables_perm_add(opal, project, subject, type = "user", permission)
@@ -97,13 +97,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -118,7 +118,7 @@ Examples
diff --git a/docs/reference/opal.tables_perm_delete.html b/docs/reference/opal.tables_perm_delete.html
index 58317fa1..c6c2bbb4 100644
--- a/docs/reference/opal.tables_perm_delete.html
+++ b/docs/reference/opal.tables_perm_delete.html
@@ -69,7 +69,7 @@ Delete a permission from any table of a project
- opal.tables_perm_delete(opal, project, subject, type = "user")
+ opal.tables_perm_delete(opal, project, subject, type = "user")
@@ -93,13 +93,13 @@ Arguments
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
@@ -114,7 +114,7 @@ Examples
diff --git a/docs/reference/opal.task.html b/docs/reference/opal.task.html
index 5f63c0bb..9f2abe58 100644
--- a/docs/reference/opal.task.html
+++ b/docs/reference/opal.task.html
@@ -69,7 +69,7 @@ Get a task
- opal.task(opal, id)
+ opal.task(opal, id)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task(o, '1')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.task_cancel.html b/docs/reference/opal.task_cancel.html
index 4d2f68ff..a6d3af66 100644
--- a/docs/reference/opal.task_cancel.html
+++ b/docs/reference/opal.task_cancel.html
@@ -69,7 +69,7 @@ Cancel a task
- opal.task_cancel(opal, id)
+ opal.task_cancel(opal, id)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_cancel(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_cancel(o, '1')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.task_wait.html b/docs/reference/opal.task_wait.html
index e46c9ad1..c75baf8d 100644
--- a/docs/reference/opal.task_wait.html
+++ b/docs/reference/opal.task_wait.html
@@ -69,7 +69,7 @@ Wait for a task to complete.
- opal.task_wait(opal, id, max = NULL)
+ opal.task_wait(opal, id, max = NULL)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_wait(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_wait(o, '1')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.tasks.html b/docs/reference/opal.tasks.html
index b03cca25..bbc1909c 100644
--- a/docs/reference/opal.tasks.html
+++ b/docs/reference/opal.tasks.html
@@ -69,7 +69,7 @@ Get the tasks
- opal.tasks(opal, df = TRUE)
+ opal.tasks(opal, df = TRUE)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tasks(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tasks(o)
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.taxonomies.html b/docs/reference/opal.taxonomies.html
index 6eb7c9fc..7fdeb65c 100644
--- a/docs/reference/opal.taxonomies.html
+++ b/docs/reference/opal.taxonomies.html
@@ -71,7 +71,7 @@ Get taxonomies
- opal.taxonomies(opal, locale = "en", df = TRUE)
+ opal.taxonomies(opal, locale = "en", df = TRUE)
@@ -102,11 +102,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomies(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomies(o)
+opal.logout(o)
+}
@@ -121,7 +121,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy.html b/docs/reference/opal.taxonomy.html
index 588356cb..830f2f20 100644
--- a/docs/reference/opal.taxonomy.html
+++ b/docs/reference/opal.taxonomy.html
@@ -69,7 +69,7 @@ Get a taxonomy
- opal.taxonomy(opal, taxonomy)
+ opal.taxonomy(opal, taxonomy)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_delete.html b/docs/reference/opal.taxonomy_delete.html
index 56a28d51..16c5fe75 100644
--- a/docs/reference/opal.taxonomy_delete.html
+++ b/docs/reference/opal.taxonomy_delete.html
@@ -69,7 +69,7 @@ Delete a taxonomy
- opal.taxonomy_delete(opal, taxonomy)
+ opal.taxonomy_delete(opal, taxonomy)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_delete(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_delete(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_download.html b/docs/reference/opal.taxonomy_download.html
index bde9b7cc..72ddba73 100644
--- a/docs/reference/opal.taxonomy_download.html
+++ b/docs/reference/opal.taxonomy_download.html
@@ -69,7 +69,7 @@ Download a taxonomy file
- opal.taxonomy_download(opal, taxonomy, destination = NULL)
+ opal.taxonomy_download(opal, taxonomy, destination = NULL)
@@ -101,11 +101,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.taxonomy_upload.html b/docs/reference/opal.taxonomy_upload.html
index f64a1c9c..33aa2918 100644
--- a/docs/reference/opal.taxonomy_upload.html
+++ b/docs/reference/opal.taxonomy_upload.html
@@ -71,7 +71,7 @@ Upload a taxonomy file
- opal.taxonomy_upload(opal, path)
+ opal.taxonomy_upload(opal, path)
@@ -98,11 +98,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
+opal.logout(o)
+}
@@ -117,7 +117,7 @@ Examples
diff --git a/docs/reference/opal.terms.html b/docs/reference/opal.terms.html
index 42d3ba1c..4514444d 100644
--- a/docs/reference/opal.terms.html
+++ b/docs/reference/opal.terms.html
@@ -69,7 +69,7 @@ Get the terms of a vocabulary
- opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
+ opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)
@@ -108,11 +108,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
@@ -127,7 +127,7 @@ Examples
diff --git a/docs/reference/opal.token.html b/docs/reference/opal.token.html
index 139cfb7f..2b23254c 100644
--- a/docs/reference/opal.token.html
+++ b/docs/reference/opal.token.html
@@ -71,7 +71,7 @@ Get a personal access token
- opal.token(opal, name)
+ opal.token(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_datashield_create.html b/docs/reference/opal.token_datashield_create.html
index 3eb7cd13..2f127a6b 100644
--- a/docs/reference/opal.token_datashield_create.html
+++ b/docs/reference/opal.token_datashield_create.html
@@ -71,7 +71,7 @@ Create a personal access token for Datashield usage
- opal.token_datashield_create(opal, name, projects = NULL)
+ opal.token_datashield_create(opal, name, projects = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_datashield_create(o, 'ds-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_datashield_create(o, 'ds-1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.token_delete.html b/docs/reference/opal.token_delete.html
index 780eb5ed..402a3d26 100644
--- a/docs/reference/opal.token_delete.html
+++ b/docs/reference/opal.token_delete.html
@@ -71,7 +71,7 @@ Delete a personal access token
- opal.token_delete(opal, name)
+ opal.token_delete(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_delete(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_delete(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_r_create.html b/docs/reference/opal.token_r_create.html
index b0b36787..c8222189 100644
--- a/docs/reference/opal.token_r_create.html
+++ b/docs/reference/opal.token_r_create.html
@@ -71,13 +71,13 @@ Create a personal access token for R usage
- opal.token_r_create(
- opal,
- name,
- projects = NULL,
- access = NULL,
- commands = c("export")
-)
+ opal.token_r_create(
+ opal,
+ name,
+ projects = NULL,
+ access = NULL,
+ commands = c("export")
+)
@@ -121,11 +121,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
+opal.logout(o)
+}
@@ -140,7 +140,7 @@ Examples
diff --git a/docs/reference/opal.token_renew.html b/docs/reference/opal.token_renew.html
index 72208339..e11a4f33 100644
--- a/docs/reference/opal.token_renew.html
+++ b/docs/reference/opal.token_renew.html
@@ -71,7 +71,7 @@ Renew an inactive personal access token
- opal.token_renew(opal, name)
+ opal.token_renew(opal, name)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_renew(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_renew(o, 'sql-1')
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.token_sql_create.html b/docs/reference/opal.token_sql_create.html
index b618980e..d65e177c 100644
--- a/docs/reference/opal.token_sql_create.html
+++ b/docs/reference/opal.token_sql_create.html
@@ -71,7 +71,7 @@ Create a personal access token for SQL usage
- opal.token_sql_create(opal, name, projects = NULL)
+ opal.token_sql_create(opal, name, projects = NULL)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_sql_create(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_sql_create(o, 'sql-1')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.tokens.html b/docs/reference/opal.tokens.html
index 59d4edfa..703771e5 100644
--- a/docs/reference/opal.tokens.html
+++ b/docs/reference/opal.tokens.html
@@ -71,7 +71,7 @@ Get the personal access tokens
- opal.tokens(opal, df = TRUE)
+ opal.tokens(opal, df = TRUE)
@@ -97,11 +97,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tokens(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tokens(o)
+opal.logout(o)
+}
