Ingest to phylogenetic #125
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| name: Ingest to phylogenetic | |
| defaults: | |
| run: | |
| # This is the same as GitHub Action's `bash` keyword as of 20 June 2023: | |
| # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsshell | |
| # | |
| # Completely spelling it out here so that GitHub can't change it out from under us | |
| # and we don't have to refer to the docs to know the expected behavior. | |
| shell: bash --noprofile --norc -eo pipefail {0} | |
| 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 5pm UTC (1pm EDT/10am PDT) since curation by NCBI happens on the East Coast. | |
| # We were running into invalid zip archive errors at 9am PDT, so hoping an hour | |
| # delay will lower the error frequency | |
| - cron: '0 17 * * *' | |
| workflow_dispatch: | |
| inputs: | |
| ingest_image: | |
| description: 'Specific container image to use for ingest workflow (will override the default of "nextstrain build")' | |
| required: false | |
| phylogenetic_image: | |
| description: 'Specific container image to use for phylogenetic workflow (will override the default of "nextstrain build")' | |
| required: false | |
| jobs: | |
| ingest: | |
| permissions: | |
| id-token: write | |
| uses: ./.github/workflows/ingest-ncbi.yaml | |
| secrets: inherit | |
| with: | |
| image: ${{ inputs.ingest_image }} | |
| # Check if ingest results include new data by checking for the cache | |
| # of the file with the results' Metadata.sh256sum (which should have been added within upload-to-s3) | |
| # GitHub will remove any cache entries that have not been accessed in over 7 days, | |
| # so if the workflow has not been run over 7 days then it will trigger phylogenetic. | |
| check-new-data: | |
| needs: [ingest] | |
| runs-on: ubuntu-latest | |
| outputs: | |
| cache-hit: ${{ steps.check-cache.outputs.cache-hit }} | |
| steps: | |
| - name: Get sha256sum | |
| id: get-sha256sum | |
| env: | |
| AWS_DEFAULT_REGION: ${{ vars.AWS_DEFAULT_REGION }} | |
| run: | | |
| segments=( | |
| 'ha' | |
| 'mp' | |
| 'na' | |
| 'np' | |
| 'ns' | |
| 'pa' | |
| 'pb1' | |
| 'pb2' | |
| ) | |
| s3_urls=("s3://nextstrain-data/files/workflows/avian-flu/h5n1/metadata.tsv.zst") | |
| for segment in "${segments[@]}"; do | |
| s3_urls+=("s3://nextstrain-data/files/workflows/avian-flu/h5n1/${segment}/sequences.fasta.zst") | |
| done | |
| # Code below is modified from ingest/upload-to-s3 | |
| # https://github.com/nextstrain/ingest/blob/c0b4c6bb5e6ccbba86374d2c09b42077768aac23/upload-to-s3#L23-L29 | |
| no_hash=0000000000000000000000000000000000000000000000000000000000000000 | |
| for s3_url in "${s3_urls[@]}"; do | |
| s3path="${s3_url#s3://}" | |
| bucket="${s3path%%/*}" | |
| key="${s3path#*/}" | |
| s3_hash="$(aws s3api head-object --no-sign-request --bucket "$bucket" --key "$key" --query Metadata.sha256sum --output text 2>/dev/null || echo "$no_hash")" | |
| echo "${s3_hash}" | tee -a ingest-ncbi-output-sha256sum | |
| done | |
| - name: Check cache | |
| id: check-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ingest-ncbi-output-sha256sum | |
| key: ingest-output-sha256sum-${{ hashFiles('ingest-ncbi-output-sha256sum') }} | |
| lookup-only: true | |
| phylogenetic: | |
| needs: [check-new-data] | |
| if: ${{ needs.check-new-data.outputs.cache-hit != 'true' }} | |
| permissions: | |
| id-token: write | |
| uses: ./.github/workflows/phylogenetic-ncbi.yaml | |
| secrets: inherit | |
| with: | |
| image: ${{ inputs.phylogenetic_image }} |