Fix alt dockerfile #362
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| name: Python-Apollo | |
| on: ["push", "pull_request"] | |
| jobs: | |
| test-python-apollo: | |
| name: test-python-apollo | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.9] | |
| steps: | |
| - name: Checkout Apollo | |
| uses: actions/checkout@v2 | |
| - name: Set up JDK 1.8 | |
| uses: actions/setup-java@v1 | |
| with: | |
| java-version: 1.8 | |
| - name: Run Apollo | |
| run: | | |
| cp test/config/python-apollo-config.groovy apollo-config.groovy | |
| date | |
| ./grailsw run-app & | |
| echo "Sleeping here while Apollo builds" | |
| sleep 240 | |
| echo "Done sleeping, I hope it is working" | |
| curl -i 'http://localhost:8080/apollo/annotator/system' | |
| - name: Setup python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Checkout Pypi | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: galaxy-genome-annotation/python-apollo | |
| path: python-apollo | |
| ref: master | |
| - name: Python install | |
| run: | | |
| pwd | |
| cd python-apollo | |
| pip install "setuptools==68.2.2" nose apollo | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Bootstrap | |
| run: | | |
| pwd | |
| echo "Testing if awake" | |
| curl -i 'http://localhost:8080/apollo/annotator/system' | |
| cd python-apollo | |
| pwd | |
| export ARROW_GLOBAL_CONFIG_PATH=`pwd`/test-data/local-apollo2-arrow.yml | |
| echo "Testing arrow command" | |
| arrow users get_users | |
| echo $ARROW_GLOBAL_CONFIG_PATH | |
| ls $ARROW_GLOBAL_CONFIG_PATH | |
| cat $ARROW_GLOBAL_CONFIG_PATH | |
| ./bootstrap_apollo.sh --nodocker | |
| - name: Run tests | |
| run: | | |
| pwd | |
| cd python-apollo | |
| pwd | |
| export ARROW_GLOBAL_CONFIG_PATH=`pwd`/test-data/local-apollo2-arrow.yml | |
| python setup.py nosetests | |
| - uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.gradle/caches | |
| ~/.gradle/wrapper | |
| key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }} | |
| restore-keys: | | |
| ${{ runner.os }}-gradle- | |
| - name: Cache local Maven repository | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.m2/repository | |
| key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-maven- |