Update python-app.yml #14
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| name: OMERO | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| test: | |
| name: Run integration tests against OMERO | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout omero-test-infra | |
| uses: actions/checkout@main | |
| with: | |
| repository: ome/omero-test-infra | |
| path: .omero | |
| - name: Launch OMERO test database | |
| run: .omero/compose up -d | |
| env: | |
| ROOTPASS: omero | |
| POSTGRES_IMAGE: postgres | |
| POSTGRES_VERSION: 10 | |
| POSTGRES_PASSWORD: postgres | |
| OMERO_SERVER_IMAGE: openmicroscopy/omero-server | |
| OMERO_SERVER_VERSION: 5 | |
| OMERO_SERVER_TCP: "4063:" | |
| OMERO_SERVER_SSL: "4064:" | |
| OMERO_WEB_IMAGE: openmicroscopy/omero-web-standalone | |
| OMERO_WEB_VERSION: 5 | |
| OMERO_WEB_PORT: "4080:" | |
| BUILD_IMAGE: adoptopenjdk:11-jdk-hotspot-bionic | |
| - name: checkout arc_omero | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| cache: 'pip' # caching pip dependencies | |
| - name: Build arc_omero | |
| run: | | |
| mkdir bftools | |
| unzip -d ./bftools bftools.zip | |
| wget https://downloads.openmicroscopy.org/bio-formats/7.2.0/artifacts/bftools.zip | |
| pip install --upgrade pip | |
| pip install "omero-cli-transfer @ git+https://github.com/MicheleBortol/omero-cli-transfer.git@omero_arc_importer" | |
| pip install ".[dev]" | |
| - name: Import datasets | |
| run: | | |
| export PATH=$(pwd)/bftools:$PATH | |
| omero login --user root --password omero localhost | |
| omero transfer prepare --plugin arc_omero test/data/arcs/Resolve/assays/ResolveMolecularCartography/dataset | |
| omero transfer unpack --folder test/data/arcs/Resolve/assays/ResolveMolecularCartography/dataset | |
| - name: Run tests | |
| run: | | |
| pip install pytest | |
| - name: Checkout omero-test-infra | |
| uses: actions/checkout@main | |
| with: | |
| repository: ome/omero-test-infra | |
| path: .omero | |
| - name: Stop OMERO test database | |
| run: .omero/compose down |