EVA-3365 Filter by taxonomy when getting active contigs #772
Workflow file for this run
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| name: Run tests | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| # Temporarily run tests on the feature branch until merged to master | |
| branches: [ master, feature/ws-contig-alias-integration ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| mongodb-version: [4.0.18] | |
| java-version: [1.8] | |
| python-version: [3.7] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Setup Java JDK | |
| uses: actions/[email protected] | |
| # The Java version to make available on the path. Takes a whole or semver Java version, or 1.x syntax (e.g. 1.8 => Java 8.x). Early access versions can be specified in the form of e.g. 14-ea, 14.0.0-ea, or 14.0.0-ea.28 | |
| with: | |
| java-version: ${{ matrix.java-version }} | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install numpy pandas psycopg2-binary pgpasslib | |
| - name: Install and Start MongoDB | |
| run: | | |
| wget http://fastdl.mongodb.org/linux/mongodb-linux-x86_64-${{ matrix.mongodb-version }}.tgz | |
| tar xfz mongodb-linux-x86_64-${{ matrix.mongodb-version }}.tgz | |
| export PATH=`pwd`/mongodb-linux-x86_64-${{ matrix.mongodb-version }}/bin:$PATH | |
| mkdir -p data/db | |
| mongod --dbpath=data/db & | |
| mongod --version | |
| - name: Run Maven tests | |
| run: mvn test | |
| - name: Run Python tests | |
| run: | | |
| cd eva-accession-import-automation | |
| python -m tests.test_generate_custom_assembly_report -v |