Update avro (#44) #164
Workflow file for this run
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| name: CWL Avro Testing | |
| on: [push] | |
| jobs: | |
| Build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| - name: Set up Python 3.x | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| architecture: 'x64' | |
| # upgrade pip? | |
| - run: sudo pip install --upgrade pip | |
| # install a specific version of the cwl dependencies to test with | |
| - run: pip3.10 install --user importlib-resources==6.1.1 | |
| - run: pip3.10 install --user setuptools==69.0.2 | |
| - run: pip3.10 install --user cwl-runner cwltool==3.1.20230201224320 schema-salad==8.4.20230201194352 | |
| - run: git clone https://github.com/common-workflow-language/common-workflow-language | |
| # convert CWL schema salad CWL to standard Avro json | |
| - run: schema-salad-tool --print-avro common-workflow-language/v1.0/CommonWorkflowLanguage.yml > cwl.avsc | |
| # get rid of invalid avro symbols | |
| - run: sed '/draft-3/d' cwl.avsc > cwl.edited.avsc | |
| - run: sed -i '/draft-2/d' cwl.edited.avsc | |
| - run: sed -i '/draft-4/d' cwl.edited.avsc | |
| - run: sed -i '/dev4/d' cwl.edited.avsc | |
| - run: sed -i '/v1.0/d' cwl.edited.avsc | |
| # Replace the namespace generated by schema-salad-tool with our namespace, "io.cwl.avro" so | |
| # that the generated Java models will have this package name. | |
| - run: sed -i 's/org.w3id.cwl.cwl/io.cwl.avro/g' cwl.edited.avsc | |
| - run: sed -i 's/org.w3id.cwl.salad/io.cwl.avro/g' cwl.edited.avsc | |
| # get rid of symbols that screw up javadoc (not sure if invalid avro schema) | |
| - run: sed -i 's/<A>/A/g' cwl.edited.avsc | |
| - run: sed -i 's/<B>/B/g' cwl.edited.avsc | |
| - run: sed -i 's/<C>/C/g' cwl.edited.avsc | |
| - run: wget https://repo1.maven.org/maven2/org/apache/avro/avro-tools/1.11.3/avro-tools-1.11.3.jar | |
| # generate Java model classes. | |
| - run: java -jar avro-tools-1.11.3.jar compile schema -fieldVisibility public cwl.edited.avsc cwl-temp | |
| - run: find cwl-temp/ -type f -exec sed -i 's/io.cwl.avro.Any/Object/g' {} \; | |
| - run: rm cwl-temp/io/cwl/avro/Any.java | |
| # There are 5 subdirectories in cwl-temp/io/cwl/avro that have the same name as a file | |
| # Fix ArraySchema conflict | |
| - run: mv cwl-temp/io/cwl/avro/ArraySchema cwl-temp/io/cwl/avro/ArraySchemaPackage | |
| - run: find cwl-temp/ -type f -exec sed -i 's/io.cwl.avro.ArraySchema.type/io.cwl.avro.ArraySchemaPackage.type/g' {} \; | |
| # Fix Directory conflict | |
| - run: mv cwl-temp/io/cwl/avro/Directory cwl-temp/io/cwl/avro/DirectoryPackage | |
| - run: find cwl-temp/ -type f -exec sed -i 's/io.cwl.avro.Directory.class\$/io.cwl.avro.DirectoryPackage.class$/g' {} \; | |
| # Fix EnumSchema conflict | |
| - run: mv cwl-temp/io/cwl/avro/EnumSchema cwl-temp/io/cwl/avro/EnumSchemaPackage | |
| - run: find cwl-temp/ -type f -exec sed -i 's/io.cwl.avro.EnumSchema.type/io.cwl.avro.EnumSchemaPackage.type/g' {} \; | |
| # Fix File conflict | |
| - run: mv cwl-temp/io/cwl/avro/File cwl-temp/io/cwl/avro/FilePackage | |
| - run: find cwl-temp/ -type f -exec sed -i 's/io.cwl.avro.File.class\$/io.cwl.avro.FilePackage.class$/g' {} \; | |
| # Fix RecordSchema conflict | |
| - run: mv cwl-temp/io/cwl/avro/RecordSchema cwl-temp/io/cwl/avro/RecordSchemaPackage | |
| - run: find cwl-temp/ -type f -exec sed -i 's/io.cwl.avro.RecordSchema.type/io.cwl.avro.RecordSchemaPackage.type/g' {} \; | |
| # Copy generated java classes | |
| - run: rm -Rf cwlavro-generated/src/main/java/io/cwl/avro | |
| - run: cp -R cwl-temp/io/cwl/avro cwlavro-generated/src/main/java/io/cwl/avro | |
| - run: echo "the output below should show that the generated API more-or-less matches the checked-in API for convenience" | |
| - run: git diff | |
| - name: Set up JDK | |
| uses: actions/setup-java@v4 | |
| with: | |
| java-version: '17.0.4+8' | |
| distribution: 'adopt' | |
| - if: "!contains(github.ref, 'dependabot')" | |
| name: Initialize CodeQL | |
| uses: github/codeql-action/init@v3 | |
| with: | |
| languages: java | |
| - run: mvn -B clean install | |
| - if: "!contains(github.ref, 'dependabot')" | |
| name: Perform CodeQL Analysis | |
| uses: github/codeql-action/analyze@v3 |