Merge pull request #580 from Sage-Bionetworks/develop

Release 23.11.1

R/schematic_rest_api.R

@@ -21,8 +21,8 @@ check_success <- function(x){
 manifest_download <- function(url = "http://localhost:3001/v1/manifest/download", access_token, asset_view, dataset_id, as_json=TRUE, new_manifest_name=NULL) {
   request <- httr::GET(
     url = url,
+    httr::add_headers(Authorization = sprintf("Bearer %s", access_token)),
     query = list(
-      access_token = access_token,
       asset_view = asset_view,
       dataset_id = dataset_id,
       as_json = as_json,
@@ -61,6 +61,7 @@ manifest_generate <- function(url="http://localhost:3001/v1/manifest/generate",
                               strict_validation = FALSE) {
 
   req <- httr::GET(url,
+                   httr::add_headers(Authorization = sprintf("Bearer %s", access_token)),
                    query = list(
                      schema_url=schema_url,
                      title=title,
@@ -69,7 +70,6 @@ manifest_generate <- function(url="http://localhost:3001/v1/manifest/generate",
                      dataset_id=dataset_id,
                      asset_view=asset_view,
                      output_format=output_format,
-                     access_token = access_token,
                      strict_validation = strict_validation
                    ))
 
@@ -161,12 +161,11 @@ model_submit <- function(url="http://localhost:3001/v1/model/submit",
                          use_schema_label=TRUE, manifest_record_type="table_and_file", file_name,
                          table_manipulation="replace", hide_blanks=FALSE) {
   req <- httr::POST(url,
-                    #add_headers(Authorization=paste0("Bearer ", pat)),
+                    httr::add_headers(Authorization = sprintf("Bearer %s", access_token)),
                     query=list(
                       schema_url=schema_url,
                       data_type=data_type,
                       dataset_id=dataset_id,
-                      access_token=access_token,
                       restrict_rules=restrict_rules,
                       json_str=json_str,
                       asset_view=asset_view,
@@ -230,11 +229,10 @@ storage_project_datasets <- function(url="http://localhost:3001/v1/storage/proje
                                      access_token) {
 
   req <- httr::GET(url,
-                    #add_headers(Authorization=paste0("Bearer ", pat)),
+                   httr::add_headers(Authorization = sprintf("Bearer %s", access_token)),
                     query=list(
                       asset_view=asset_view,
-                      project_id=project_id,
-                      access_token=access_token)
+                      project_id=project_id)
   )
 
   check_success(req)
@@ -254,9 +252,9 @@ storage_projects <- function(url="http://localhost:3001/v1/storage/projects",
                              access_token) {
 
   req <- httr::GET(url,
+                   httr::add_headers(Authorization = sprintf("Bearer %s", access_token)),
                    query = list(
-                     asset_view=asset_view,
-                     access_token=access_token
+                     asset_view=asset_view
                    ))
 
   check_success(req)
@@ -280,13 +278,12 @@ storage_dataset_files <- function(url="http://localhost:3001/v1/storage/dataset/
                                   full_path=FALSE, access_token) {
 
   req <- httr::GET(url,
-                   #add_headers(Authorization=paste0("Bearer ", pat)),
+                   httr::add_headers(Authorization = sprintf("Bearer %s", access_token)),
                    query=list(
                      asset_view=asset_view,
                      dataset_id=dataset_id,
                      file_names=file_names,
-                     full_path=full_path,
-                     access_token=access_token))
+                     full_path=full_path))
   check_success(req)
   httr::content(req)
 
@@ -302,9 +299,9 @@ get_asset_view_table <- function(url="http://localhost:3001/v1/storage/assets/ta
                                  access_token, asset_view, return_type="json") {
 
   req <- httr::GET(url,
+                   httr::add_headers(Authorization = sprintf("Bearer %s", access_token)),
                    query=list(
                      asset_view=asset_view,
-                     access_token=access_token,
                      return_type=return_type))
 
   check_success(req)

global.R

@@ -31,6 +31,8 @@ ncores <- availableCores()
 message(sprintf("Available cores: %s", ncores))
 plan(multicore, workers = ncores)
 
+options(shiny.maxRequestSize=32*1024^2)
+
 # import R files
 source_files <- list.files(c("functions", "modules"), pattern = "*\\.R$", recursive = TRUE, full.names = TRUE)
 sapply(source_files, FUN = source)

server.R

@@ -35,7 +35,7 @@ shinyServer(function(input, output, session) {
   ######## session global variables ########
   # read config in
   if (grepl("dev", dcc_config_file)) {
-    def_config <- fromJSON("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/dev/demo/dca-template-config.json")
+    def_config <- fromJSON("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/dev-old/demo/dca-template-config.json")
   } else if (grepl("staging", dcc_config_file)) {
     def_config <- fromJSON("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/staging/demo/dca-template-config.json")
   } else def_config <- fromJSON("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/main/demo/dca-template-config.json")
@@ -235,7 +235,7 @@ shinyServer(function(input, output, session) {
     if (!file.exists(conf_file())){
       if (grepl("dev", dcc_config_file)) {
         conf_file(
-          file.path("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/dev",
+          file.path("https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/dev-old",
                     conf_file()
           )
         )
@@ -323,6 +323,21 @@ shinyServer(function(input, output, session) {
     shinyjs::enable("btn_template_select")
   })
 
