unify data_source keyword, and return organism for images #368
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| name: Build | |
| on: | |
| push: | |
| tags: | |
| branches: | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| services: | |
| postgres: | |
| image: postgres:16 | |
| env: | |
| POSTGRES_USER: postgress | |
| POSTGRES_PASSWORD: passwprd | |
| POSTGRES_DB: postgress | |
| max_wal_size: 4GB | |
| ports: | |
| - 5432/tcp | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| elasticsearch: | |
| image: elasticsearch:8.8.1 | |
| ports: | |
| - 9200/tcp | |
| env: | |
| es_api_basic_auth_username: "elastic" | |
| ELASTIC_PASSWORD: "elasticsearch_user_password" | |
| options: -e="discovery.type=single-node" --health-cmd="curl -k -u elastic:elasticsearch_user_password https://localhost:9200/_cluster/health" --health-interval=10s --health-timeout=5s --health-retries=10 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| #test the app before bulding the image | |
| - name: Install dependencies and test | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt; | |
| # Configure database url | |
| python manage.py set_database_configuration -u localhost -s ${{ job.services.postgres.ports[5432] }} -n postgress -p passwprd -w omero1 -d omero -b omero.pgdump | |
| export PGPASSWORD=passwprd; | |
| echo $PGPASSWORD | |
| psql -h localhost -U postgress -p ${{ job.services.postgres.ports[5432] }} -c 'CREATE DATABASE omero' | |
| # configure elasticsearch | |
| python manage.py set_elasticsearch_configuration -e localhost:${{ job.services.elasticsearch.ports[9200] }} | |
| # download and extract the database backup file | |
| wget https://downloads.openmicroscopy.org/images/omero_db_searchengine.zip -P app_data | |
| unzip app_data/omero_db_searchengine.zip -d app_data/ | |
| # run restore omero database | |
| python manage.py restore_postgresql_database | |
| # run indexing indexing | |
| python manage.py get_index_data_from_database -b False | |
| # set up the seond database | |
| rm app_data/omero_db_searchengine.zip | |
| rm app_data/omero.pgdump | |
| wget https://github.com/khaledk2/ice-archh-64/releases/download/new_re_db/omero_train.zip -P app_data | |
| unzip app_data/omero_train.zip -d app_data/ | |
| rm app_data/omero_train.zip | |
| python manage.py set_database_configuration -u localhost -s ${{ job.services.postgres.ports[5432] }} -n postgress -p passwprd -w omero_train -d omero_train -b omero_train.pgdump | |
| echo $PGPASSWORD | |
| psql -h localhost -U postgress -p ${{ job.services.postgres.ports[5432] }} -c 'CREATE DATABASE omero_train' | |
| python manage.py restore_postgresql_database -s omero_train | |
| python manage.py get_index_data_from_database -b False -s omero_train | |
| rm app_data/omero_train.pgdump | |
| # run tests | |
| python -m unittest discover -s unit_tests | |
| upload: | |
| needs: build | |
| if: startsWith(github.ref, 'refs/tags') | |
| runs-on: ubuntu-latest | |
| env: | |
| name: openmicroscopy/omero-searchengine | |
| steps: | |
| - name: Get prefix | |
| id: getprefix | |
| run: | | |
| if [ ! -z ${{ env.name }} ]; then | |
| echo "prefix=${{ env.name }}:" >> $GITHUB_OUTPUT | |
| else | |
| echo "prefix=${{ github.repository }}:" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Get other tags | |
| id: gettags | |
| uses: jupyterhub/[email protected] | |
| with: | |
| githubToken: ${{ secrets.GITHUB_TOKEN }} | |
| prefix: "${{ steps.getprefix.outputs.prefix }}" | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v1 | |
| - uses: actions/checkout@v2 | |
| - name: Login to DockerHub | |
| uses: docker/login-action@v1 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| - name: display docker account | |
| run: echo ${{ secrets.DOCKER_LOGIN }} | |
| - name: Build and push | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: . | |
| file: deployment/docker/rockylinux/Dockerfile | |
| push: true | |
| tags: ${{ join(fromJson(steps.gettags.outputs.tags)) }} |