Update Zenodo Record with New Version #15
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| 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 (<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>). </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" |