Merge pull request #284 from vimc/mrc-2337

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: orderly
 Title: Lightweight Reproducible Reporting
-Version: 1.2.38
+Version: 1.2.39
 Description: Order, create and store reports from R.  By defining a
     lightweight interface around the inputs and outputs of an
     analysis, a lot of the repetitive work for reproducible research

NAMESPACE

@@ -50,5 +50,4 @@ export(orderly_use_gitignore)
 export(orderly_use_package)
 export(orderly_use_resource)
 export(orderly_use_source)
-export(orderly_workflow)
 importFrom(R6,R6Class)

NEWS.md

@@ -1,3 +1,7 @@
+# orderly 1.2.39
+
+* Remove `orderly_workflow` in favour of supporting workflows through orderly.server (mrc-2275)
+
 # orderly 1.2.38
 
 * Much clearer error message where dependency resolution fails due to a query dependency (vimc-4499)

R/db2.R

@@ -8,7 +8,7 @@
 ## namespace/module feature so that implementation details can be
 ## hidden away a bit further.
 
-orderly_schema_version <- "1.2.34"
+orderly_schema_version <- "1.2.39"
 orderly_schema_table <- "orderly_schema"
 orderly_table_list <- "orderly_schema_tables"
 
@@ -429,16 +429,13 @@ report_data_import <- function(con, name, id, config) {
 
   if (!is.null(dat_rds$meta$workflow)) {
     sql_batch <- "SELECT id FROM workflow WHERE id = $1"
-    if (nrow(DBI::dbGetQuery(con, sql_batch, dat_rds$meta$workflow$id)) == 0L) {
-      workflow <- data_frame(
-        id = dat_rds$meta$workflow$id,
-        name = dat_rds$meta$workflow$name
-      )
+    if (nrow(DBI::dbGetQuery(con, sql_batch, dat_rds$meta$workflow)) == 0L) {
+      workflow <- data_frame(id = dat_rds$meta$workflow)
       DBI::dbWriteTable(con, "workflow", workflow, append = TRUE)
     }
     report_version_workflow <- data_frame(
       report_version = id,
-      workflow_id = dat_rds$meta$workflow$id
+      workflow_id = dat_rds$meta$workflow
     )
     DBI::dbWriteTable(con, "report_version_workflow", report_version_workflow,
                       append = TRUE)

R/main.R

@@ -30,10 +30,6 @@ cli_args_process <- function(args) {
     dat$options$parameters <- cli_args_process_batch_parameters(
       dat$options$parameter, dat$options$file)
     dat$options$name <- dat$options[["<name>"]] # docopt bug?
-  } else if (dat$command == "workflow") {
-    dat$options$parameters <- cli_args_process_run_parameters(
-      dat$options$parameter)
-    dat$options$name <- dat$options[["<name>"]] # docopt bug?
   }
 
   dat
@@ -55,8 +51,7 @@ Commands:
   cleanup      Remove drafts and dangling data
   rebuild      Rebuild the database
   migrate      Migrate the archive
-  batch        Run a batch of reports
-  workflow     Run a workflow"
+  batch        Run a batch of reports"
 
 cli_args_preprocess <- function(args) {
   ## This will work ok for filtering away unwanted arguments *if* the
@@ -144,14 +139,15 @@ usage_run <- "Usage:
   orderly run [options] <name> [<parameter>...]
 
 Options:
-  --instance=NAME  Database instance to use (if instances are configured)
-  --no-commit      Do not commit the report
-  --print-log      Print the log (rather than storing it)
-  --id-file=FILE   File to write the id into
-  --ref=REF        Git reference (branch or sha) to use
-  --fetch          Fetch git before updating reference
-  --pull           Pull git before running report
-  --message=TEXT   A message explaining why the report was run
+  --instance=NAME     Database instance to use (if instances are configured)
+  --no-commit         Do not commit the report
+  --print-log         Print the log (rather than storing it)
+  --id-file=FILE      File to write the id into
+  --ref=REF           Git reference (branch or sha) to use
+  --fetch             Fetch git before updating reference
+  --pull              Pull git before running report
+  --message=TEXT      A message explaining why the report was run
+  --workflow-id=TEXT  The ID of the workflow this report is run as part of
 
 Parameters, if given, must be passed through in key=value pairs"
 
@@ -176,6 +172,7 @@ main_do_run <- function(x) {
   fetch <- x$options$fetch
   pull <- x$options$pull
   message <- x$options$message
+  workflow_id <- x$options$workflow_id
 
   if (print_log) {
     sink(stderr(), type = "output")
@@ -188,7 +185,8 @@ main_do_run <- function(x) {
   id <- orderly_run_internal(name, parameters, root = config,
                              id_file = id_file, instance = instance,
                              ref = ref, fetch = fetch, message = message,
-                             commit = commit, capture_log = !print_log)
+                             commit = commit, capture_log = !print_log,
+                             workflow_id = workflow_id)
   message("id:", id)
 }
 
