upload-to-zenodo.yml

name: Update Zenodo Record with New Version

on:
  workflow_dispatch:

jobs:
  update-zenodo-record:
    runs-on: ubuntu-latest

    steps:
      - name: Checkout Repository
        uses: actions/checkout@v4

      - name: Install curl and jq
        run: sudo apt-get install -y curl jq

      - name: Discard Current Draft
        run: |
          discard_response=$(curl -s -X POST -H "Authorization: Bearer ${{ secrets.ZENODO_ACCESS_TOKEN }}" \
                              "https://zenodo.org/api/deposit/depositions/${{ secrets.ZENODO_DEPOSITION_ID }}/actions/discard")
          echo "Discard Response: $discard_response"
          if echo "$discard_response" | grep -q '"status": 403'; then
            echo "Failed to discard the draft. The draft might be locked or in an invalid state."
            exit 1
          fi

      - name: Create a New Version of the Deposition
        id: new_version
        run: |
          # Attempt to create a new version and capture the full response
          response=$(curl -s -X POST -H "Authorization: Bearer ${{ secrets.ZENODO_ACCESS_TOKEN }}" \
                        "https://zenodo.org/api/deposit/depositions/${{ secrets.ZENODO_DEPOSITION_ID }}/actions/newversion")
          
          echo "Response: $response"

          # Extract the latest draft URL from the response
          new_draft_url=$(echo "$response" | jq -r '.links.latest_draft')
          if [[ "$new_draft_url" == "null" || -z "$new_draft_url" ]]; then
            echo "Failed to retrieve the latest draft URL. Response was: $response"
            exit 1
          fi

          # Fetch the new draft deposition details
          new_draft_response=$(curl -s -H "Authorization: Bearer ${{ secrets.ZENODO_ACCESS_TOKEN }}" "$new_draft_url")
          
          echo "New Draft Response: $new_draft_response"

          # Extract necessary information for the next steps
          new_deposition_id=$(echo "$new_draft_response" | jq -r '.id')
          new_bucket_url=$(echo "$new_draft_response" | jq -r '.links.bucket')
          
          if [[ "$new_deposition_id" == "null" || -z "$new_deposition_id" ]]; then
            echo "Failed to retrieve the new deposition ID. New draft response was: $new_draft_response"
            exit 1
          fi
          
          echo "New Deposition ID: $new_deposition_id"
          echo "New Bucket URL: $new_bucket_url"

          echo "new_deposition_id=$new_deposition_id" >> $GITHUB_ENV
          echo "new_bucket_url=$new_bucket_url" >> $GITHUB_ENV

      - name: Debug New Bucket URL
        run: echo "$new_bucket_url"

      - name: Upload files to Zenodo
        run: |
          for file in data/*.ttl; do
            curl --progress-bar -H "Authorization: Bearer ${{ secrets.ZENODO_ACCESS_TOKEN }}" \
                  --upload-file $file "$new_bucket_url/$(basename $file)"
          done

      - name: Update Metadata for New Version
        run: |
          metadata=$(cat <<EOF 
          {
          "metadata": {
          "title": "Adverse Outcome Pathway Wiki RDF",
          "doi": "10.5281/zenodo.***",  # Replace with your actual DOI
          "publication_date": "2023-10-31",  # Use the existing publication date
          "description": "<p>This dataset is the RDF generated from the AOP-Wiki data release&nbsp;(<a href=\"https://aopwiki.org/downloads\">aopwiki.org/downloads</a>). It was generated using a Jupyter notebook that is available on GitHub (<a href=\"https://github.com/marvinm2/AOPWikiRDF\">github.com/marvinm2/AOPWikiRDF</a>), and the process and additional description of the RDF have been published (<a href=\"https://doi.org/10.1089/aivt.2021.0010\">doi.org/10.1089/aivt.2021.0010</a>).&nbsp;</p>",
          "access_right": "open",
          "creators": [
          {
          "name": "Martens, Marvin",
          "affiliation": "Department of Bioinformatics (BiGCaT), NUTRIM, Maastricht University, Maastricht, the Netherlands",
          "orcid": "0000-0003-2230-0840"
          },
          {
          "name": "Willighagen, Egon",
          "affiliation": "Department of Bioinformatics (BiGCaT), NUTRIM, Maastricht University, Maastricht, the Netherlands",
          "orcid": "0000-0001-7542-0286"
          },
          {
          "name": "Evelo, Chris",
          "affiliation": "Department of Bioinformatics (BiGCaT), NUTRIM, Maastricht University, Maastricht, the Netherlands",
          "orcid": "0000-0002-5301-3142"
          }
          ],
          #    "keywords": [
          #      "AOP-Wiki",
          #      "Resource Description Framework",
          #      "Adverse Outcome Pathways"
          #    ],
          "related_identifiers": [
          {
          "identifier": "10.1089/aivt.2021.0010",
          "relation": "references",
          "resource_type": "publication-article",
          "scheme": "doi"
          }
          ],
          "references": [
          "10.1089/aivt.2021.0010"
          ],
          "language": "eng",
          "grants": [
          {"id": "10.13039/501100000780::814572"},
          {"id": "10.13039/501100000780::681002"},
          {"id": "10.13039/501100000780::814425"},
          {"id": "10.13039/501100000780::731075"},
          {"id": "10.13039/501100003246::36952"}
          ],
          "license": "cc-by-4.0",
          "communities": [
          {
          "identifier": "nsc"
          },
          {
          "identifier": "vhp4safety"
          },
          {
          "identifier": "nanosolveit"
          }
          ],
          "notes": "Funded by the European Union's Horizon 2020 (EU 2020) research and innovation program under grant agreement no. 681002 (EU-ToxRisk), grant agreement no. 814572 (NanoSolveIT), grant agreement no. 814425 (RiskGONE), EINFRA-22-2016 program under grant agreement no. 731075 (OpenRiskNet), and VHP4Safety, which is funded by the Netherlands Research Council (NWO) 'Netherlands Research Agenda: Research on Routes by Consortia' (NWA-ORC 1292.19.272)",
          "upload_type": "dataset"
          }
          }
          EOF
          )
          curl -H "Authorization: Bearer ${{ secrets.ZENODO_ACCESS_TOKEN }}" \
               -H "Content-Type: application/json" \
               -X PUT --data "$metadata" "https://zenodo.org/api/deposit/depositions/$new_deposition_id"


      - name: Publish Updated Zenodo Record
        run: |
          curl -H "Authorization: Bearer ${{ secrets.ZENODO_ACCESS_TOKEN }}" \
               -H "Content-Type: application/json" \
               -X POST "https://zenodo.org/api/deposit/depositions/$new_deposition_id/actions/publish"