Patch/study registration

new_project/Dockerfile

@@ -1,10 +1,10 @@
-FROM ghcr.io/nf-osi/nfportalutils:develop@sha256:103c21eea8c9a2c0e438880f28b03827e4285bc4e71f3141f5fdcf28a6b813ce
+FROM ghcr.io/nf-osi/nfportalutils:develop@sha256:32e4820eb9e5a7aecc51413a796c7d470c215182ffc3f20f3d2148c55de49077
 
 ARG USERNAME=nfosi
 ARG USER_UID=1001
 ARG USER_GID=1000
 
-RUN apt-get update -qq && \
+RUN apt-get update && \
     apt-get install -y jq
 
 # Create the user

new_project/README.md

@@ -1,17 +1,16 @@
 ## New Project
 
-Create new project(s) given study JSON data following the [NF schema](). 
+Create new project(s) based on study data following the [NF study schema](https://github.com/nf-osi/dcc-site/blob/main/lib/study-schema.json). 
 
 ### Examples
 
 See files under tests for examples of what these study data look like.
-For testing, add `-e PROFILE=TEST` when running (see below). This will create the project but register it with the [test fixture Studies table](https://www.synapse.org/#!Synapse:syn27353709/tables/) instead of the production Studies table.
 
 #### Test
 
 Single study:
-`docker run -v "$(pwd)":/app -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN -e PROFILE=TEST ghcr.io/nf-osi/jobs-new-project tests/study_basic.json`
+`docker run -v "$(pwd)":/app -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN ghcr.io/nf-osi/jobs-new-project tests/study_basic.json`
 
 Multiple studies:
-`docker run -v "$(pwd)":/app -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN -e PROFILE=TEST ghcr.io/nf-osi/jobs-new-project tests/study_two_datasets.json tests/study_same_data_labels.json`
+`docker run -v "$(pwd)":/app -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN ghcr.io/nf-osi/jobs-new-project tests/study_two_datasets.json tests/study_same_data_labels.json`
 

new_project/new_project_from_json.R

@@ -43,8 +43,9 @@ setup_from_config <- function(config_file) {
     DATASETS <- make.unique(DATASETS, sep = " ")
     DATASETS <- as.list(DATASETS)
     for(i in seq_along(DATA_DEPOSIT)) {
-      # Set attributes -- note that properties not present resolve to NULL, which is OK 
+      # Set selected attributes -- note that properties not present resolve to NULL, which is OK 
       attr(DATASETS[[i]], "assay") <- DATA_DEPOSIT[[i]]$dataAssay
+      attr(DATASETS[[i]], "dataType") <- DATA_DEPOSIT[[i]]$dataType
       attr(DATASETS[[i]], "description") <- DATA_DEPOSIT[[i]]$dataDescription
       attr(DATASETS[[i]], "progressReportNumber") <- DATA_DEPOSIT[[i]]$dataProgressReportNumber
       attr(DATASETS[[i]], "contentType") <- "dataset"
@@ -67,28 +68,26 @@ setup_from_config <- function(config_file) {
   PROJECT_ID <- created_project$properties$id
   FILEVIEW_ID <- attr(created_project, "fileview")
 
-  # Register
-  STUDY_TABLE_ID <- if(Sys.getenv("PROFILE") == "TEST") "syn27353709" else "syn16787123"
-  nfportalutils::register_study(name = NAME,
-                                project_id = PROJECT_ID,
-                                abstract = SUMMARY, 
-                                lead =  LEAD_CSV,
-                                institution = INSTITUTION, 
-                                focus = FOCUS, 
-                                manifestation = MANIFESTATIONS,
-                                fileview_id = FILEVIEW_ID,
-                                funder = FUNDER,
-                                initiative = INITIATIVE,
-                                grant_doi = GRANT_DOI,
-                                study_table_id = STUDY_TABLE_ID)
-
-  # Add to scope of master portal fileview
-  nfportalutils::register_study_files(PROJECT_ID)
-
   # Write new syn id to config 
   cat("Writing", PROJECT_ID, "to", config_file, "\n")
   command <- paste0('jq \'. += { "studyId" : "',  PROJECT_ID, '" }\' ', config_file, ' > tmp.json && mv tmp.json ' , config_file)
   system(command)
+
+  # Register with some translations
+  config$studyLeads <- config$PI
+  config$studyFileviewId <- FILEVIEW_ID
+  config$studyName <- config$name
+  config$institutions <- config$institution
+  config$manifestation <- config$diseaseManifestation
+  nfportalutils::register_study(id = PROJECT_ID,
+                                study_meta = config,
+                                summary = SUMMARY,
+                                study_summary_table = "syn16787123",
+                                portal_project_view = "syn52677631")
+
+  # Add to scope of master portal fileview
+  nfportalutils::register_study_files(PROJECT_ID)
+
 }
 
 for(config in configs) {