@@ -116,7 +116,7 @@ Examples
diff --git a/docs/reference/opal.unload_package.html b/docs/reference/opal.unload_package.html
index cb7ded42..6b5ebac0 100644
--- a/docs/reference/opal.unload_package.html
+++ b/docs/reference/opal.unload_package.html
@@ -69,7 +69,7 @@ Unload package
- opal.unload_package(opal, pkg)
+ opal.unload_package(opal, pkg)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.unload_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.unload_package(o, 'stats')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.valueset.html b/docs/reference/opal.valueset.html
index 7bbd50a4..d0c5c00a 100644
--- a/docs/reference/opal.valueset.html
+++ b/docs/reference/opal.valueset.html
@@ -69,7 +69,7 @@ Get the values of an entity
- opal.valueset(opal, datasource, table, identifier)
+ opal.valueset(opal, datasource, table, identifier)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.variable.html b/docs/reference/opal.variable.html
index 3e2e9155..2269ea5d 100644
--- a/docs/reference/opal.variable.html
+++ b/docs/reference/opal.variable.html
@@ -69,7 +69,7 @@ Get a variable of a table
- opal.variable(opal, datasource, table, variable)
+ opal.variable(opal, datasource, table, variable)
@@ -107,11 +107,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
@@ -126,7 +126,7 @@ Examples
diff --git a/docs/reference/opal.variable_summary.html b/docs/reference/opal.variable_summary.html
index 75fda252..5686692d 100644
--- a/docs/reference/opal.variable_summary.html
+++ b/docs/reference/opal.variable_summary.html
@@ -69,14 +69,14 @@ Get summary statistics of a variable of a table
- opal.variable_summary(
- opal,
- datasource,
- table,
- variable,
- cached = TRUE,
- nature = NULL
-)
+ opal.variable_summary(
+ opal,
+ datasource,
+ table,
+ variable,
+ cached = TRUE,
+ nature = NULL
+)
@@ -124,11 +124,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
@@ -143,7 +143,7 @@ Examples
diff --git a/docs/reference/opal.variables.html b/docs/reference/opal.variables.html
index e1072df8..3ea90c87 100644
--- a/docs/reference/opal.variables.html
+++ b/docs/reference/opal.variables.html
@@ -69,7 +69,7 @@ Get variables of a table
- opal.variables(opal, datasource, table, locale = "en", df = TRUE)
+ opal.variables(opal, datasource, table, locale = "en", df = TRUE)
@@ -111,11 +111,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variables(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variables(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
@@ -130,7 +130,7 @@ Examples
diff --git a/docs/reference/opal.version_compare.html b/docs/reference/opal.version_compare.html
index f9a8bc44..b8a11b96 100644
--- a/docs/reference/opal.version_compare.html
+++ b/docs/reference/opal.version_compare.html
@@ -71,7 +71,7 @@ Compare
- opal.version_compare(opal, version)
+ opal.version_compare(opal, version)
@@ -93,11 +93,11 @@ Value
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.version_compare(o, "2.6.0")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.version_compare(o, "2.6.0")
+opal.logout(o)
+}
@@ -112,7 +112,7 @@ Examples
diff --git a/docs/reference/opal.vocabularies.html b/docs/reference/opal.vocabularies.html
index 2a4ae4ac..edaf165e 100644
--- a/docs/reference/opal.vocabularies.html
+++ b/docs/reference/opal.vocabularies.html
@@ -69,7 +69,7 @@ Get the vocabularies of a taxonomy
- opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
+ opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)
@@ -104,11 +104,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabularies(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabularies(o, 'Mlstr_area')
+opal.logout(o)
+}
@@ -123,7 +123,7 @@ Examples
diff --git a/docs/reference/opal.vocabulary.html b/docs/reference/opal.vocabulary.html
index 8dd847d4..18c471f7 100644
--- a/docs/reference/opal.vocabulary.html
+++ b/docs/reference/opal.vocabulary.html
@@ -69,7 +69,7 @@ Get a taxonomy vocabulary
- opal.vocabulary(opal, taxonomy, vocabulary)
+ opal.vocabulary(opal, taxonomy, vocabulary)
@@ -100,11 +100,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
@@ -119,7 +119,7 @@ Examples
diff --git a/docs/reference/opal.workspace_restore.html b/docs/reference/opal.workspace_restore.html
index 192c945b..705b823a 100644
--- a/docs/reference/opal.workspace_restore.html
+++ b/docs/reference/opal.workspace_restore.html
@@ -69,7 +69,7 @@ Restore a R workspace from a opal.
- opal.workspace_restore(opal, ws)
+ opal.workspace_restore(opal, ws)
@@ -92,11 +92,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_restore(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_restore(o, 'test')
+opal.logout(o)
+}
@@ -111,7 +111,7 @@ Examples
diff --git a/docs/reference/opal.workspace_rm.html b/docs/reference/opal.workspace_rm.html
index e33cf1d2..4bce81f9 100644
--- a/docs/reference/opal.workspace_rm.html
+++ b/docs/reference/opal.workspace_rm.html
@@ -69,7 +69,7 @@ Remove a R workspace from a opal.
- opal.workspace_rm(opal, ws, user = NULL)
+ opal.workspace_rm(opal, ws, user = NULL)
@@ -96,11 +96,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_rm(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_rm(o, 'test')
+opal.logout(o)
+}
@@ -115,7 +115,7 @@ Examples
diff --git a/docs/reference/opal.workspace_save.html b/docs/reference/opal.workspace_save.html
index 074274e0..aa974933 100644
--- a/docs/reference/opal.workspace_save.html
+++ b/docs/reference/opal.workspace_save.html
@@ -69,7 +69,7 @@ Save the current session in a opal R workspace.
- opal.workspace_save(opal, save = TRUE)
+ opal.workspace_save(opal, save = TRUE)
@@ -98,14 +98,14 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# provide a workspace ID
-opal.workspace_save(o, 'test')
-# or use default one
-id <- opal.workspace_save(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# provide a workspace ID
+opal.workspace_save(o, 'test')
+# or use default one
+id <- opal.workspace_save(o)
+opal.logout(o)
+}
@@ -120,7 +120,7 @@ Examples
diff --git a/docs/reference/opal.workspaces.html b/docs/reference/opal.workspaces.html
index 83f92fdc..f4b0c155 100644
--- a/docs/reference/opal.workspaces.html
+++ b/docs/reference/opal.workspaces.html
@@ -69,7 +69,7 @@ Get the R workspaces from a opal.
- opal.workspaces(opal)
+ opal.workspaces(opal)
@@ -88,11 +88,11 @@ See also
Examples
- if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspaces(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspaces(o)
+opal.logout(o)
+}
@@ -107,7 +107,7 @@ Examples
diff --git a/docs/reference/opalr-package.html b/docs/reference/opalr-package.html
index acf0539c..7a3957ef 100644
--- a/docs/reference/opalr-package.html
+++ b/docs/reference/opalr-package.html
@@ -99,7 +99,7 @@ Author
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index db0185af..5d5b6ce2 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -123,6 +123,12 @@
/reference/dot-verbose.html
+
+ /reference/dsadmin.activity.html
+
+
+ /reference/dsadmin.activity_summary.html
+
/reference/dsadmin.get_method.html
@@ -144,6 +150,9 @@
/reference/dsadmin.installed_package.html
+
+ /reference/dsadmin.log.html
+
/reference/dsadmin.package_description.html
@@ -231,6 +240,12 @@
/reference/index.html
+
+ /reference/oadmin.activity.html
+
+
+ /reference/oadmin.activity_summary.html
+
/reference/oadmin.install_bioconductor_package.html
@@ -258,6 +273,15 @@
/reference/oadmin.installed_packages.html
+
+ /reference/oadmin.log.html
+
+
+ /reference/oadmin.log_rest.html
+
+
+ /reference/oadmin.log_sql.html
+
/reference/oadmin.package_description.html
@@ -426,6 +450,9 @@
/reference/opal.logout.html
+
+ /reference/opal.perms.html
+
/reference/opal.post.html
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics.
+
+
+
+
+ oadmin.activity(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+ Arguments
+- opal +
Opal connection object.
+
+
+- user +
Optional user name.
+
+
+- profile +
Optional profile name.
+
+
+- from +
Optional start date.
+
+
+- to +
Optional end date.
+
+
+- df +
Return a data.frame (default is TRUE)
+
+
+
+
+ Examples
+if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity(o)
+# user and profile specific session metrics
+oadmin.activity(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+ Get the recorded R session metrics, grouped by profile and user.
+
+
+
+
+ oadmin.activity_summary(
+ opal,
+ user = NULL,
+ profile = NULL,
+ from = NULL,
+ to = NULL,
+ df = TRUE
+)
+
+
+ Arguments
+- opal +
Opal connection object.
+
+
+- user +
Optional user name.
