DB Refresh (Objects API) #31312
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| name: DB Refresh (Objects API) | |
| on: | |
| schedule: | |
| # - cron: '0 5 * * *' # every day 5am GMT (12/1am EST/EDT) | |
| - cron: '*/20 * * * *' # every 20 minutes | |
| # - cron: '0 * * * *' # every hour on the hour | |
| workflow_dispatch: | |
| inputs: | |
| since: | |
| # A timestamp by which new data should be fetched. If not present, will look up the last time the DB was | |
| # refreshed and fetch new data from that time. Valid formats: | |
| # - Simple date timestamp, YYYY-MM-DD, e.g. 2022-02-22. | |
| # - ISO 8601 datetime with timezone offset, YYYY-MM-DDTHH:MM:SS.SSSSSS+HH:MM, e.g. 2022-02-22T22:22:22.222222+00:00. | |
| description: 'Optional: YYYY-MM-DD or YYYY-MM-DDTHH:MM:SS.SSSSSS+HH:MM' | |
| required: false | |
| type: string | |
| cset-ids: | |
| # Space-delimited list of integers representing codeset IDs | |
| description: 'Optional: Space-delimited list of integers representing codeset IDs' | |
| required: false | |
| type: string | |
| repository_dispatch: | |
| types: [refresh-db] | |
| jobs: | |
| refresh-db: | |
| # runs-on: ubuntu-18.04 | |
| runs-on: ubuntu-latest | |
| steps: | |
| # Set up | |
| - name: Checkout repository and submodules | |
| uses: actions/checkout@v2 | |
| - name: Set up Python version | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.10' | |
| - name: Print commit hash & branch for rollbacks & troubleshooting | |
| run: | | |
| echo "Commit hash: ${{ github.sha }}" | |
| echo "Branch: ${{ github.ref }}" | |
| - name: 'Create env file' | |
| run: | | |
| mkdir env | |
| echo "${{ secrets.ENV_FILE }}" > env/.env | |
| - name: Create and start virtual environment | |
| run: | | |
| python3 -m venv venv | |
| source venv/bin/activate | |
| - name: Install dependencies | |
| run: | | |
| # Reactivate install upgrades of pip, wheel, &/or setuptools if needed | |
| # python -m pip install --upgrade pip | |
| # pip install --upgrade wheel | |
| # pip install --upgrade setuptools | |
| # VS Hub SDK w/ OAuth disabled: https://github.com/jhu-bids/TermHub/issues/863 | |
| # TOKEN=$(grep '^PALANTIR_ENCLAVE_AUTHENTICATION_BEARER_TOKEN=' env/.env | cut -d'=' -f2) | |
| # python3 -m pip install vshub_sdk --upgrade --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.artifacts.main.repository.9bc9cc56-4b8c-4560-9bfb-fba8ade55246/contents/release/pypi/simple" --extra-index-url "https://:${TOKEN}@unite.nih.gov/artifacts/api/repositories/ri.foundry-sdk-asset-bundle.main.artifacts.repository/contents/release/pypi/simple" | |
| pip install -r requirements.txt | |
| # Refresh | |
| - name: Refresh db | |
| run: | | |
| if [ -n "${{ github.event.inputs.cset-ids }}" ] && [ -n "${{ github.event.inputs.since }}" ]; then | |
| echo "Error: Both 'cset-ids' and 'since' were provided. These inputs are mutually exclusive." | |
| exit 1 | |
| elif [ -n "${{ github.event.inputs.cset-ids }}" ]; then | |
| python backend/db/refresh.py --cset-ids ${{ github.event.inputs.cset-ids }} | |
| elif [ -n "${{ github.event.inputs.since }}" ]; then | |
| python backend/db/refresh.py --since ${{ github.event.inputs.since }} | |
| else | |
| python backend/db/refresh.py | |
| fi | |
| - name: Commit changes to documentation | |
| uses: stefanzweifel/git-auto-commit-action@v4 | |
| with: | |
| commit_message: Updating documentation in docs/backend/db/analysis.md | |
| # fetch-missing-csets: Deactivated because various tweaks and default re-refresh buffer solve this problem, and | |
| # also test-missing-csets is there as a redundancy. Original context: | |
| # https://github.com/jhu-bids/TermHub/issues/573 https://github.com/jhu-bids/TermHub/issues/574 | |
| # - name: Fetch missing csets | |
| # run: make fetch-missing-csets | |
| # Test | |
| # todo: add more tests, ideally | |
| - name: Test missing csets | |
| run: make test-missing-csets |