Merge branch 'master' of https://github.com/edmcouncil/idmp into IDMP…

…-735

.github/workflows/unit_tests_run.yml

@@ -6,14 +6,6 @@ on:
   push:
   pull_request:
     branches: ["master"]
-  workflow_dispatch:
-    inputs:
-      gsrs_version:
-        description: "GSRS dataset version"
-        required: false
-      gsrs_cache_rebuild:
-        description: "Whether to rebuild cache"
-        required: false
 
 permissions:
   contents: read
@@ -49,64 +41,3 @@ jobs:
         with:
           name: merged-ontology
           path: AboutIDMPDev-ReferenceIndividuals.ttl
-  GSRS:
-    runs-on: ubuntu-latest
-    env:
-      GSRS_VERSION: ${{ inputs.gsrs_version || '2023-12-14' }}
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Java 11
-        uses: actions/setup-java@v4
-        with:
-          distribution: "temurin"
-          java-version: "11"
-          cache: "maven"
-      - name: Install Dependencies & Prepare IDMP Ontologies
-        run: |
-          ./etc/unit_tests/dependencies.sh
-      - name: GSRS Cache
-        id: gsrs-caches
-        uses: actions/cache@v4
-        with:
-          path: |
-            gsrs-transformed.ttl
-          key: gsrs-public-data-${{ env.GSRS_VERSION }}|transformation-files-${{ hashFiles('etc/transformation/GSRS/*.rqg') }}
-      - name: Download and Extract GSRS Version ${{ env.GSRS_VERSION }}
-        if: steps.gsrs-caches.outputs.cache-hit != 'true' || inputs.gsrs_cache_rebuild == 'true'
-        run: |
-          url=https://gsrs.ncats.nih.gov/downloads/dump-public-${{ env.GSRS_VERSION }}.gsrs
-          sudo wget --no-verbose -m -nH -nd -O public_data.gz $url
-          gunzip public_data.gz
-          jq -c -s '.' public_data > public_data.json
-      - name: Transform GSRS
-        if: steps.gsrs-caches.outputs.cache-hit != 'true' || inputs.gsrs_cache_rebuild == 'true'
-        run: |
-          queries=(gsrs-public-data-identifiers gsrs-public-data-names gsrs-public-data-relationships gsrs-public-data-substances)
-          for query in "${queries[@]}"; do
-            echo "Transforming $query.rqg"
-            java -Xmx8G -jar sparql-generate.jar -l INFO -q etc/transformation/GSRS/$query.rqg -o $query.ttl
-          done
-          result=gsrs-transformed.ttl
-          rm -rf $result
-          for query in "${queries[@]}"; do
-            cat $query.ttl >>$result
-          done
-      - name: Combine GSRS with IDMP
-        run: |
-          source_files=(gsrs-transformed.ttl AboutIDMPDev-ReferenceIndividuals.ttl)
-          output_file=gsrs-final.ttl
-          # Loop through the source files and append their contents to the output file
-          for file in "${source_files[@]}"; do
-            cat $file >> $output_file
-          done
-      - name: Run unit tests using Apache Jena
-        run: |
-          java -Xmx8G -jar etc/unit_tests/target/unit-test-runner-1.0.jar \
-            -ontology_location ./gsrs-final.ttl \
-            -root_folder etc/unit_tests/ \
-            -cq_source etc/CQ/Example/ \
-            -config_file configs/gsrs_tests_config.yaml
-          if [ $? != 0 ];
-          then
-          exit $?
-          fi