Merge branch 'IDMP-616' of https://github.com/edmcouncil/idmp into ID… #1487
Workflow file for this run
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| # This workflow will run test for IDMP project | |
| name: IDMP Automation Test | |
| 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 | |
| jobs: | |
| IDMP: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Java 11 | |
| uses: actions/setup-java@v3 | |
| with: | |
| distribution: "temurin" | |
| java-version: "11" | |
| cache: "maven" | |
| - name: Install Dependencies & Prepare IDMP Ontologies | |
| run: | | |
| ./etc/unit_tests/dependencies.sh | |
| - name: Run unit tests using Apache Jena | |
| run: | | |
| java -Xmx5G -jar etc/unit_tests/target/unit-test-runner-1.0.jar \ | |
| -ontology_location ./AboutIDMPDev-ReferenceIndividuals.ttl \ | |
| -root_folder etc/unit_tests/ \ | |
| -cq_source etc/CQ/Example/ \ | |
| -config_file configs/idmp_tests_config.yaml | |
| if [ $? != 0 ]; | |
| then | |
| exit $? | |
| fi | |
| - name: Archive merged ontology on failure | |
| uses: actions/upload-artifact@v3 | |
| if: always() | |
| with: | |
| name: merged-ontology | |
| path: AboutIDMPDev-ReferenceIndividuals.ttl | |
| GSRS: | |
| runs-on: ubuntu-latest | |
| env: | |
| GSRS_VERSION: ${{ inputs.gsrs_version || '2022-12-15' }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Java 11 | |
| uses: actions/setup-java@v3 | |
| with: | |
| distribution: "temurin" | |
| java-version: "11" | |
| cache: "maven" | |
| - name: Install Dependencies & Prepare IDMP Ontologies | |
| run: | | |
| ./etc/unit_tests/dependencies.sh | |
| - name: GSRS Cache | |
| id: gsrs-caches | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| gsrs-transformed.ttl | |
| key: gsrs-public-data-${{ 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 $query.rqg" | |
| java -Xmx5G -jar sparql-generate.jar -l INFO -q etc/transformation/GSRS/$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 -Xmx5G -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 |