+
+
+- profile +
Optional profile name.
+
+
+- from +
Optional start date.
+
+
+- to +
Optional end date.
+
+
+- df +
Return a data.frame (default is TRUE)
+
+
+
+
+ Examples
+if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# all sessions metrics
+oadmin.activity_summary(o)
+# user and profile specific session metrics
+oadmin.activity_summary(o, user = 'dsuser', profile = 'default')
+# user sessions in a time range
+oadmin.activity_summary(o, user = "dsuser", from = "2022-07-01", to = "2023-01-01")
+opal.logout(o)
+}
+oadmin.install_bioconductor_package(opal, pkg, profile = NULL)oadmin.install_bioconductor_package(opal, pkg, profile = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_bioconductor_package(o, 'GWASTools')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_bioconductor_package(o, 'GWASTools')
+opal.logout(o)
+}
Examples
oadmin.install_cran_package(opal, pkg, profile = NULL)oadmin.install_cran_package(opal, pkg, profile = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_cran_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_cran_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
Examples
oadmin.install_devtools(opal, profile = NULL)oadmin.install_devtools(opal, profile = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_devtools(o)
+opal.logout(o)
+}
Examples
oadmin.install_github_package(
- opal,
- pkg,
- username = getOption("github.user"),
- ref = "master",
- profile = NULL
-)oadmin.install_github_package(
+ opal,
+ pkg,
+ username = getOption("github.user"),
+ ref = "master",
+ profile = NULL
+)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_github_package(o, 'opalr', 'obiba')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_github_package(o, 'opalr', 'obiba')
+opal.logout(o)
+}
Examples
oadmin.install_local_package(opal, path, profile = NULL)oadmin.install_local_package(opal, path, profile = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# install a pre-built local archive file
-oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
-# or build archive file from local package source (in current working folder)
-oadmin.install_local_package(o, devtools::build())
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# install a pre-built local archive file
+oadmin.install_local_package(o, '~/Rserve_1.8-7.tar.gz')
+# or build archive file from local package source (in current working folder)
+oadmin.install_local_package(o, devtools::build())
+opal.logout(o)
+}
Examples
oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)oadmin.install_package(opal, pkg, repos = NULL, profile = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.install_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.install_package(o, 'xxx')
+opal.logout(o)
+}
Examples
oadmin.installed_devtools(opal, profile = NULL)oadmin.installed_devtools(opal, profile = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_devtools(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_devtools(o)
+opal.logout(o)
+}
Examples
oadmin.installed_package(opal, pkg, profile = NULL)oadmin.installed_package(opal, pkg, profile = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_package(o, 'xxx')
-oadmin.installed_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_package(o, 'xxx')
+oadmin.installed_package(o, 'stats')
+opal.logout(o)
+}
Examples
oadmin.installed_packages(opal, profile = NULL)oadmin.installed_packages(opal, profile = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.installed_packages(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.installed_packages(o)
+opal.logout(o)
+}
Examples
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal main logs
+
+
+
+
+ oadmin.log(opal, all = TRUE)
+
+
+ Arguments
+- opal +
Opal connection object.
+
+
+- all +
Get all or only latest log messages.
+
+
+
+
+ Examples
+if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal REST API logs
+
+
+
+
+ oadmin.log_rest(opal, all = TRUE)
+
+
+ Arguments
+- opal +
Opal connection object.
+
+
+- all +
Get all or only latest log messages.
+
+
+
+
+ Examples
+if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_rest(o)
+opal.logout(o)
+}
+
+
+
+
+
+
+
+
+
+
+
+
+ Get Opal SQL API logs
+
+
+
+
+ oadmin.log_sql(opal, all = TRUE)
+
+
+ Arguments
+- opal +
Opal connection object.
+
+
+- all +
Get all or only latest log messages.
+
+
+
+
+ Examples
+if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.log_sql(o)
+opal.logout(o)
+}
+oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)oadmin.package_description(opal, pkg, fields = NULL, profile = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.package_description(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.package_description(o, 'stats')
+opal.logout(o)
+}
Examples
oadmin.perm(opal)oadmin.perm(opal)Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
oadmin.perm_add(opal, subject, type = "user", permission)oadmin.perm_add(opal, subject, type = "user", permission)Arguments
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
oadmin.perm_delete(opal, subject, type = "user")oadmin.perm_delete(opal, subject, type = "user")Arguments
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
oadmin.r_perm(opal)oadmin.r_perm(opal)Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
oadmin.r_perm_add(opal, subject, type = "user", permission = "use")oadmin.r_perm_add(opal, subject, type = "user", permission = "use")Arguments
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
oadmin.r_perm_delete(opal, subject, type = "user")oadmin.r_perm_delete(opal, subject, type = "user")Arguments
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
-oadmin.r_perm(o)
-oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.r_perm_add(o, c('andrei', 'valentina'), 'user', 'use')
+oadmin.r_perm(o)
+oadmin.r_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
oadmin.remove_package(opal, pkg, profile = NULL)oadmin.remove_package(opal, pkg, profile = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.remove_package(o, 'xxx')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.remove_package(o, 'xxx')
+opal.logout(o)
+}
Examples
oadmin.system_metrics(opal)oadmin.system_metrics(opal)Arguments
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_metrics(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_metrics(o)
+opal.logout(o)
+}
Examples
oadmin.system_perm(opal)oadmin.system_perm(opal)Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
oadmin.system_perm_add(opal, subject, type = "user", permission)oadmin.system_perm_add(opal, subject, type = "user", permission)Arguments
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
oadmin.system_perm_delete(opal, subject, type = "user")oadmin.system_perm_delete(opal, subject, type = "user")Arguments
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
-oadmin.system_perm(o)
-oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.system_perm_add(o, c('andrei', 'valentina'), 'user', 'project_add')
+oadmin.system_perm(o)
+oadmin.system_perm_delete(o, c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
oadmin.user_add(opal, name, groups = NULL, password = NULL)oadmin.user_add(opal, name, groups = NULL, password = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+opal.logout(o)
+}
Examples
oadmin.user_delete(opal, name)oadmin.user_delete(opal, name)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_delete(o, "foo")
+opal.logout(o)
+}
Examples
oadmin.user_enable(opal, name, enabled = TRUE)oadmin.user_enable(opal, name, enabled = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_enable(o, "foo", enabled = FALSE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_enable(o, "foo", enabled = FALSE)
+opal.logout(o)
+}
Examples
oadmin.user_exists(opal, name)oadmin.user_exists(opal, name)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-if (!oadmin.user_exists(o, "foo"))
- oadmin.user_add(o, "foo", password = "bar123")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+if (!oadmin.user_exists(o, "foo"))
+ oadmin.user_add(o, "foo", password = "bar123")
+opal.logout(o)
+}
Examples
oadmin.user_profile_delete(opal, name)oadmin.user_profile_delete(opal, name)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_profile_delete(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_profile_delete(o, "foo")
+opal.logout(o)
+}
Examples
oadmin.user_profiles(opal, df = TRUE)oadmin.user_profiles(opal, df = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.user_profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.user_profiles(o)
+opal.logout(o)
+}
Examples
oadmin.user_reset_password(opal, name, password = NULL)oadmin.user_reset_password(opal, name, password = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
-oadmin.user_reset_password(o, "foo", password = "password1234")
-oadmin.user_rm(o, "foo")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+pwd <- oadmin.user_add(o, "foo", groups = c("datashield", "CNSIM"))
+oadmin.user_reset_password(o, "foo", password = "password1234")
+oadmin.user_rm(o, "foo")
+opal.logout(o)
+}
Examples
oadmin.users(opal, df = TRUE)oadmin.users(opal, df = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-oadmin.users(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+oadmin.users(o)
+opal.logout(o)
+}
Examples
opal.annotate(opal, datasource, table, annotations)opal.annotate(opal, datasource, table, annotations)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+annots <- opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.annotate(o, 'CPTP', 'Cag_coreqx', annots)
+opal.logout(o)
+}
Examples
opal.annotations(opal, datasource, table)opal.annotations(opal, datasource, table)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.annotations(o, 'CPTP', 'Coreqx_final')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.annotations(o, 'CPTP', 'Coreqx_final')
+opal.logout(o)
+}
Examples
Arguments
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.as_md_table(opal.variables(o, 'datashield', 'CNSIM1'))
+opal.logout(o)
+}
Examples
opal.assign.data(opal, symbol, value, async = FALSE)opal.assign.data(opal, symbol, value, async = FALSE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# push an arbitrary data frame to the R server
-opal.assign.data(o, "D", mtcars)
-# push an arbitrary vector to the R server
-opal.assign.data(o, "C", mtcars$cyl)
-# push a string
-opal.assign.data(o, "S", "Hello!")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# push an arbitrary data frame to the R server
+opal.assign.data(o, "D", mtcars)
+# push an arbitrary vector to the R server
+opal.assign.data(o, "C", mtcars$cyl)
+# push a string
+opal.assign.data(o, "S", "Hello!")
