Patch main-ci workflow (#434)

* Bump schematic testing to 24.4.1

* Refine workflow build commit step

* Update test

* Rebuild NF.jsonld, json

* Use v4 to resolve deprecation notice

* Add another control test manifest

* Update test config with new mock manifest

* Remove restriction GE rules

* Update the new control manifest

---------

Co-authored-by: nf-osi[bot] <[email protected]>

.github/workflows/main-ci.yml

@@ -6,6 +6,7 @@ on:
     branches: [main]
     paths:
       - 'modules/**'
+      - '.github/workflows/main-ci.yml'
 
   workflow_dispatch:
 
@@ -37,12 +38,18 @@ jobs:
           make PortalDataset
           make PortalStudy
     
-      - name: Commit files
+      - name: Commit files if there are changes
         run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "nf-osi[bot]"
-          git add .
-          git commit -m "Rebuild NF.jsonld, json"
+          if [[ $(git diff --exit-code) ]]; then 
+            echo "Changes in src modules affect final jsonld or json artifacts and will be committed"
+            git config --local user.email "[email protected]"
+            git config --local user.name "nf-osi[bot]"
+            git add .
+            git commit -m "Rebuild NF.jsonld, json"
+          else 
+            echo "Changes in src modules did not affect final jsonld or json artifacts"
+            echo "Note that tests will still be run in the next job"
+          fi
     
       - name: Push changes
         uses: ad-m/github-push-action@master
@@ -53,7 +60,7 @@ jobs:
 
   # Additionally test PRs
   test:
-    name: Test with schematic
+    name: Test with schematic current version
     needs: [build]
     runs-on: ubuntu-latest
     env:
@@ -62,7 +69,7 @@ jobs:
       pull-requests: write
     strategy:
       matrix:
-        schematic-version: [24.2.1]
+        schematic-version: [24.4.1]  # cannot actually do parallel/concurrent testing and need to do sequential because of API rate limits
 
     steps:
       - uses: actions/checkout@v4
@@ -80,7 +87,7 @@ jobs:
 
       - name: Sanity-check successful installation and version
         run: pip show schematicpy
-      
+
       - name: Test generate
         working-directory: tests/generate
         continue-on-error: true
@@ -96,17 +103,17 @@ jobs:
       - name: Create test suite report
         working-directory: tests
         continue-on-error: true
-        run: docker run -v $(pwd):/tests rocker/tidyverse R -e "rmarkdown::render('tests/test-suite-report.Rmd')"
+        run: docker run -v $(pwd):/tests -e SCHEMATIC=${{ matrix.schematic-version }} rocker/tidyverse R -e "rmarkdown::render('tests/test-suite-report.Rmd')"
 
       - name: Report on test suite as PR comment
         uses: mshick/add-pr-comment@v2
         with:
-          message-id: test-suite-report
+          message-id: test-suite-report-${{ matrix.schematic-version }}
           message-path: |
             tests/test-suite-report.md
 
       - name: Upload test artifacts
-        uses: actions/upload-artifact@v3
+        uses:  actions/upload-artifact@v4
         with:
           name: test-logs-${{ matrix.schematic-version }}
           path: tests/**/logs

tests/test-suite-report.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "Test Suite Report"
+title: "Test Suite Report `r Sys.getenv('SCHEMATIC')`"
 output:
   github_document:
     html_preview: false

tests/validate/GenomicsAssayTemplate_control.csv

@@ -0,0 +1,5 @@
+Component,Filename,fileFormat,resourceType,dataType,dataSubtype,assay,individualID,species,sex,age,ageUnit,diagnosis,nf1Genotype,nf2Genotype,modelSystemName,parentSpecimenID,specimenID,aliquotID,tumorType,platform,nucleicAcidSource,specimenPreparationMethod,specimenType,runType,libraryStrand,libraryPrep,libraryPreparationMethod,readPair,readLength,readDepth,targetDepth,batchID
+GenomicsAssayTemplate,a,fastq,experimentalData,geneExpression,raw,RNA-seq,A,Homo sapiens,Female,20,years,Neurofibromatosis type 1,,,JHU 2-079-CL,,A1,,Not Applicable,Illumina NovaSeq 6000,,RNAlater,,pairedEnd,FirstStranded,,TruSeq standard total RNA library kit,,150,,,
+GenomicsAssayTemplate,b,fastq,experimentalData,geneExpression,raw,RNA-seq,B,Homo sapiens,Female,20,years,Neurofibromatosis type 1,,,JHU 2-079-CL,,B2,,Not Applicable,Illumina NovaSeq 6000,,RNAlater,,pairedEnd,FirstStranded,,TruSeq standard total RNA library kit,,150,,,
+GenomicsAssayTemplate,c,fastq,experimentalData,geneExpression,raw,RNA-seq,C,Homo sapiens,Female,20,years,Neurofibromatosis type 1,,,JHU 2-079-CL,,C3,,Not Applicable,Illumina NovaSeq 6000,,RNAlater,,pairedEnd,FirstStranded,,TruSeq standard total RNA library kit,,150,,,
+GenomicsAssayTemplate,d,fastq,experimentalData,geneExpression,raw,RNA-seq,D,Homo sapiens,Female,20,years,Neurofibromatosis type 1,,,JHU 2-079-CL,,D4,,Not Applicable,Illumina NovaSeq 6000,,RNAlater,,pairedEnd,FirstStranded,,TruSeq standard total RNA library kit,,150,,,

tests/validate/config.json

@@ -7,6 +7,14 @@
       }
   },
   "tests": [
+    {
+    "manifest": "GenomicsAssayTemplate_control.csv",
+    "template": "GenomicsAssayTemplate",
+    "expect_pass": true,
+    "expectation": "There should be no issue with this template.",
+    "comment": "Optional attributes are filled (sometimes nonsensically just to make sure there's something), in contrast with templates 0-2.",
+    "issue": ["https://github.com/Sage-Bionetworks/schematic/issues/819"]
+    },
     {
       "manifest": "GenomicsAssayTemplate_0.csv",
       "template": "GenomicsAssayTemplate",

tests/validate/run_config.sh

@@ -20,7 +20,7 @@ for i in ${!MANIFESTS[@]}
 do
   echo ">>>>>>> Testing ${MANIFESTS[$i]} "
   schematic model --config config.yml \
-  validate -mp ${MANIFESTS[$i]} -dt ${TEMPLATES[$i]} -rr 2>&1 | tee $LOG_DIR/${MANIFESTS[$i]%.*}.txt
+  validate -mp ${MANIFESTS[$i]} -dt ${TEMPLATES[$i]} 2>&1 | tee $LOG_DIR/${MANIFESTS[$i]%.*}.txt
 done
 
 echo "Cleaning up test fixtures and intermediates..."