Update upload-to-zenodo.yml

marvinm2 · Aug 21, 2024 · dea56bc · dea56bc
1 parent 5f15e8f
commit dea56bc
Showing 1 changed file with 68 additions and 74 deletions.
diff --git a/.github/workflows/upload-to-zenodo.yml b/.github/workflows/upload-to-zenodo.yml
@@ -72,84 +72,78 @@ jobs:
 
       - name: Update Metadata for New Version
         run: |
-          metadata='{
-            "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"
-            }
-          }'
+          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 }}" \