DON'T MERGE! Production db not clean #849
Workflow file for this run
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| # name: Qiita CI | |
| on: | |
| push: | |
| branches: [ dev ] | |
| pull_request: | |
| jobs: | |
| # derived from https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml | |
| nonclearDB: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| include: | |
| - cover_package: "qiita_db" | |
| # - cover_package: "qiita_pet qiita_core qiita_ware" | |
| services: | |
| postgres: | |
| # Docker Hub image | |
| image: postgres:13.4 | |
| env: | |
| POSTGRES_DB: postgres | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| COVER_PACKAGE: ${{ matrix.cover_package }} | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| # based on https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml#L44-L72 | |
| - 5432/tcp | |
| steps: | |
| # Downloads a copy of the code in your repository before running CI tests | |
| - name: Check out repository code | |
| uses: actions/checkout@v2 | |
| - name: Setup for conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: '3.9' | |
| - name: Basic dependencies install | |
| env: | |
| COVER_PACKAGE: ${{ matrix.cover_package }} | |
| shell: bash -l {0} | |
| run: | | |
| echo "Testing: " $COVER_PACKAGE | |
| # pull out the port so we can modify the configuration file easily | |
| pgport=${{ job.services.postgres.ports[5432] }} | |
| sed -i "s/PORT = 5432/PORT = $pgport/" qiita_core/support_files/config_test.cfg | |
| # SMJ: set to productive mode! | |
| sed -i "s/TEST_ENVIRONMENT = TRUE/TEST_ENVIRONMENT = FALSE/" qiita_core/support_files/config_test.cfg | |
| # PGPASSWORD is read by pg_restore, which is called by the build_db process. | |
| export PGPASSWORD=postgres | |
| # Setting up main qiita conda environment | |
| conda config --add channels conda-forge | |
| conda deactivate | |
| conda create --quiet --yes -n qiita python=3.9 pip libgfortran numpy nginx cython redis | |
| conda env list | |
| conda activate qiita | |
| pip install -U pip | |
| pip install sphinx sphinx-bootstrap-theme nose-timer Click coverage | |
| # Configuring SSH | |
| cp /etc/ssh/sshd_config sshd_config | |
| echo "RSAAuthentication yes" > sshd_config | |
| echo "PubkeyAuthentication yes" > sshd_config | |
| echo "StrictModes no" > sshd_config | |
| sudo mv sshd_config /etc/ssh/sshd_config | |
| sudo systemctl restart ssh | |
| - name: Webdis install | |
| shell: bash -l {0} | |
| run: | | |
| sudo apt-get -y install libevent-dev | |
| git clone https://github.com/nicolasff/webdis | |
| cd webdis | |
| make | |
| - name: Main install | |
| shell: bash -l {0} | |
| run: | | |
| conda activate qiita | |
| export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt | |
| export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg | |
| export REDBIOM_HOST="http://localhost:7379" | |
| pip install . --no-binary redbiom | |
| # 10.2022 | |
| # this is for redbiom / biom-format (so fine to delete in the future) | |
| pip install future | |
| pwd | |
| mkdir ~/.qiita_plugins | |
| # SMJ: don't install any plugins! ~/.qiita_plugins directory should remain empty | |
| - name: Starting services | |
| shell: bash -l {0} | |
| run: | | |
| conda activate qiita | |
| export QIITA_ROOTCA_CERT=`pwd`/qiita_core/support_files/ci_rootca.crt | |
| export QIITA_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg | |
| export REDBIOM_HOST="http://localhost:7379" | |
| echo "1. Setting up redis" | |
| redis-server --daemonize yes --port 7777 | |
| redis-server --daemonize yes --port 6379 | |
| echo "2. Starting webdis" | |
| pushd webdis | |
| ./webdis & | |
| popd | |
| echo "3. Starting redbiom: " $REDBIOM_HOST | |
| curl -s http://localhost:7379/FLUSHALL > /dev/null | |
| redbiom --version | |
| redbiom admin scripts-writable | |
| redbiom admin create-context --name "qiita-test" --description "qiita-test context" | |
| redbiom admin load-sample-metadata --metadata `pwd`/qiita_db/support_files/test_data/templates/1_19700101-000000.txt | |
| redbiom admin load-sample-metadata-search --metadata `pwd`/qiita_db/support_files/test_data/templates/1_19700101-000000.txt | |
| redbiom admin load-sample-data --table `pwd`/qiita_db/support_files/test_data/processed_data/1_study_1001_closed_reference_otu_table.biom --context qiita-test --tag 4 | |
| redbiom admin load-sample-data --table `pwd`/qiita_db/support_files/test_data/processed_data/1_study_1001_closed_reference_otu_table-for_redbiom_tests.biom --context qiita-test --tag 5 | |
| echo "4. Setting up nginx" | |
| mkdir -p /usr/share/miniconda/envs/qiita/var/run/nginx/ | |
| nginx -c ${PWD}/qiita_pet/nginx_example.conf | |
| echo "5. Setting up qiita" | |
| conda activate qiita | |
| # adapt environment_script for private qiita plugins from travis to github actions. | |
| sed 's#export PATH="/home/travis/miniconda3/bin:$PATH"; source #source /home/runner/.profile; conda #' -i qiita_db/support_files/patches/54.sql | |
| qiita-env make #--no-load-ontologies | |
| PGPASSWORD=postgres psql -U postgres --host=localhost --port=32768 -d qiita_test -c "SELECT * FROM qiita.software;" | |
| PGPASSWORD=postgres psql -U postgres --host=localhost --port=32768 -d qiita_test -c "SELECT * FROM qiita.default_workflow;" | |