Fetch and ingest #158
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| name: Fetch and ingest | |
| on: | |
| schedule: | |
| # Note times are in UTC, which is 1 or 2 hours behind CET depending on daylight savings. | |
| # | |
| # Note the actual runs might be late. | |
| # Numerous people were confused, about that, including me: | |
| # - https://github.community/t/scheduled-action-running-consistently-late/138025/11 | |
| # - https://github.com/github/docs/issues/3059 | |
| # | |
| # Note, '*' is a special character in YAML, so you have to quote this string. | |
| # | |
| # Docs: | |
| # - https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows#schedule | |
| # | |
| # Tool that deciphers this particular format of crontab string: | |
| # - https://crontab.guru/ | |
| # | |
| # Runs at 4pm UTC (12pm EDT) since curation by NCBI happens on the East Coast. | |
| - cron: '0 16 * * 2' | |
| repository_dispatch: | |
| types: | |
| - fetch-and-ingest | |
| # Manually triggered using GitHub's UI | |
| workflow_dispatch: | |
| inputs: | |
| trial_name: | |
| description: 'Short name for a trial run. WARNING: without this we will overwrite files in s3://nextstrain-data/files/workflows/rsv' | |
| jobs: | |
| set_config_overrides: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - id: s3_dst | |
| run: | | |
| S3_DST=s3://nextstrain-data/files/workflows/rsv | |
| if [[ -n "$TRIAL_NAME" ]]; then | |
| S3_DST+=/trial/"$TRIAL_NAME" | |
| fi | |
| echo "s3_dst=$S3_DST" >> "$GITHUB_OUTPUT" | |
| env: | |
| TRIAL_NAME: ${{ inputs.trial_name }} | |
| - id: trigger_rebuild | |
| run: | | |
| TRIGGER_REBUILD=true | |
| if [[ -n "$TRIAL_NAME" ]]; then | |
| TRIGGER_REBUILD=false | |
| fi | |
| echo "trigger_rebuild=$TRIGGER_REBUILD" >> "$GITHUB_OUTPUT" | |
| outputs: | |
| s3_dst: ${{ steps.s3_dst.outputs.s3_dst }} | |
| trigger_rebuild: ${{ steps.trigger_rebuild.outputs.trigger_rebuild }} | |
| fetch-and-ingest: | |
| needs: [set_config_overrides] | |
| permissions: | |
| id-token: write | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
| secrets: inherit | |
| with: | |
| runtime: aws-batch | |
| run: | | |
| nextstrain build \ | |
| --aws-batch \ | |
| --detach \ | |
| --no-download \ | |
| --cpus 8 \ | |
| --memory 32gib \ | |
| --env PAT_GITHUB_DISPATCH="$GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH" \ | |
| --env S3_DST \ | |
| --env TRIGGER_REBUILD \ | |
| ingest \ | |
| --configfiles config/config.yaml config/optional.yaml \ | |
| --config s3_dst="$S3_DST" trigger_rebuild="$TRIGGER_REBUILD" \ | |
| --printshellcmds | |
| env: | | |
| S3_DST: ${{ needs.set_config_overrides.outputs.s3_dst }} | |
| TRIGGER_REBUILD: ${{ needs.set_config_overrides.outputs.trigger_rebuild }} |