+opal.logout(o)
+}
Examples
opal.assign(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- async = FALSE
-)opal.assign(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ async = FALSE
+)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-# push an arbitrary data frame to the R server
-#opal.assign(o, "D", mtcars)
-# push an arbitrary vector to the R server
-#opal.assign(o, "C", mtcars$cyl)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+# push an arbitrary data frame to the R server
+#opal.assign(o, "D", mtcars)
+# push an arbitrary vector to the R server
+#opal.assign(o, "C", mtcars$cyl)
+opal.logout(o)
+}
Examples
opal.assign.resource(opal, symbol, value, async = FALSE)opal.assign.resource(opal, symbol, value, async = FALSE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a resource and make some operation on it
-opal.assign.resource(o, "D", "datashield.cram1")
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a resource and make some operation on it
+opal.assign.resource(o, "D", "datashield.cram1")
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
Examples
opal.assign.script(opal, symbol, value, async = FALSE)opal.assign.script(opal, symbol, value, async = FALSE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a function and call it
-opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
-opal.execute(o, "hello('Mr Bean')")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a function and call it
+opal.assign.script(o, 'hello', quote(function(x) { print(paste0('Hello ', x , '!'))}))
+opal.execute(o, "hello('Mr Bean')")
+opal.logout(o)
+}
Examples
opal.assign.table(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = NULL,
- updated.name = NULL,
- class = "data.frame",
- async = FALSE
-)opal.assign.table(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = NULL,
+ updated.name = NULL,
+ class = "data.frame",
+ async = FALSE
+)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a list of variables from table CNSIM1
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
-opal.execute(o, "colnames(D)")
-# assign a table CNSIM1 with a identifiers column
-opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
-opal.execute(o, "colnames(H)")
-# assign all the variables matching 'LAB' from table HOP of opal object o
-opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
-opal.execute(o, "colnames(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a list of variables from table CNSIM1
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
+opal.execute(o, "colnames(D)")
+# assign a table CNSIM1 with a identifiers column
+opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
+opal.execute(o, "colnames(H)")
+# assign all the variables matching 'LAB' from table HOP of opal object o
+opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
+opal.execute(o, "colnames(D)")
+opal.logout(o)
+}
Examples
opal.assign.table.tibble(
- opal,
- symbol,
- value,
- variables = NULL,
- missings = FALSE,
- identifiers = NULL,
- id.name = "id",
- with.factors = FALSE,
- updated.name = NULL,
- async = FALSE
-)opal.assign.table.tibble(
+ opal,
+ symbol,
+ value,
+ variables = NULL,
+ missings = FALSE,
+ identifiers = NULL,
+ id.name = "id",
+ with.factors = FALSE,
+ updated.name = NULL,
+ async = FALSE
+)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# assign a table and make some operation on it
-opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
-opal.execute(o, "class(D)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# assign a table and make some operation on it
+opal.assign.table.tibble(o, 'D', 'datashield.CNSIM1')
+opal.execute(o, "class(D)")
+opal.logout(o)
+}
Examples
opal.attribute_values(attributes, namespace = NULL, name = "label")opal.attribute_values(attributes, namespace = NULL, name = "label")See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.attribute_values(var$attributes)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+var <- opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.attribute_values(var$attributes)
+opal.logout(o)
+}
Examples
opal.command(opal, id, wait = FALSE)opal.command(opal, id, wait = FALSE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command(o, '1234')
+opal.logout(o)
+}
Examples
opal.command_result(opal, id, wait = FALSE)opal.command_result(opal, id, wait = FALSE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_result(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_result(o, '1234')
+opal.logout(o)
+}
Examples
opal.command_rm(opal, id)opal.command_rm(opal, id)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.command_rm(o, '1234')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.command_rm(o, '1234')
+opal.logout(o)
+}
Examples
opal.commands(opal, df = TRUE)opal.commands(opal, df = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands(o)
+opal.logout(o)
+}
Examples
opal.commands_rm(opal)opal.commands_rm(opal)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.commands_rm(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.commands_rm(o)
+opal.logout(o)
+}
Examples
opal.datasource(opal, datasource)opal.datasource(opal, datasource)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasource(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasource(o, 'CNSIM')
+opal.logout(o)
+}
Examples
opal.datasources(opal, df = TRUE)opal.datasources(opal, df = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.datasources(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.datasources(o)
+opal.logout(o)
+}
Examples
opal.delete(opal, ..., query = list(), callback = NULL)opal.delete(opal, ..., query = list(), callback = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.delete(o, 'some', 'resource')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.delete(o, 'some', 'resource')
+opal.logout(o)
+}
Examples
opal.execute(opal, script, async = FALSE)opal.execute(opal, script, async = FALSE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute(o, "x <- 'foo'")
-opal.execute(o, "ls()")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute(o, "x <- 'foo'")
+opal.execute(o, "ls()")
+opal.logout(o)
+}
Examples
opal.execute.source(opal, path, async = FALSE)opal.execute.source(opal, path, async = FALSE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.execute.source(o, "myscript.R")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.execute.source(o, "myscript.R")
+opal.logout(o)
+}
Examples
opal.file(opal, path, key = NULL)opal.file(opal, path, key = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.file(o, '/home/administrator/joins/join-src-3.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.file(o, '/home/administrator/joins/join-src-3.csv')
+opal.logout(o)
+}
Examples
opal.file_cp(opal, source, destination)opal.file_cp(opal, source, destination)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# copy a file to another folder
-opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# copy recursively a folder to another folder
-opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# copy a file to another folder
+opal.file_cp(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# copy recursively a folder to another folder
+opal.file_cp(o, '/home/administrator/export', '/home/userx/deliverables')
+opal.logout(o)
+}
Examples
opal.file_download(opal, source, destination = NULL, key = NULL)opal.file_download(opal, source, destination = NULL, key = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# download a file
-opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
-# download a file encrypted by a key: resulting file is a zip with an encrypted content
-opal.file_download(o, '/home/administrator/export/some-data.csv',
- destination='some-data.zip', key='AZF57893FBDE')
-# download, create destination folder and rename file
-opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
-# download a folder
-opal.file_download(o, '/home/administrator/export', 'export.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# download a file
+opal.file_download(o, '/home/administrator/joins/join-src-3.csv')
+# download a file encrypted by a key: resulting file is a zip with an encrypted content
+opal.file_download(o, '/home/administrator/export/some-data.csv',
+ destination='some-data.zip', key='AZF57893FBDE')
+# download, create destination folder and rename file
+opal.file_download(o, '/home/administrator/spss/DatabaseTest.sav', 'spss/test.sav')
+# download a folder
+opal.file_download(o, '/home/administrator/export', 'export.zip')
+opal.logout(o)
+}
Examples
opal.file_ls(opal, path)opal.file_ls(opal, path)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# list content of a folder
-opal.file_ls(o, '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# list content of a folder
+opal.file_ls(o, '/home/administrator')
+opal.logout(o)
+}
Examples
opal.file_mkdir(opal, path, parents = FALSE)opal.file_mkdir(opal, path, parents = FALSE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+opal.file_mkdir(o, '/home/administrator/test', parents = TRUE)
+opal.logout(o)
+}
Examples
opal.file_mkdir_tmp(opal)opal.file_mkdir_tmp(opal)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a folder
-path <- opal.file_mkdir_tmp(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a folder
+path <- opal.file_mkdir_tmp(o)
+opal.logout(o)
+}
Examples
opal.file_mv(opal, source, destination)opal.file_mv(opal, source, destination)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# move a file to another folder
-opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
-# rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/administrator/export/some-data.csv')
-# move and rename a file
-opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
- '/home/userx/deliverables/some-data.csv')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# move a file to another folder
+opal.file_mv(o, '/home/administrator/export/some-data.csv', '/home/userx/deliverables')
+# rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/administrator/export/some-data.csv')
+# move and rename a file
+opal.file_mv(o, '/home/administrator/export/some-data-20170123.csv',
+ '/home/userx/deliverables/some-data.csv')
+opal.logout(o)
+}
Examples
opal.file_read(opal, source, destination)opal.file_read(opal, source, destination)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# read into folder
-opal.file_read(o,"DatabaseTest.sav", "/tmp")
-# read and rename
-opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
-# user home expansion
-opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# read into folder
+opal.file_read(o,"DatabaseTest.sav", "/tmp")
+# read and rename
+opal.file_read(o,"test/DatabaseTest.sav", "/tmp/Test.sav")
+# user home expansion
+opal.file_read(o,"DatabaseTest.sav", "~/coucou/pwel.sav")
+opal.logout(o)
+}
Examples
opal.file_rm(opal, path)opal.file_rm(opal, path)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# remove a file
-opal.file_rm(o, '/home/administrator/export/some-data.csv')
-# remove recursively a folder
-opal.file_rm(o, '/home/administrator/export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# remove a file
+opal.file_rm(o, '/home/administrator/export/some-data.csv')
+# remove recursively a folder
+opal.file_rm(o, '/home/administrator/export')
+opal.logout(o)
+}
Examples
opal.file_unzip(opal, source, destination, key = NULL)opal.file_unzip(opal, source, destination, key = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# unzip
-path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# unzip
+path <- opal.file_unzip(o, "/tmp/TESTING.zip", "/home/administrator")
+opal.logout(o)
+}
Examples
opal.file_upload(opal, source, destination, all.files = TRUE)opal.file_upload(opal, source, destination, all.files = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# upload a file
-opal.file_upload(o, 'some_data.csv', '/home/administrator')
-# upload a folder
-opal.file_upload(o, 'some_data', '/home/administrator')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# upload a file
+opal.file_upload(o, 'some_data.csv', '/home/administrator')
+# upload a folder
+opal.file_upload(o, 'some_data', '/home/administrator')
+opal.logout(o)
+}
Examples
opal.file_write(opal, source, destination = NULL)opal.file_write(opal, source, destination = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# user home expansion
-opal.file_write(o, "~/spss/DatabaseTest.sav")
-# rename file
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
-# create sub-folder
-opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# user home expansion
+opal.file_write(o, "~/spss/DatabaseTest.sav")
+# rename file
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "x.sav")
+# create sub-folder
+opal.file_write(o, "/home/administrator/spss/DatabaseTest.sav", "test/x.sav")
+opal.logout(o)
+}
Examples
opal.get(
- opal,
- ...,
- query = list(),
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)opal.get(
+ opal,
+ ...,
+ query = list(),
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.get(o, 'project', 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.get(o, 'project', 'CNSIM')
+opal.logout(o)
+}
Examples
opal.load_package(opal, pkg)opal.load_package(opal, pkg)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.load_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.load_package(o, 'stats')
+opal.logout(o)
+}
Examples
See also
Examples
-if (FALSE) {
-#### The below examples illustrate the different ways to login in opal ####
-
-# explicite username/password login
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
- # explicite personal access token login
-o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login using options and user credentials
-options(opal.username = 'administrator',
- opal.password = 'password',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using options and personal access token
-options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
- opal.url = 'https://opal-demo.obiba.org')
-o <- opal.login()
-opal.logout(o)
-
-# login using ssl key pair
-options(opal.opts = list(
- sslcert = 'my-publickey.pem',
- sslkey = 'my-privatekey.pem'))
-o <- opal.login(url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-
-# login with a R server profile
-o <- opal.login(username = 'administrator', password = 'password',
- url = 'https://opal-demo.obiba.org', profile = 'default')
-opal.logout(o)
-}
+ if (FALSE) {
+#### The below examples illustrate the different ways to login in opal ####
+
+# explicite username/password login
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+ # explicite personal access token login
+o <- opal.login(token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login using options and user credentials
+options(opal.username = 'administrator',
+ opal.password = 'password',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using options and personal access token
+options(opal.token = 'HYG16LO0VaX4O0UardNbiqmr2ByBpRke',
+ opal.url = 'https://opal-demo.obiba.org')
+o <- opal.login()
+opal.logout(o)
+
+# login using ssl key pair
+options(opal.opts = list(
+ sslcert = 'my-publickey.pem',
+ sslkey = 'my-privatekey.pem'))
+o <- opal.login(url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+
+# login with a R server profile
+o <- opal.login(username = 'administrator', password = 'password',
+ url = 'https://opal-demo.obiba.org', profile = 'default')
+opal.logout(o)
+}
Examples
opal.logout(opal, save = FALSE)opal.logout(opal, save = FALSE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.logout(o)
+}
Examples
+
+
+
+
+
+
+
+
+
+
+
+ Get the permissions of a subject. If the subject is a user, the permissions of +the groups to which the user belongs are also added to the result.
+
+
+
+
+ opal.perms(opal, subject, type = "user")
+
+ Arguments
+- opal +
Opal connection object.
+
+
+- subject +
A subject identifier: user or group name.
+
+
+- type +
The type of subject: user (default) or group.
+
+
+
+ Value
+ + +A data.frame with columns: subject, type, target (path to the opal object to which +the permission applies), target_type and perm (the permission name)
+
+
+
+
+ See also
+Other table functions:
+opal.resource_view_create(),
+opal.resource_view_reconnect(),
+opal.table_create(),
+opal.table_delete(),
+opal.table_dictionary_get(),
+opal.table_dictionary_update(),
+opal.table_exists(),
+opal.table_export(),
+opal.table_get(),
+opal.table_import(),
+opal.table_perm_add(),
+opal.table_perm_delete(),
+opal.table_perm(),
+opal.table_save(),
+opal.table_truncate(),
+opal.table_view_create(),
+opal.table_view_update()
+
+
+ Examples
+if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.perms(o, 'andrei')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
+opal.post(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- acceptType = "application/json",
- outFile = NULL,
- callback = NULL
-)opal.post(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ acceptType = "application/json",
+ outFile = NULL,
+ callback = NULL
+)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.post(o, 'some', 'resources', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.post(o, 'some', 'resources', body = '{"some":"value"}')
+opal.logout(o)
+}
Examples
opal.profiles(opal, df = TRUE)opal.profiles(opal, df = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.profiles(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.profiles(o)
+opal.logout(o)
+}
Examples
opal.project(opal, project)opal.project(opal, project)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project(o, 'datashield')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project(o, 'datashield')
+opal.logout(o)
+}
Examples
opal.project_backup(
- opal,
- project,
- archive,
- viewsAsTables = FALSE,
- override = TRUE,
- wait = TRUE
-)opal.project_backup(
+ opal,
+ project,
+ archive,
+ viewsAsTables = FALSE,
+ override = TRUE,
+ wait = TRUE
+)Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
-opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE')
+opal.file_download(o, '/home/administrator/backup/GREENSPACE', 'GREENSPACE.zip')
+opal.logout(o)
+}
Examples
opal.project_command(opal, project, id)opal.project_command(opal, project, id)Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
-opal.project_command(opal, 'GREENSPACE', id)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+id <- opal.project_backup(o, 'GREENSPACE', '/home/administrator/backup/GREENSPACE', wait = FALSE)
+opal.project_command(opal, 'GREENSPACE', id)
+opal.logout(o)
+}
Examples
opal.project_create(
- opal,
- project,
- database = NULL,
- title = NULL,
- description = NULL,
- tags = NULL,
- exportFolder = NULL
-)opal.project_create(
+ opal,
+ project,
+ database = NULL,
+ title = NULL,
+ description = NULL,
+ tags = NULL,
+ exportFolder = NULL
+)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with named database
-opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
-# with default database
-opal.project_create(o, 'test_default_db', database = TRUE)
-# no database, for views and resources only
-opal.project_create(o, 'test_no_db')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with named database
+opal.project_create(o, 'test', database='opal_data', title='This is a test', tags=list('Test'))
+# with default database
+opal.project_create(o, 'test_default_db', database = TRUE)
+# no database, for views and resources only
+opal.project_create(o, 'test_no_db')
+opal.logout(o)
+}
Examples
opal.project_delete(opal, project, archive = FALSE, silent = TRUE)opal.project_delete(opal, project, archive = FALSE, silent = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_delete(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_delete(o, 'test')
+opal.logout(o)
+}
Examples
opal.project_exists(opal, project)opal.project_exists(opal, project)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_exists(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_exists(o, 'test')
