Harvest from ORCID #15
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Harvest from ORCID | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| orcid: | |
| description: 'ORCID identifier to harvest from' | |
| required: true | |
| jobs: | |
| get-orcid: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| dois: ${{ steps.harvest.outputs.dois }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Python Deps | |
| shell: bash | |
| run: pip install -r requirements.txt | |
| - name: Harvest DOIs | |
| shell: bash | |
| id: harvest | |
| run: python harvest.py orcid -orcid ${{ github.event.inputs.orcid }} -print >> $GITHUB_OUTPUT | |
| prepare-dois: | |
| name: Prepare Matrix Output of DOIs | |
| needs: [get-orcid] | |
| runs-on: ubuntu-latest | |
| outputs: | |
| dois: ${{ steps.step1.outputs.matrix }} | |
| env: | |
| DOI: ${{ needs.get-orcid.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-latest | |
| needs: [prepare-dois] | |
| 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 | |
| - 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: ${{ secrets.RDMTOK }} | |
| id: harvest | |
| run: python harvest.py doi -doi "${{matrix.doi}}" -actor ${{github.actor}} >> $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 ${{steps.harvest.outputs.error}} | |
| false | |
| write-output: | |
| name: Write Output | |
| runs-on: ubuntu-latest | |
| needs: [harvest] | |
| outputs: | |
| result: "${{ 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: write DOI | |
| run: | | |
| python save_dois.py '${{steps.read.outputs.result}}' | |
| - name: Commit File | |
| uses: EndBug/add-and-commit@v9 | |
| with: | |
| message: 'Update harvested_dois.txt' | |
| add: "['harvested_dois.txt']" | |
| report-status: | |
| name: Report Status | |
| runs-on: ubuntu-latest | |
| needs: [write-output] | |
| outputs: | |
| result: "${{ 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}}' |