Fix FDA24 #391
Workflow file for this run
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| name: Autofill & Build | |
| on: | |
| pull_request_target: | |
| branches: [ master ] | |
| jobs: | |
| autofill_and_build: | |
| runs-on: ubuntu-latest | |
| services: | |
| covid-drdb-devdb: | |
| image: postgres:latest | |
| env: | |
| POSTGRES_HOST_AUTH_METHOD: trust | |
| ports: | |
| - 5432:5432 | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| steps: | |
| - name: Checkout payload repository | |
| uses: actions/checkout@v3 | |
| with: | |
| path: covid-drdb-payload | |
| - name: Checkout covid-drdb repository | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: hivdb/covid-drdb | |
| path: covid-drdb | |
| - name: Checkout PR | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| cd covid-drdb-payload | |
| gh pr checkout ${{ github.event.pull_request.number }} | |
| - name: Run autofill-payload | |
| run: | | |
| set -e | |
| cd covid-drdb | |
| docker run --rm -v $GITHUB_WORKSPACE/covid-drdb:/covid-drdb -v $GITHUB_WORKSPACE/covid-drdb-payload:/covid-drdb-payload hivdb/covid-drdb-builder:latest pipenv run python -m drdb.entry autofill-payload /covid-drdb-payload | |
| - name: Validate the results | |
| env: | |
| POSTGRES_PORT: 5432 | |
| POSTGRES_HOST: localhost | |
| run: | | |
| set -e | |
| cd covid-drdb | |
| mkdir -p local/sqls | |
| docker run --rm -v="$(pwd)":/covid-drdb/ -v="$(dirname $(pwd))"/covid-drdb-payload:/covid-drdb/payload hivdb/covid-drdb-builder:latest scripts/export-sqls.sh | |
| psql -v ON_ERROR_STOP=1 -U postgres -h localhost -f local/sqls/01_schema.sql | |
| psql -v ON_ERROR_STOP=1 -U postgres -h localhost -f local/sqls/02_data_tables.sql | |
| psql -v ON_ERROR_STOP=1 -U postgres -h localhost -f local/sqls/03_derived_tables.sql | |
| - name: Check for changes and commit | |
| run: | | |
| git config --global user.name "HIVDB Bot" | |
| git config --global user.email "hivdbteam@stanford.edu" | |
| cd covid-drdb-payload | |
| git add . | |
| git diff --cached --quiet || git commit -m "Autogenerated data updated by HIVDB Bot" | |
| echo "committed=$?" >> $GITHUB_ENV | |
| - name: Push changes | |
| if: env.committed == 0 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| set -e | |
| cd covid-drdb-payload | |
| git remote add headrepo https://${GITHUB_TOKEN}@github.com/${{ github.event.pull_request.head.repo.full_name }}.git | |
| git push headrepo ${{ github.event.pull_request.head.ref }} | |
| gh pr edit ${{ github.event.pull_request.number }} --add-label "autofilled" |