+opal.logout(o)
+}
Examples
opal.project_perm(opal, project)opal.project_perm(opal, project)Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
opal.project_perm_add(
- opal,
- project,
- subject,
- type = "user",
- permission = "administrate"
-)opal.project_perm_add(
+ opal,
+ project,
+ subject,
+ type = "user",
+ permission = "administrate"
+)Arguments
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
opal.project_perm_delete(opal, project, subject, type = "user")opal.project_perm_delete(opal, project, subject, type = "user")Arguments
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.project_perm(o, 'CNSIM')
-opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.project_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.project_perm(o, 'CNSIM')
+opal.project_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
opal.project_restore(
- opal,
- project,
- archive,
- key = NULL,
- override = TRUE,
- wait = TRUE
-)opal.project_restore(
+ opal,
+ project,
+ archive,
+ key = NULL,
+ override = TRUE,
+ wait = TRUE
+)Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# create the project to restore, with the default database (to store tables)
-opal.project_create(o, 'GREENSPACE2', database = TRUE)
-# upload backup zip and launch restore task
-opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
-opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# create the project to restore, with the default database (to store tables)
+opal.project_create(o, 'GREENSPACE2', database = TRUE)
+# upload backup zip and launch restore task
+opal.file_upload(o, 'GREENSPACE.zip', '/home/administrator')
+opal.project_restore(o, 'GREENSPACE2', '/home/administrator/GREENSPACE.zip')
+opal.logout(o)
+}
Examples
opal.projects(opal, df = TRUE)opal.projects(opal, df = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects(o)
+opal.logout(o)
+}
Examples
opal.projects_databases(opal)opal.projects_databases(opal)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.projects_databases(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.projects_databases(o)
+opal.logout(o)
+}
Examples
opal.put(
- opal,
- ...,
- query = list(),
- body = "",
- contentType = "application/x-rscript",
- callback = NULL
-)opal.put(
+ opal,
+ ...,
+ query = list(),
+ body = "",
+ contentType = "application/x-rscript",
+ callback = NULL
+)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.put(o, 'some', 'resource', 'toupdate', body = '{"some":"value"}')
+opal.logout(o)
+}
Examples
opal.report(
- input,
- output = NULL,
- progress = FALSE,
- verbose = FALSE,
- boot_style = NULL
-)opal.report(
+ input,
+ output = NULL,
+ progress = FALSE,
+ verbose = FALSE,
+ boot_style = NULL
+)Arguments
Examples
-if (FALSE) {
-opal.report('input.Rmd', 'report', progress=TRUE)
-}
+ if (FALSE) {
+opal.report('input.Rmd', 'report', progress=TRUE)
+}
Examples
opal.report_md(inputFile, progress, verbose)opal.report_md(inputFile, progress, verbose)opal.resource(opal, project, resource)opal.resource(opal, project, resource)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
Examples
opal.resource_create(
- opal,
- project,
- name,
- url,
- description = NULL,
- format = NULL,
- package = NULL,
- identity = NULL,
- secret = NULL
-)opal.resource_create(
+ opal,
+ project,
+ name,
+ url,
+ description = NULL,
+ format = NULL,
+ package = NULL,
+ identity = NULL,
+ secret = NULL
+)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_create(o, 'RSRC', 'CNSIM4',
- url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
- format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_create(o, 'RSRC', 'CNSIM4',
+ url = 'opal+https://opal-demo.obiba.org/ws/files/projects/RSRC/CNSIM3.zip',
+ format = 'csv', secret = 'EeTtQGIob6haio5bx6FUfVvIGkeZJfGq')
+opal.logout(o)
+}
Examples
opal.resource_delete(opal, project, resource, silent = TRUE)opal.resource_delete(opal, project, resource, silent = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_delete(o, "RSRC", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_delete(o, "RSRC", "CNSIM4")
+opal.logout(o)
+}
Examples
opal.resource_exists(opal, project, resource)opal.resource_exists(opal, project, resource)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_exists(o, 'RSRC', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_exists(o, 'RSRC', 'CNSIM1')
+opal.logout(o)
+}
Examples
opal.resource_extension_create(
- opal,
- project,
- name,
- provider,
- factory,
- parameters,
- description = NULL,
- credentials = NULL
-)opal.resource_extension_create(
+ opal,
+ project,
+ name,
+ provider,
+ factory,
+ parameters,
+ description = NULL,
+ credentials = NULL
+)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
- provider = 'dsOmics', factory = 'ga4gh-htsget',
- parameters = list(
- host = 'https://htsget.ga4gh.org',
- sample = '1000genomes.phase1.chr1',
- reference = '1',
- start = '1',
- end = '100000',
- format = 'GA4GHVCF'
- )
-)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_extension_create(o, 'RSRC', 'ga4gh_1000g',
+ provider = 'dsOmics', factory = 'ga4gh-htsget',
+ parameters = list(
+ host = 'https://htsget.ga4gh.org',
+ sample = '1000genomes.phase1.chr1',
+ reference = '1',
+ start = '1',
+ end = '100000',
+ format = 'GA4GHVCF'
+ )
+)
+opal.logout(o)
+}
Examples
opal.resource_get(opal, project, resource)opal.resource_get(opal, project, resource)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
-# then interpret locally the resource object (load the appropriate R packages)
-library(resourcer)
-# coerce to a data.frame
-as.data.frame(res)
-# or get the resource client object for low-level interactions
-rescli <- resourcer::newResourceClient(res)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+res <- opal.resource_get(o, 'RSRC', 'CNSIM1')
+# then interpret locally the resource object (load the appropriate R packages)
+library(resourcer)
+# coerce to a data.frame
+as.data.frame(res)
+# or get the resource client object for low-level interactions
+rescli <- resourcer::newResourceClient(res)
+opal.logout(o)
+}
Examples
opal.resource_perm(opal, project, resource)opal.resource_perm(opal, project, resource)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
opal.resource_perm_add(
- opal,
- project,
- resource,
- subject,
- type = "user",
- permission
-)opal.resource_perm_add(
+ opal,
+ project,
+ resource,
+ subject,
+ type = "user",
+ permission
+)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
opal.resource_perm_delete(opal, project, resource, subject, type = "user")opal.resource_perm_delete(opal, project, resource, subject, type = "user")See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resource_perm(o, 'CNSIM', 'CNSIM1')
-opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resource_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resource_perm(o, 'CNSIM', 'CNSIM1')
+opal.resource_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
opal.resource_view_create(
- opal,
- project,
- table,
- resource,
- type = "Participant",
- idColumn = NULL,
- profile = NULL
-)opal.resource_view_create(
+ opal,
+ project,
+ table,
+ resource,
+ type = "Participant",
+ idColumn = NULL,
+ profile = NULL
+)Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_reconnect(),
opal.table_create(),
opal.table_delete(),
@@ -139,14 +140,14 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
- resource = "RSRC.FEMALE_2439", idColumn = "Name")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+opal.resource_view_create(o, "CNSIM", "FEMALE_2439",
+ resource = "RSRC.FEMALE_2439", idColumn = "Name")
+opal.logout(o)
+}
Examples
Reconnect an Opal view to its underlying resource
opal.resource_view_reconnect(opal, project, table)opal.resource_view_reconnect(opal, project, table)Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.table_create(),
opal.table_delete(),
@@ -113,14 +114,14 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view over a resource
-opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
-# re-initialize the view's connection to the resource
-opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view over a resource
+opal.resource_view_create(o, "CNSIM", "CNSIM4", resource = "RSRC.CNSIM1")
+# re-initialize the view's connection to the resource
+opal.resource_view_reconnect(o, "CNSIM", "CNSIM4")
+opal.logout(o)
+}
Examples
Get the resource references of a project
opal.resources(opal, project, df = TRUE)opal.resources(opal, project, df = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources(o, 'RSRC')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources(o, 'RSRC')
+opal.logout(o)
+}
Examples
opal.resources_perm(opal, project)opal.resources_perm(opal, project)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
opal.resources_perm_add(opal, project, subject, type = "user", permission)opal.resources_perm_add(opal, project, subject, type = "user", permission)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM')
-opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM')
+opal.resources_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
opal.resources_perm_delete(opal, project, subject, type = "user")opal.resources_perm_delete(opal, project, subject, type = "user")See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.resources_perm(o, 'CNSIM', 'CNSIM1')
-opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.resources_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.resources_perm(o, 'CNSIM', 'CNSIM1')
+opal.resources_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
opal.rm(opal, symbol)opal.rm(opal, symbol)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.rm(o, 'D')
+opal.logout(o)
+}
Examples
opal.sql(opal, query, project = NULL, id.name = "_id")opal.sql(opal, query, project = NULL, id.name = "_id")Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from CNSIM1
- where LAB_HDL is not null
- group by GENDER',
- 'CNSIM')
-# without project context
-opal.sql(o,
