Fetch pathway figures and metadata from date range #1
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| name: Fetch pathway figures and metadata from date range | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "0 1-7 1-3 1,4,7,10 *" # For 9PM-3AM ET (1-7 AM UTC), for the first 3 days of every Jan, Apr, Jul, Oct. | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.head_ref || github.ref }} | |
| cancel-in-progress: false # to allow multiple runs to queue up rather than clobber | |
| jobs: | |
| check: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| status: ${{ steps.early.outputs.status }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - id: early | |
| name: Date check | |
| run: | | |
| last_run_date=$(sed -n 's/^last_run:[[:space:]]*\([[:digit:]]\{4\}\/[[:digit:]]\{2\}\/[[:digit:]]\{2\}\).*$/\1/p' query_config.yml) | |
| today_date="$(date +'%Y/%m/%d')" | |
| if [[ "$last_run_date" < "$today_date" ]]; then | |
| echo "status=proceed" >> $GITHUB_OUTPUT | |
| else | |
| echo "status=quit" >> $GITHUB_OUTPUT | |
| echo "Nothing more to collect at this time (see last_run date). Skipping other steps..." | |
| fi | |
| scrape: | |
| needs: check | |
| if: ${{needs.check.outputs.status == 'proceed' }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Install Packages | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libcurl4-openssl-dev | |
| Rscript -e 'install.packages(c("rentrez", "xml2", "httr", "yaml", "stringr", "lubridate"))' | |
| - name: Run R Script to Fetch Figures | |
| run: Rscript scripts/fetch_figures_v2.R || true #commit files even if R crashes | |
| - name: Commit, pull with rebase (any remote changes during this run), and then push | |
| run: | | |
| git config --global user.name 'GitHub Action' | |
| git config --global user.email '[email protected]' | |
| git add . | |
| if git diff --exit-code --staged; then | |
| echo "No changes" | |
| else | |
| git commit -m 'new figures from pmc; updated config and log' | |
| git pull --rebase | |
| git push --force-with-lease | |
| fi | |