Patch/update image

new_project/Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/nf-osi/nfportalutils:develop-reticulate-1.28
+FROM ghcr.io/nf-osi/nfportalutils@sha256:b16251a7091aebcb8a789589b4adfbcea0fb23b50bbc20031dde8733fce1ac98
 
 ARG USERNAME=nfosi
 ARG USER_UID=1001

new_project/README.md

@@ -8,9 +8,11 @@ See files under tests for examples of what these study data look like.
 
 #### Test
 
+Note that `PROFILE=TEST` skips registration of the newly created study in the public portal. 
+
 Single study:
-`docker run -v "$(pwd)":/app -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN ghcr.io/nf-osi/jobs-new-project tests/study_basic.json`
+`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`
 
 Multiple studies:
-`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`
+`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`
 

new_project/new_project_from_json.R

@@ -5,9 +5,12 @@ configs <- commandArgs(trailingOnly = TRUE)
 library(nfportalutils)
 syn_login()
 
+
+register_check <- Sys.getenv("PROFILE") == "TEST"
 # Note that dataset folders must have unique names (Synapse won't create duplicates)
 # Since this can't be enforced at the JSON schema level, we adjust folder names using `make.unique` as necessary
-setup_from_config <- function(config_file) {
+#' @param register_study Depends on whether PROFILE=TEST. 
+setup_from_config <- function(config_file, skip_register = register_check) {
 
   config <- jsonlite::read_json(config_file)
 
@@ -52,6 +55,17 @@ setup_from_config <- function(config_file) {
     }
   }
 
+  # Non-data -- see schema for allowed resources
+  OTHER_RESOURCES <- NULL
+  if(length(config$nonDataResources)) {
+    resources <- unique(sapply(config$nonDataResources, `[[`, "resourceType"))
+    cat("Non-data resources:", resources, "\n")
+    if(length(resources)) {
+      if(grep("protocol", resources)) OTHER_RESOURCES <- append(OTHER_RESOURCES, "Protocols")
+      if(grep("tool", resources)) OTHER_RESOURCES <- append(OTHER_RESOURCES, "Tools")
+    }
+  }
+
   # Create
   created_project <- new_project(name = NAME,
                                  pi = PI_CSV,
@@ -63,6 +77,7 @@ setup_from_config <- function(config_file) {
                                  initiative = INITIATIVE,
                                  publicview = INITPUBLICVIEW,
                                  datasets = DATASETS,
+                                 other_resources = OTHER_RESOURCES
                                  )
 
   PROJECT_ID <- created_project$properties$id
@@ -79,14 +94,16 @@ setup_from_config <- function(config_file) {
   config$studyName <- config$name
   config$institutions <- config$institution
   config$manifestation <- config$diseaseManifestation
-  nfportalutils::register_study(id = PROJECT_ID,
+
+  if(skip_register) cat("Study not registered since profile detected is TEST", "\n")
+  if(!skip_register) 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)
+  if(!skip_register) nfportalutils::register_study_files(PROJECT_ID)
 
 }
 

new_project/tests/study_other_resources.json

@@ -0,0 +1,47 @@
+{
+  "schemaVersion": "v0.9",
+  "NFID": "Test_Project",
+  "name": "NF Test Study - Other Resources",
+  "summary": "This study has non-data resources included.",
+  "fundingAgency": "NIH-NCI",
+  "initiative": "Developmental and HyperActive Ras Tumor Specialized Programs of Research Excellence",
+  "grantID": "",
+  "grantStartDate": "2020-09-01",
+  "grantEndDate": "2030-08-31",
+  "diseaseFocus": "Neurofibromatosis type 1",
+  "diseaseManifestation": "Plexiform Neurofibroma",
+  "PI": [
+    "John Doe",
+    "Jane Doe"
+  ],
+  "PIEmail": "[email protected]",
+  "dataLead": [
+    "John Doe",
+    "Jane Doe"
+  ],
+  "institution": [
+    "Stanford University",
+    "Harvard University"
+  ],
+  "dataDeposit": [
+    {
+      "dataRelatedAim": "Aim 1",
+      "dataLabel": "ChIP-seq",
+      "dataType": "chromatinActivity",
+      "dataAssay": "ChIP-seq",
+      "dataSpecies": "Homo sapiens"
+    }
+  ],
+  "nonDataResources": [
+    {
+      "relatedAim": "Aim 1",
+      "resourceType": "protocol",
+      "label": "Protocol 1"
+    },
+    {
+        "relatedAim": "Aim 2",
+        "resourceType": "protocol",
+        "label": "Protocol 2"
+    }
+  ]
+}

new_project/tests/study_principals_proliferate.json

@@ -0,0 +1,23 @@
+{
+  "schemaVersion": "v0.9000",
+  "NFID": "Test_Multiple_Principals",
+  "name": "NF Test Study - A Basic Study With Multiple PIs",
+  "summary": "An NF Demo Project with multiple `synPrincipal`s.",
+  "fundingAgency": "Demo",
+  "initiative": "",
+  "grantDOI": "https://doi.org/xxx",
+  "grantStartDate": "2020-01-01",
+  "grantEndDate": "2021-01-01",
+  "embargoEndDate": "2022-10-01",
+  "diseaseFocus": "Neurofibromatosis type 1",
+  "diseaseManifestation": "Behavioral",
+  "PI": "NF Service",
+  "PIEmail": "[email protected]",
+  "dataLead": "NF Service",
+  "dataLeadEmail": "[email protected]",
+  "synPrincipal": ["avu", "anngvu"],
+  "institution": [
+    "Sage Bionetworks"
+  ],
+  "notes": ""
+}