- 'select avg(LAB_HDL) as HDL_AVG, GENDER
- from `CNSIM.CNSIM1`
- where LAB_HDL is not null
- group by GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from CNSIM1
+ where LAB_HDL is not null
+ group by GENDER',
+ 'CNSIM')
+# without project context
+opal.sql(o,
+ 'select avg(LAB_HDL) as HDL_AVG, GENDER
+ from `CNSIM.CNSIM1`
+ where LAB_HDL is not null
+ group by GENDER')
+opal.logout(o)
+}
Examples
opal.sql_history(
- opal,
- project = NULL,
- offset = 0,
- limit = 100,
- user = NULL,
- df = TRUE
-)opal.sql_history(
+ opal,
+ project = NULL,
+ offset = 0,
+ limit = 100,
+ user = NULL,
+ df = TRUE
+)Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# with project context
-opal.sql_history(o, 'CNSIM')
-# without project context
-opal.sql_history(o, NA)
-# with or without project context
-opal.sql_history(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# with project context
+opal.sql_history(o, 'CNSIM')
+# without project context
+opal.sql_history(o, NA)
+# with or without project context
+opal.sql_history(o)
+opal.logout(o)
+}
Examples
opal.symbol_import(
- opal,
- symbol,
- project,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)opal.symbol_import(
+ opal,
+ symbol,
+ project,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_import(o, 'D', 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_import(o, 'D', 'test')
+opal.logout(o)
+}
Examples
opal.symbol_rm(opal, symbol)opal.symbol_rm(opal, symbol)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_rm(o, 'D')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_rm(o, 'D')
+opal.logout(o)
+}
Examples
opal.symbol_save(opal, symbol, destination)opal.symbol_save(opal, symbol, destination)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbol_save(o, 'D', 'test.sav')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbol_save(o, 'D', 'test.sav')
+opal.logout(o)
+}
Examples
opal.symbols(opal)opal.symbols(opal)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.symbols(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.symbols(o)
+opal.logout(o)
+}
Examples
opal.table(opal, datasource, table, counts = FALSE)opal.table(opal, datasource, table, counts = FALSE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
Examples
opal.table_create(opal, project, table, type = "Participant", tables = NULL)opal.table_create(opal, project, table, type = "Participant", tables = NULL)Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_delete(),
@@ -122,15 +123,15 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a raw table
-opal.table_create(o, "CNSIM", "CNSIM4")
-# make a view
-opal.table_create(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a raw table
+opal.table_create(o, "CNSIM", "CNSIM4")
+# make a view
+opal.table_create(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
Examples
Delete a Opal table
opal.table_delete(opal, project, table, silent = TRUE)opal.table_delete(opal, project, table, silent = TRUE)Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,11 +116,11 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_delete(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_delete(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
Examples
Get the dictionary of a Opal table
opal.table_dictionary_get(opal, project, table)opal.table_dictionary_get(opal, project, table)Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -109,11 +110,11 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+dico <- opal.table_dictionary_get(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
Examples
Update the dictionary of a Opal table
opal.table_dictionary_update(
- opal,
- project,
- table,
- variables,
- categories = NULL
-)opal.table_dictionary_update(
+ opal,
+ project,
+ table,
+ variables,
+ categories = NULL
+)Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -124,23 +125,23 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-variables <- tibble::tribble(
- ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
- "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
- "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
- "disp", "decimal", "Disp label", NA, NA, 1, 3
-)
-categories <- tibble::tribble(
- ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
- "cyl", "4", 0, "Four", "Quatre",
- "cyl", "6", 0, "Six", "Six",
- "cyl", "8", 1, "Height", "Huit"
-)
-opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+variables <- tibble::tribble(
+ ~name, ~valueType, ~`label:en`, ~`Namespace::Name`, ~unit, ~repeatable, ~index,
+ "mpg", "decimal", "Mpg label", "Value1", "years", 0, 1,
+ "cyl", "decimal", "Cyl label", "Value2", "kg/m2", 0, 2,
+ "disp", "decimal", "Disp label", NA, NA, 1, 3
+)
+categories <- tibble::tribble(
+ ~variable, ~name, ~missing, ~`label:en`, ~`label:fr`,
+ "cyl", "4", 0, "Four", "Quatre",
+ "cyl", "6", 0, "Six", "Six",
+ "cyl", "8", 1, "Height", "Huit"
+)
+opal.table_dictionary_update(o, "test", "mtcars", variables, categories)
+opal.logout(o)
+}
Examples
Check a Opal table exists
opal.table_exists(opal, project, table, view = NA)opal.table_exists(opal, project, table, view = NA)Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -116,16 +117,16 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# check table exists
-opal.table_exists(o, "CNSIM", "CNSIM1")
-# check table exists AND is a NOT a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
-# check table exists AND is a view
-opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# check table exists
+opal.table_exists(o, "CNSIM", "CNSIM1")
+# check table exists AND is a NOT a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = FALSE)
+# check table exists AND is a view
+opal.table_exists(o, "CNSIM", "CNSIM1", view = TRUE)
+opal.logout(o)
+}
Examples
Export a table as a file
opal.table_export(
- opal,
- project,
- table,
- file,
- identifiers = NULL,
- id.name = "id",
- wait = TRUE
-)opal.table_export(
+ opal,
+ project,
+ table,
+ file,
+ identifiers = NULL,
+ id.name = "id",
+ wait = TRUE
+)Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -140,12 +141,12 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
- file = "/home/administrator/cnsim1.sav")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_export(o, "CNSIM", "CNSIM1",
+ file = "/home/administrator/cnsim1.sav")
+opal.logout(o)
+}
Examples
Get a Opal table as a tibble
opal.table_get(
- opal,
- project,
- table,
- id.name = "id",
- variables = NULL,
- missings = TRUE
-)opal.table_get(
+ opal,
+ project,
+ table,
+ id.name = "id",
+ variables = NULL,
+ missings = TRUE
+)Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -132,11 +133,11 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+opal.logout(o)
+}
Examples
Import a file as table
opal.table_import(
- opal,
- file,
- project,
- table,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant",
- wait = TRUE
-)opal.table_import(
+ opal,
+ file,
+ project,
+ table,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant",
+ wait = TRUE
+)Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -151,11 +152,11 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_import(o, '/home/administrator/mydataset.rds', 'test', 'mytable')
+opal.logout(o)
+}
Examples
Get the permissions on a table
opal.table_perm(opal, project, table)opal.table_perm(opal, project, table)Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -115,13 +116,13 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
Add or update a permission on a table
opal.table_perm_add(opal, project, table, subject, type = "user", permission)opal.table_perm_add(opal, project, table, subject, type = "user", permission)Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
Delete a permission from a table
opal.table_perm_delete(opal, project, table, subject, type = "user")opal.table_perm_delete(opal, project, table, subject, type = "user")Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -117,13 +118,13 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
-opal.table_perm(o, 'CNSIM', 'CNSIM1')
-opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_perm_add(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user', 'view')
+opal.table_perm(o, 'CNSIM', 'CNSIM1')
+opal.table_perm_delete(o, 'CNSIM', 'CNSIM1', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
Save a local tibble as a Opal table
opal.table_save(
- opal,
- tibble,
- project,
- table,
- overwrite = TRUE,
- force = FALSE,
- identifiers = NULL,
- policy = "required",
- id.name = "id",
- type = "Participant"
-)opal.table_save(
+ opal,
+ tibble,
+ project,
+ table,
+ overwrite = TRUE,
+ force = FALSE,
+ identifiers = NULL,
+ policy = "required",
+ id.name = "id",
+ type = "Participant"
+)Value
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -162,15 +163,15 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
-# do some (meta)data transformations, then save in opal's database
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
-# or overwrite data only (keep original data dictionary)
-opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+cqx <- opal.table_get(o, "CPTP", "Cag_coreqx")
+# do some (meta)data transformations, then save in opal's database
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = TRUE, force = TRUE)
+# or overwrite data only (keep original data dictionary)
+opal.table_save(o, cqx, "CPTP", "Cag_coreqx", overwrite = 'values', force = TRUE)
+opal.logout(o)
+}
Examples
Truncate a Opal table
opal.table_truncate(opal, project, table)opal.table_truncate(opal, project, table)Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -111,11 +112,11 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.table_truncate(o, "CNSIM", "CNSIM1")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.table_truncate(o, "CNSIM", "CNSIM1")
+opal.logout(o)
+}
Examples
Create an Opal view over tables
opal.table_view_create(opal, project, table, tables, type = "Participant")opal.table_view_create(opal, project, table, tables, type = "Participant")Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -122,13 +123,13 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+opal.logout(o)