@@ -387,49 +385,6 @@ main_do_batch <- function(x) {
   message("ids:", paste(ids, collapse = ", "))
 }
 
-## 9. workflow
-usage_workflow <- "Usage:
-  orderly workflow [options] <name> [<parameter>...]
-
-Options:
-  --print-log      Print the log (rather than storing it)
-  --ref=REF        Git reference (branch or sha) to use
-  --pull           Pull git before running report
-  --instance=NAME  Database instance to use (if instances are configured)
-  --message=TEXT   A message explaining why the workflow was run
-
-Parameters, if given, must be passed through in key=value pairs"
-
-main_do_workflow <- function(x) {
-  ## TODO: Get some classed errors though here and then write out
-  ## information about whether or not things worked and why they
-  ## didn't.  Possible issues (in order)
-  ##
-  ## * orderly report not found
-  ## * error while preparing (e.g., package not found)
-  ## * error while running report
-  ## * error checking artefacts
-  config <- orderly_config(x$options$root, TRUE)
-  name <- x$options$name
-  instance <- x$options$instance
-  print_log <- x$options$print_log
-  ref <- x$options$ref
-  pull <- x$options$pull
-  message <- x$options$message
-
-  if (print_log) {
-    sink(stderr(), type = "output")
-    on.exit(sink(NULL, type = "output"))
-  } else {
-    config$add_run_option("capture_log", TRUE)
-  }
-
-  git_pull_ref(pull, ref, config, message = "Can't use --pull with --ref.")
-
-  output <- orderly_workflow_internal(name, root = config, instance = instance,
-                                      message = message, ref = ref)
-  message("ids:", paste(output, collapse = ", "))
-}
 
 write_script <- function(path, versioned = FALSE) {
   if (!isTRUE(is_directory(path))) {
@@ -476,10 +431,7 @@ cli_commands <- function() {
                       target = main_do_migrate),
        batch = list(name = "batch run reports",
                       usage = usage_batch,
-                      target = main_do_batch),
-       workflow = list(name = "run workflow",
-                       usage = usage_workflow,
-                       target = main_do_workflow))
+                      target = main_do_batch))
 }
 
 

R/orderly_version.R

@@ -8,7 +8,7 @@ orderly_version <- R6::R6Class(
 
     id = NULL,
     batch_id = NULL,
-    workflow_info = NULL,
+    workflow_id = NULL,
     workdir = NULL,
 
     envvar = NULL,
@@ -354,7 +354,7 @@ orderly_version <- R6::R6Class(
            tags = private$tags,
            git = private$preflight_info$git,
            batch_id = private$batch_id,
-           workflow = private$workflow_info,
+           workflow = private$workflow_id,
            data = private$postflight_info$data_info,
            view = private$postflight_info$view_info)
     },
@@ -423,7 +423,7 @@ orderly_version <- R6::R6Class(
                             use_draft = FALSE, remote = NULL,
                             ## These might move around a bit
                             id_file = NULL, batch_id = NULL,
-                            workflow_info = NULL, ref = NULL, fetch = FALSE,
+                            workflow_id = NULL, ref = NULL, fetch = FALSE,
                             capture_log = FALSE) {
       logfile <- tempfile()
       capture_log <- capture_log %||%
@@ -441,7 +441,7 @@ orderly_version <- R6::R6Class(
                               path_orderly_log(private$workdir)))
           }
           private$batch_id <- batch_id
-          private$workflow_info <- workflow_info
+          private$workflow_id <- workflow_id
           private$fetch()
           self$run_execute(echo)
           self$run_cleanup()

R/paths.R

@@ -48,10 +48,6 @@ path_orderly_envir_yml <- function(path) {
   file.path(path, "orderly_envir.yml")
 }
 
-path_orderly_workflow_dir <- function(path, workflow_name) {
-  file.path(path, "workflows", paste0(workflow_name, ".yml"))
-}
-
 path_orderly_log <- function(path) {
   file.path(path, "orderly.log")
 }

R/recipe_run.R

@@ -128,13 +128,13 @@ orderly_run_internal <- function(name = NULL, parameters = NULL, envir = NULL,
                                  remote = NULL, tags = NULL,
                                  # specific to run_internal
                                  id_file = NULL, batch_id = NULL,
-                                 workflow_info = NULL, fetch = FALSE,
+                                 workflow_id = NULL, fetch = FALSE,
                                  ref = NULL, capture_log = NULL,
                                  commit = FALSE) {
   version <- orderly_version$new(name, root, locate)
   id <- version$run_internal(parameters, instance, envir, message, tags, echo,
                              use_draft, remote, id_file, batch_id,
-                             workflow_info, ref, fetch, capture_log)
+                             workflow_id, ref, fetch, capture_log)
   if (commit) {
     version$commit(capture_log)
   }

inst/database/schema.yml

@@ -253,7 +253,6 @@ report_version_batch:
 workflow:
   columns:
     - id: {type: TEXT}
-    - name: {type: TEXT}
 
 report_version_workflow:
   columns: