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Caruana 2023

Caruana 2023 #130

Workflow file for this run

name: Prepare autofilled template for library metadata
on:
issue_comment:
types: [created]
jobs:
Autofill:
# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
if: >
contains(github.event.comment.html_url, '/pull/') &&
startsWith(github.event.comment.body, '@spaam-bot please autofill') &&
github.repository == 'SPAAM-community/AncientMetagenomeDir'
runs-on: ubuntu-latest
continue-on-error: true
permissions:
pull-requests: write
env:
PR_NUMBER: ${{ github.event.number }}
steps:
- uses: actions/checkout@v4
with:
## from: https://github.com/actions/checkout/issues/331
ref: ${{ github.event_name == 'issue_comment' && format('refs/pull/{0}/head', github.event.issue.number) }}
# indication that the autofill is being attempted
- name: React on comment
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
with:
comment-id: ${{ github.event.comment.id }}
reactions: eyes
token: ${{ secrets.GITHUB_TOKEN }}
# install AMDirT
- uses: actions/setup-python@v4
with:
python-version: "3.9"
architecture: "x64"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install amdirt==1.6.2
pip install jsonschema==4.17.0
# Get context of PR...
- name: get context
run: |
echo "${{ github.head_ref }}"
echo "${{ github.event.number }}"
tail ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv
git --no-pager log --oneline | head
# Run the autofill script
- name: run autofill
run: |
table=$(echo "${{github.event.comment.body}}" | cut -d ' ' -f 4)
project=$(echo "${{github.event.comment.body}}" | cut -d ' ' -f 5)
bash assets/utility/autofill-wrapper.sh -t $table -p $project 2>&1 | tee autofill-log.txt
- uses: actions/upload-artifact@v4
id: artifact-upload-step
with:
name: autofill-results
path: |
TEMPLATE_*libraries.tsv
autofill-log.txt
# Prepare the results
- name: prepare results
run: |
bash assets/utility/autofill-report.sh -l autofill-log.txt -i ${{ github.run_id }} -u ${{ steps.artifact-upload-step.outputs.artifact-url }}
# Post results
- name: comment PR success
if: always()
uses: mshick/add-pr-comment@v2
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
message-path: autofill-report.md
refresh-message-position: true
# indication that the autofill attempt was completed
- name: React on succesful comment
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
with:
comment-id: ${{ github.event.comment.id }}
reactions: +1
token: ${{ secrets.GITHUB_TOKEN }}