+  observeEvent(input$info_box, {
+
+    nx_report_info(
+      title = sprintf("DCA for %s", dcc_config_react()$project_name),
+      tags$ul(
+        if (!is.na(dcc_config_react()$dca_help_link)) tags$li(tags$a(href = dcc_config_react()$dca_help_link, "DCA Help Docs", target = "_blank")),
+        if (!is.na(dcc_config_react()$portal_help_link)) tags$li(tags$a(href = dcc_config_react()$portal_help_link, "Portal Help Docs", target = "_blank")),
+        if (!is.na(dcc_config_react()$data_model_info)) tags$li(tags$a(href = dcc_config_react()$data_model_info, "Data Model Info", target = "_blank")),
+        tags$li(tags$a(href = paste0("https://www.synapse.org/#!Synapse:", selected$master_asset_view()), paste("Asset View:", selected$master_asset_view()), target = "_blank")),
+        tags$li("DCA version: ", dca_version),
+        tags$li("Schematic version: ", schematic_version),
+      )
+    )
+  })
+
   # Goal of this observer is to get all of the folders within the selected
   # project.
   observeEvent(input$btn_project, {
@@ -631,6 +646,7 @@ shinyServer(function(input, output, session) {
                         p("Try again or contact the DCC for help"),
                         p("For debugging: ", manifest_data())
                       ))
+      hide(selector = "#NXReportButton") # hide OK button so users can't continue
       shinyjs::enable("btn_template_select")
       updateTabsetPanel(session, "tab_template_select")
     } else {
@@ -980,6 +996,7 @@ shinyServer(function(input, output, session) {
                         p("For debugging: ", manifest_id())
                       )
       )
+      hide(selector = "#NXReportButton") # hide OK button so users can't continue
     } else {
       manifest_path <- tags$a(href = paste0("https://www.synapse.org/#!Synapse:", manifest_id()), manifest_id(), target = "_blank")
 

tests/testthat/test_schematic_rest_api.R

@@ -4,7 +4,7 @@ context("test schematic rest api wrappers")
 ### schematic server URL https://github.com/Sage-Bionetworks/schematic/tree/develop/api
 ### If not available, skip these tests.
 
-schematic_url <- "https://schematic.api.sagebionetworks.org"
+schematic_url <- "https://schematic-dev.api.sagebionetworks.org"
 ping <- try(httr::GET(schematic_url), silent = TRUE)
 skip_it <- function(skip=ping) {
   if (inherits(ping, "try-error")) skip(sprintf("schematic server URL unavailable (%s). Is it running locally?", schematic_url)) #nolint
@@ -20,7 +20,7 @@ test_that("manifest_generate returns a URL if sucessful", {
   skip_it()
 
   url <- manifest_generate(url=file.path(schematic_url, "v1/manifest/generate"),
-    schema_url = schema_url, input_token = Sys.getenv("SNYAPSE_PAT"),
+    schema_url = schema_url, access_token = Sys.getenv("SNYAPSE_PAT"),
     title="Test biospecimen", data_type="Biospecimen",
     use_annotations = FALSE,
     dataset_id="syn33715357", asset_view="syn33715412",

ui.R

@@ -107,9 +107,12 @@ ui <- shinydashboardPlus::dashboardPage(
       # add sidebar footer here
       tags$a(
         id = "sidebar_footer", `data-toggle` = "tab",
-        tags$footer(HTML(' Powered by <i class="far fa-heart"></i> and Sage Bionetworks'))
+        tags$footer(
+          actionButton("info_box", "About Data Curator", icon("circle-info"), class="btn-primary-color"),
+          HTML('&#12288 Powered by <i class="far fa-heart"></i> and Sage Bionetworks')
+        )
       )
-    )
+     )
     )
   ),
   dashboardBody(
@@ -120,7 +123,8 @@ ui <- shinydashboardPlus::dashboardPage(
   ),
   uiOutput("sass"),
   # load dependencies
-  use_notiflix_report(width = "400px"),
+  use_notiflix_report(width = "500px", messageMaxLength = 10000,
+                      titleMaxLength = 100),
   use_waiter(),
   tabItems(
   # second tab content
@@ -294,9 +298,6 @@ ui <- shinydashboardPlus::dashboardPage(
   ),
   # waiter loading screen
   dcWaiter("show", landing = TRUE)
-  ),
-  footer = dashboardFooter(
-    left = sprintf("DCA %s - Schematic %s", dca_version, schematic_version)
   )
 )