DEVOPS-2101 Update Dockerize Config #34
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| name: Assembly Homology Service tests | |
| on: | |
| pull_request: | |
| types: | |
| - opened | |
| - reopened | |
| - synchronize | |
| - ready_for_review | |
| push: | |
| # run workflow when merging to main or develop | |
| branches: | |
| - main | |
| - master | |
| - develop | |
| jobs: | |
| assembly_homology_tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - java: '8' | |
| mongo: 'mongodb-linux-x86_64-ubuntu2204-7.0.4' | |
| - java: '11' | |
| mongo: 'mongodb-linux-x86_64-ubuntu2004-4.4.29' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up java | |
| uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'temurin' | |
| java-version: ${{matrix.java}} | |
| - name: Install dependencies and set up test config | |
| shell: bash | |
| run: | | |
| export HOMEDIR=`pwd` | |
| # move to parent dir of homedir to install binaries etc | |
| cd .. | |
| # Set up mash | |
| wget https://github.com/marbl/Mash/releases/download/v2.0/mash-Linux64-v2.0.tar | |
| tar -xf mash-Linux64-v2.0.tar | |
| cd mash-Linux64-v2.0 | |
| MP=`pwd` | |
| echo "MASH_PATH=$MP" >> "$GITHUB_ENV" | |
| cd .. | |
| # set up mongo | |
| wget -q http://fastdl.mongodb.org/linux/${{matrix.mongo}}.tgz | |
| tar xfz ${{matrix.mongo}}.tgz | |
| export MONGOD=`pwd`/${{matrix.mongo}}/bin/mongod | |
| # set up test config | |
| cd $HOMEDIR | |
| cp -n test.cfg.example test.cfg | |
| sed -i "s#^test.mongo.exe.*#test.mongo.exe=$MONGOD#" test.cfg | |
| cat test.cfg | |
| - name: Run tests | |
| shell: bash | |
| run: | | |
| PATH=$PATH:$MASH_PATH | |
| echo $PATH | |
| ./gradlew test | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true |