+}
Examples
Update the table references and the entity filter of an Opal view
opal.table_view_update(opal, project, table, tables = NULL, where = NULL)opal.table_view_update(opal, project, table, tables = NULL, where = NULL)Arguments
See also
Other table functions:
+opal.perms(),
opal.resource_view_create(),
opal.resource_view_reconnect(),
opal.table_create(),
@@ -121,28 +122,28 @@
See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# make a view
-opal.table_view_create(o, "CNSIM", "CNSIM123",
- c("CNSIM.CNSIM1"))
-
-# update the table references
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
-
-# update the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
-
-# remove the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
-
-# update both the table references and the entity filter
-opal.table_view_update(o, "CNSIM", "CNSIM123",
- tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
- where = "$('LAB_TSC').ge(5)")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# make a view
+opal.table_view_create(o, "CNSIM", "CNSIM123",
+ c("CNSIM.CNSIM1"))
+
+# update the table references
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"))
+
+# update the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "$('LAB_TSC').ge(5)")
+
+# remove the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123", where = "")
+
+# update both the table references and the entity filter
+opal.table_view_update(o, "CNSIM", "CNSIM123",
+ tables = c("CNSIM.CNSIM1", "CNSIM.CNSIM2", "CNSIM.CNSIM3"),
+ where = "$('LAB_TSC').ge(5)")
+opal.logout(o)
+}
Examples
Get tables of a datasource
opal.tables(opal, datasource, counts = FALSE, df = TRUE)opal.tables(opal, datasource, counts = FALSE, df = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables(o, 'CNSIM')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables(o, 'CNSIM')
+opal.logout(o)
+}
Examples
opal.tables_perm(opal, project)opal.tables_perm(opal, project)Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
opal.tables_perm_add(opal, project, subject, type = "user", permission)opal.tables_perm_add(opal, project, subject, type = "user", permission)Arguments
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
opal.tables_perm_delete(opal, project, subject, type = "user")opal.tables_perm_delete(opal, project, subject, type = "user")Arguments
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
-opal.tables_perm(o, 'CNSIM')
-opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tables_perm_add(o, 'CNSIM', c('andrei', 'valentina'), 'user', 'administrate')
+opal.tables_perm(o, 'CNSIM')
+opal.tables_perm_delete(o, 'CNSIM', c('andrei', 'valentina'), 'user')
+opal.logout(o)
+}
Examples
opal.task(opal, id)opal.task(opal, id)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task(o, '1')
+opal.logout(o)
+}
Examples
opal.task_cancel(opal, id)opal.task_cancel(opal, id)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_cancel(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_cancel(o, '1')
+opal.logout(o)
+}
Examples
opal.task_wait(opal, id, max = NULL)opal.task_wait(opal, id, max = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.task_wait(o, '1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.task_wait(o, '1')
+opal.logout(o)
+}
Examples
opal.tasks(opal, df = TRUE)opal.tasks(opal, df = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tasks(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tasks(o)
+opal.logout(o)
+}
Examples
opal.taxonomies(opal, locale = "en", df = TRUE)opal.taxonomies(opal, locale = "en", df = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomies(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomies(o)
+opal.logout(o)
+}
Examples
opal.taxonomy(opal, taxonomy)opal.taxonomy(opal, taxonomy)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy(o, 'Mlstr_area')
+opal.logout(o)
+}
Examples
opal.taxonomy_delete(opal, taxonomy)opal.taxonomy_delete(opal, taxonomy)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_delete(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_delete(o, 'Mlstr_area')
+opal.logout(o)
+}
Examples
opal.taxonomy_download(opal, taxonomy, destination = NULL)opal.taxonomy_download(opal, taxonomy, destination = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_download(o, 'Mlstr_area', '~/some/dir/Mlstr_area.yml')
+opal.logout(o)
+}
Examples
opal.taxonomy_upload(opal, path)opal.taxonomy_upload(opal, path)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.taxonomy_upload(o, '~/some/dir/taxo.yml')
+opal.logout(o)
+}
Examples
opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)opal.terms(opal, taxonomy, vocabulary, locale = "en", df = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.terms(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
Examples
opal.token(opal, name)opal.token(opal, name)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token(o, 'sql-1')
+opal.logout(o)
+}
Examples
opal.token_datashield_create(opal, name, projects = NULL)opal.token_datashield_create(opal, name, projects = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_datashield_create(o, 'ds-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_datashield_create(o, 'ds-1')
+opal.logout(o)
+}
Examples
opal.token_delete(opal, name)opal.token_delete(opal, name)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_delete(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_delete(o, 'sql-1')
+opal.logout(o)
+}
Examples
opal.token_r_create(
- opal,
- name,
- projects = NULL,
- access = NULL,
- commands = c("export")
-)opal.token_r_create(
+ opal,
+ name,
+ projects = NULL,
+ access = NULL,
+ commands = c("export")
+)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_r_create(o, 'r-1', access = 'READ', commands = 'export')
+opal.logout(o)
+}
Examples
opal.token_renew(opal, name)opal.token_renew(opal, name)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.token_renew(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.token_renew(o, 'sql-1')
+opal.logout(o)
+}
Examples
opal.token_sql_create(opal, name, projects = NULL)opal.token_sql_create(opal, name, projects = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-token <- opal.token_sql_create(o, 'sql-1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+token <- opal.token_sql_create(o, 'sql-1')
+opal.logout(o)
+}
Examples
opal.tokens(opal, df = TRUE)opal.tokens(opal, df = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.tokens(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.tokens(o)
+opal.logout(o)
+}
Examples
opal.unload_package(opal, pkg)opal.unload_package(opal, pkg)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.unload_package(o, 'stats')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.unload_package(o, 'stats')
+opal.logout(o)
+}
Examples
opal.valueset(opal, datasource, table, identifier)opal.valueset(opal, datasource, table, identifier)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.valueset(o, 'CNSIM', 'CNSIM1', '1008573362')
+opal.logout(o)
+}
Examples
opal.variable(opal, datasource, table, variable)opal.variable(opal, datasource, table, variable)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
Examples
opal.variable_summary(
- opal,
- datasource,
- table,
- variable,
- cached = TRUE,
- nature = NULL
-)opal.variable_summary(
+ opal,
+ datasource,
+ table,
+ variable,
+ cached = TRUE,
+ nature = NULL
+)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variable_summary(o, 'CNSIM', 'CNSIM1', 'GENDER')
+opal.logout(o)
+}
Examples
opal.variables(opal, datasource, table, locale = "en", df = TRUE)opal.variables(opal, datasource, table, locale = "en", df = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.variables(o, 'CNSIM', 'CNSIM1')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.variables(o, 'CNSIM', 'CNSIM1')
+opal.logout(o)
+}
Examples
opal.version_compare(opal, version)opal.version_compare(opal, version)Value
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
-opal.version_compare(o, "2.6.0")
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url = 'https://opal-demo.obiba.org')
+opal.version_compare(o, "2.6.0")
+opal.logout(o)
+}
Examples
opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)opal.vocabularies(opal, taxonomy, locale = "en", df = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabularies(o, 'Mlstr_area')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabularies(o, 'Mlstr_area')
+opal.logout(o)
+}
Examples
opal.vocabulary(opal, taxonomy, vocabulary)opal.vocabulary(opal, taxonomy, vocabulary)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.vocabulary(o, 'Mlstr_area', 'Lifestyle_behaviours')
+opal.logout(o)
+}
Examples
opal.workspace_restore(opal, ws)opal.workspace_restore(opal, ws)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_restore(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_restore(o, 'test')
+opal.logout(o)
+}
Examples
opal.workspace_rm(opal, ws, user = NULL)opal.workspace_rm(opal, ws, user = NULL)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspace_rm(o, 'test')
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspace_rm(o, 'test')
+opal.logout(o)
+}
Examples
opal.workspace_save(opal, save = TRUE)opal.workspace_save(opal, save = TRUE)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-# provide a workspace ID
-opal.workspace_save(o, 'test')
-# or use default one
-id <- opal.workspace_save(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+# provide a workspace ID
+opal.workspace_save(o, 'test')
+# or use default one
+id <- opal.workspace_save(o)
+opal.logout(o)
+}
Examples
opal.workspaces(opal)opal.workspaces(opal)See also
Examples
-if (FALSE) {
-o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
-opal.workspaces(o)
-opal.logout(o)
-}
+ if (FALSE) {
+o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
+opal.workspaces(o)
+opal.logout(o)
+}