Harvest from CrossRef by ROR #317
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| name: Harvest from CrossRef by ROR | |
| on: | |
| schedule: | |
| - cron: '0 15 * * 1-5' | |
| workflow_dispatch: | |
| inputs: | |
| reason: | |
| description: 'Reason' | |
| required: false | |
| default: 'Manual trigger' | |
| jobs: | |
| get-crossref: | |
| runs-on: ubuntu-24.04 | |
| outputs: | |
| dois: ${{ steps.harvest.outputs.dois }} | |
| message: ${{ steps.harvest.outputs.message }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Python Deps | |
| shell: bash | |
| run: pip install -r requirements.txt --break-system-packages | |
| - name: Harvest DOIs | |
| shell: bash | |
| id: harvest | |
| run: python harvest.py crossref -print >> $GITHUB_OUTPUT | |
| - name: Commit and Push Changes | |
| id: commit-and-push | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: 'Update run date' | |
| prepare-dois: | |
| name: Prepare Matrix Output of DOIs | |
| needs: [get-crossref] | |
| runs-on: ubuntu-24.04 | |
| outputs: | |
| dois: ${{ steps.step1.outputs.matrix }} | |
| env: | |
| DOI: ${{ needs.get-crossref.outputs.dois }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Process DOIs | |
| shell: bash | |
| run: python split_doi.py >> $GITHUB_OUTPUT | |
| id: step1 | |
| harvest: | |
| runs-on: ubuntu-24.04 | |
| needs: [prepare-dois, get-crossref] | |
| continue-on-error: true | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| doi: ${{ fromJSON(needs.prepare-dois.outputs.dois) }} | |
| outputs: | |
| dois: ${{ steps.step1.outputs.matrix }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Python Deps | |
| shell: bash | |
| run: pip install -r requirements.txt --break-system-packages | |
| - name: Make downloads folder | |
| shell: bash | |
| run: mkdir $HOME/Downloads | |
| - name: Install irdmtools | |
| shell: bash | |
| run: curl https://caltechlibrary.github.io/irdmtools/installer.sh | sh | |
| - name: Path | |
| shell: bash | |
| run: cp $HOME/bin/doi2rdm $HOME/.local/bin/. | |
| - name: Harvest DOIs | |
| shell: bash | |
| env: | |
| RDMTOK: ${{ secrets.RDMTOK }} | |
| DIMKEY: ${{ secrets.DIMKEY }} | |
| id: harvest | |
| run: python harvest.py doi -doi "${{matrix.doi}}" -actor ${{github.actor}} -message "${{needs.get-crossref.outputs.message}}" >> $GITHUB_OUTPUT | |
| - uses: cloudposse/github-action-matrix-outputs-write@main | |
| id: out | |
| with: | |
| matrix-step-name: ${{ github.job }} | |
| matrix-key: ${{ matrix.doi }} | |
| outputs: |- | |
| doi: ${{ steps.harvest.outputs.doi }} | |
| error: ${{steps.harvest.outputs.error }} | |
| - name: System error on DOI | |
| if: contains(steps.harvest.outputs.error, 'system') | |
| run: | | |
| echo ${{steps.harvest.outputs.error}} | |
| false | |
| - name: System intentionally skipped DOI | |
| if: contains(steps.harvest.outputs.error, 'skipping') | |
| run: | | |
| echo ${{steps.harvest.outputs.error}} | |
| false | |
| write-output: | |
| name: Write Output | |
| runs-on: ubuntu-24.04 | |
| needs: [harvest] | |
| outputs: | |
| result: "${{ steps.read.outputs.result }}" | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: main | |
| - name: read | |
| uses: cloudposse/github-action-matrix-outputs-read@main | |
| id: read | |
| with: | |
| matrix-step-name: harvest | |
| - name: write DOI | |
| run: | | |
| python save_dois.py '${{steps.read.outputs.result}}' | |
| - name: Commit and Push Changes | |
| id: commit-and-push | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| with: | |
| commit_message: 'Update harvested DOIs' | |
| file_pattern: 'harvested_dois.txt' | |
| report-status: | |
| name: Report Status | |
| runs-on: ubuntu-24.04 | |
| needs: [write-output] | |
| outputs: | |
| result: "${{ steps.read.outputs.result }}" | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: read | |
| uses: cloudposse/github-action-matrix-outputs-read@main | |
| id: read | |
| with: | |
| matrix-step-name: harvest | |
| - name: System error on DOI | |
| run: | | |
| python check_status.py '${{steps.read.outputs.result}}' |