[Fetch] Please include this pathway figure #18
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| name: Fetch this figure | |
| on: | |
| issues: | |
| types: [labeled] | |
| jobs: | |
| fetch-figure: | |
| if: github.event.label.name == 'fetch' | |
| runs-on: ubuntu-latest | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.issue.number }} | |
| cancel-in-progress: false # to allow multiple runs to queue up rather than clobber | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: '4.2.1' | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libcurl4-openssl-dev | |
| Rscript -e 'install.packages(c("rentrez", "xml2", "httr", "yaml", "stringr"))' | |
| - name: Extract PMCID and Figure Number | |
| id: extract | |
| run: | | |
| # Print raw issue body for debugging | |
| echo "Raw issue body:" | |
| echo "${{ github.event.issue.body }}" | |
| echo "---" | |
| # Clean and normalize the issue body | |
| cleaned_body=$(echo "${{ github.event.issue.body }}" | tr -d '\r' | tr '\n' ' ' | sed 's/[[:space:]]\+/ /g') | |
| echo "Cleaned issue body:" | |
| echo "$cleaned_body" | |
| echo "---" | |
| # Extract PMCID | |
| pmcid=$(echo "$cleaned_body" | sed -n 's/.*### PMCID *\([^ ]*\).*/\1/p') | |
| echo "Extracted PMCID: '$pmcid'" | |
| # Extract Figure Number | |
| figure_number=$(echo "$cleaned_body" | sed -n 's/.*### Figure Number *\([^ ]*\).*/\1/p') | |
| echo "Extracted Figure Number: '$figure_number'" | |
| # Set outputs | |
| echo "pmcid=$pmcid" >> $GITHUB_OUTPUT | |
| echo "figure_number=$figure_number" >> $GITHUB_OUTPUT | |
| - name: Fetch Figure | |
| run: | | |
| Rscript scripts/fetch_THIS_figure_v2.R "${{ steps.extract.outputs.pmcid }}" "${{ steps.extract.outputs.figure_number }}" | |
| - name: Create Pull Request | |
| uses: peter-evans/create-pull-request@v5 | |
| with: | |
| commit-message: Add figure ${{ steps.extract.outputs.pmcid }}_${{ steps.extract.outputs.figure_number }} | |
| title: Add figure ${{ steps.extract.outputs.pmcid }}_${{ steps.extract.outputs.figure_number }} | |
| body: | | |
| This PR adds a new figure: | |
| - PMCID: ${{ steps.extract.outputs.pmcid }} | |
| - Figure Number: ${{ steps.extract.outputs.figure_number }} | |
| branch: add-figure-${{ steps.extract.outputs.pmcid }}-${{ steps.extract.outputs.figure_number }} | |
| delete-branch: true | |
| labels: | | |
| fetch | |
| - name: Close Issue | |
| uses: peter-evans/close-issue@v3 | |
| with: | |
| issue-number: ${{ github.event.issue.number }} | |
| comment: | | |
| A new figure (ID: ${{ steps.fetch_figure.outputs.figid }}) has been fetched and a pull request has been created to add it to the repository. |