Ingest to phylogenetic #53
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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://gh.neting.ccmunity/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.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: ${{ vars.AWS_DEFAULT_REGION }} | |
run: | | |
s3_urls=( | |
"s3://nextstrain-data/files/workflows/rabies/metadata.tsv.zst" | |
"s3://nextstrain-data/files/workflows/rabies/sequences.fasta.zst" | |
) | |
# Code below is modified from ingest/upload-to-s3 | |
# https://github.com/nextstrain/ingest/blob/c0b4c6bb5e6ccbba86374d2c09b42077768aac23/upload-to-s3#L23-L29 | |
no_hash=0000000000000000000000000000000000000000000000000000000000000000 | |
for s3_url in "${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-output-sha256sum | |
done | |
- name: Check cache | |
id: check-cache | |
uses: actions/cache@v4 | |
with: | |
path: ingest-output-sha256sum | |
key: ingest-output-sha256sum-${{ hashFiles('ingest-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.yaml | |
secrets: inherit | |
with: | |
image: ${{ inputs.phylogenetic_image }} |