Merge pull request #138 from nf-osi/develop

Update prod

.github/workflows/update_model_dev.yml

@@ -0,0 +1,52 @@
+name: Update source model for dev
+
+# Update model download_url in `schematic_config.yml`
+# to point to new source URL in `develop` branch. 
+on:
+  # Note: can also run this workflow manually from the Actions tab
+  workflow_dispatch:
+    inputs:
+      source:
+        description: 'URL of new source'     
+        required: true
+
+env:
+  SOURCE_URL: ${{ github.event.inputs.source }}
+
+jobs:
+  update-model:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Check out development branch under $GITHUB_WORKSPACE
+      - uses: actions/checkout@v3
+        with:
+          ref: develop
+          persist-credentials: false
+
+      # Check steps matter more for rare occasions of manual input
+      # vs. programmatic dispatches
+      - name: Check that source link works
+        run: wget $SOURCE_URL -O model.json
+
+      # Check format as can be easy to not grab the actual raw.github URL
+      - name: Check is JSON
+        run: cat model.json | python -m simplejson.tool > validated.json
+
+      - name: Update config
+        uses: mikefarah/yq@master
+        with:
+          cmd: yq -i '.model.input.download_url = strenv(SOURCE_URL)' schematic_config.yml
+
+      - name: Commit files
+        run: |
+          git config user.email "[email protected]"
+          git config user.name "nfosi-service"
+          git commit -m "Update model source in config" -a
+    
+      - name: Push changes
+        uses: ad-m/github-push-action@master
+        with:
+          branch: ${{ github.ref }}
+          github_token: ${{ secrets.SERVICE_TOKEN }}
+

functions/validationResult.R

@@ -65,7 +65,7 @@ validationResult <- function(anno.res, template, manifest) {
 
       # create table to display errors for users
       error_table <- lapply(errors, function(i) {
-        data.frame(Row = as.numeric(i[[1]]), Column = i[[2]], Value = i[[4]][[1]], Error = i[[3]])
+        data.frame(Row = as.numeric(i[[1]]), Column = as.character(i[[2]]), Value = as.character(i[[4]][[1]]), Error = i[[3]])
       }) %>% bind_rows()
 
       # create list for hightlight function; key: error_column, value: error_value
@@ -106,4 +106,4 @@ validationResult <- function(anno.res, template, manifest) {
     errorHighlight = highlight_values,
     errorType = error_type
   ))
-}
+}

schematic_config.yml

@@ -4,25 +4,21 @@ definitions:
   creds_path: 'credentials.json'
   token_pickle: 'token.pickle'
   service_acct_creds: 'schematic_service_account_creds.json'
-
 synapse:
   master_fileview: 'syn16858331'
   manifest_folder: 'manifests'
-  manifest_basename: 'synapse_storage_manifest' 
+  manifest_basename: 'synapse_storage_manifest'
   token_creds: 'syn21088684'
   service_acct_creds: 'syn25171627'
-
 manifest:
   title: 'NF'
-  data_type: 
+  data_type:
     - 'NF'
-
 model:
   input:
-    download_url: 'https://raw.githubusercontent.com/nf-osi/nf-metadata-dictionary/v5.0.0/NF.jsonld' # url to download JSON-LD data model
+    download_url: 'https://raw.githubusercontent.com/nf-osi/nf-metadata-dictionary/v6.1.0/NF.jsonld' # url to download JSON-LD data model
     location: 'data-models/NF.jsonld' # path to JSON-LD data model
-    file_type: 'local' 
-
+    file_type: 'local'
 style:
   google_manifest:
     req_bg_color:

www/config.json

@@ -1,16 +1,23 @@
 {
   "manifest_schemas": [
-      {"display_name": "Genomics Assay", "schema_name": "GenomicsAssayTemplate", "type": "assay"},
+      {"display_name": "Whole Genome Sequencing Assay", "schema_name": "WGSTemplate", "type": "assay"},
+      {"display_name": "Whole Exome Sequencing Assay", "schema_name": "WESTemplate", "type": "assay"},
+      {"display_name": "RNA Sequencing Assay", "schema_name": "RNASeqTemplate", "type": "assay"},
+      {"display_name": "Single-cell RNA Sequencing Assay", "schema_name": "ScRNASeqTemplate", "type": "assay"},
+      {"display_name": "Epigenetics Assay", "schema_name": "EpigeneticsAssayTemplate", "type": "assay"},
       {"display_name": "PDX Genomics Assay", "schema_name": "PdxGenomicsAssayTemplate", "type": "assay"},
+      {"display_name": "Other Genomics Assay", "schema_name": "GenomicsAssayTemplate", "type": "assay"},
+      {"display_name": "Other Genomics Assay (Extended)", "schema_name": "GenomicsAssayTemplateExtended", "type": "assay"},
       {"display_name": "Imaging Assay", "schema_name": "ImagingAssayTemplate", "type": "assay"},
       {"display_name": "MRI Assay", "schema_name": "MRIAssayTemplate", "type": "assay"},
-      {"display_name": "Epigenetics Assay", "schema_name": "EpigeneticsAssayTemplate", "type": "assay"},
       {"display_name": "Pharmacokinetics Assay", "schema_name": "PharmacokineticsAssayTemplate", "type": "assay"},
       {"display_name": "Proteomics Assay", "schema_name": "ProteomicsAssayTemplate", "type": "assay"},
       {"display_name": "Plate-Based Reporter Assay", "schema_name": "PlateBasedReporterAssayTemplate", "type": "assay"},
       {"display_name": "Update Milestone Report Values", "schema_name": "UpdateMilestoneReportTemplate", "type": "assay"},
-      {"display_name": "Patient Metadata (not for annotation)", "schema_name": "PatientTimepointsTemplate", "type": "assay"},
-      {"display_name": "Clinical Assay Template", "schema_name": "ClinicalAssayTemplate", "type": "assay"}
+      {"display_name": "Clinical Assay Template", "schema_name": "ClinicalAssayTemplate", "type": "assay"},
+      {"display_name": "Processed/Aligned Sequencing Reads", "schema_name": "ProcessedAlignedReadsTemplate", "type": "assay"},
+      {"display_name": "Processed Variant Calls", "schema_name": "ProcessedVariantCallsTemplate", "type": "assay"},
+      {"display_name": "Processed Expression Data", "schema_name": "ProcessedExpressionTemplate", "type": "assay"}
     ],
   "main_fileview" : "syn16858331",
   "community" : "NF",