Merge pull request #747 from SynBioHub/updateMetadataSparql

updated edam, updated get metadata sparql for sbol3, updated model3
SynBioHub · Sep 4, 2024 · 7c99e18 · 7c99e18
2 parents c4bfc3e + 8dd55cb
commit 7c99e18
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Showing 3 changed files with 81 additions and 62 deletions.
diff --git a/frontend/components/Viewing/PageJSON/Rendering/SectionRenderer.js b/frontend/components/Viewing/PageJSON/Rendering/SectionRenderer.js
@@ -97,10 +97,12 @@ export default function SectionRenderer({ section, metadata }) {
         }
       }
     }
-    if (/^(http:\/\/edamontology\.org\/format_\d{4}|edam:format_\d{4})$/.test(section.text)) {
+    if (/^(http:\/\/edamontology\.org\/format_\d{4}|edam:format_\d{4}|https:\/\/identifiers\.org\/edam:format_\d{4})$/.test(section.text)) {
       // Normalize the section.text to the full URL format
       if (/^edam:format_\d{4}$/.test(section.text)) {
         section.text = section.text.replace(/^edam:format_(\d{4})$/, 'http://edamontology.org/format_$1');
+      } else if (/^https:\/\/identifiers\.org\/edam:format_\d{4}$/.test(section.text)) {
+        section.text = section.text.replace(/^https:\/\/identifiers\.org\/edam:format_(\d{4})$/, 'http://edamontology.org/format_$1');
       }
 
       // Now proceed with checking against the keys in edamOntology
@@ -111,6 +113,7 @@ export default function SectionRenderer({ section, metadata }) {
       }
     }
 
+
     if (section.grouped) {
       const items = section.text.split(', ');
       const content = items.map((item, index) => {

diff --git a/frontend/components/Viewing/PageJSON/Types/Model3.json b/frontend/components/Viewing/PageJSON/Types/Model3.json
@@ -1,63 +1,75 @@
-
 {
-
-    "type": "http://sbols.org/v3#Model",
-    "prefixes": [
-       "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>",
-       "PREFIX dcterms: <http://purl.org/dc/terms/>",
-       "PREFIX dc: <http://purl.org/dc/elements/1.1/>",
-       "PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>",
-       "PREFIX prov: <http://www.w3.org/ns/prov#>",
-       "PREFIX sbol: <http://sbols.org/v3#>",
-       "PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>",
-       "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>",
-       "PREFIX purl: <http://purl.obolibrary.org/obo/>"
-    ],
-    "metadata": [
-       {
-         "title": "Language",
-         "icon": "faVials",
-         "rootPredicate": "sbol:language",
-         "sections": [
-           {
-             "title": "lang",
-             "predicates": [
-             ],
-             "link": "$<This>"
-           }
-         ]
-       },
-       {
-         "title": "Framework",
-         "rootPredicate": "sbol:framework",
-         "icon": "faVials",
-         "sections": [
-           {
-             "title": "framework",
-             "predicates": [],
-             "link": "$<This>",
-             "stripAfter": "/"
-           }
-         ]
-       },
-       {
-          "title": "Model File",
-          "rootPredicate": "sbol:source",
-          "icon": "faVials",
-          "sections": [
-            {
-              "title": "mfile",
-              "predicates": [],
-              "link": "$<This>"
-            }
-          ]
+  "type": "http://sbols.org/v3#Model",
+  "prefixes": [
+    "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>",
+    "PREFIX dcterms: <http://purl.org/dc/terms/>",
+    "PREFIX dc: <http://purl.org/dc/elements/1.1/>",
+    "PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>",
+    "PREFIX prov: <http://www.w3.org/ns/prov#>",
+    "PREFIX sbol: <http://sbols.org/v3#>",
+    "PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>",
+    "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>",
+    "PREFIX purl: <http://purl.obolibrary.org/obo/>"
+  ],
+  "metadata": [
+    {
+      "title": "Language",
+      "icon": "faVials",
+      "rootPredicate": "sbol:language",
+      "sections": [
+        {
+          "title": "lang",
+          "predicates": [],
+          "link": "$<languageLink>"
+        },
+        {
+          "title": "languageLink",
+          "predicates": [],
+          "hide": true
         }
-    ],
-    "tables": [],
-    "pages": [
-      "Details",
-      "Other Properties",
-      "Member of these Collections",
-      "Attachments"
-    ]
-  }
+      ]
+    },
+    {
+      "title": "Framework",
+      "rootPredicate": "sbol:framework",
+      "icon": "faVials",
+      "sections": [
+        {
+          "title": "framework",
+          "predicates": [],
+          "link": "$<frameworkLink>",
+          "stripAfter": "/"
+        },
+        {
+          "title": "frameworkLink",
+          "predicates": [],
+          "hide": true
+        }
+      ]
+    },
+    {
+      "title": "Model File",
+      "rootPredicate": "sbol:source",
+      "icon": "faVials",
+      "sections": [
+        {
+          "title": "mfile",
+          "predicates": [],
+          "link": "$<sourceLink>"
+        },
+        {
+          "title": "sourceLink",
+          "predicates": [],
+          "hide": true
+        }
+      ]
+    }
+  ],
+  "tables": [],
+  "pages": [
+    "Details",
+    "Other Properties",
+    "Member of these Collections",
+    "Attachments"
+  ]
+}
diff --git a/frontend/sparql/getMetadata.js b/frontend/sparql/getMetadata.js
@@ -1,4 +1,5 @@
 const query = `PREFIX sbol2: <http://sbols.org/v2#>
+PREFIX sbol3: <http://sbols.org/v3#>
 PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX synbiohub: <http://synbiohub.org#>
 PREFIX dc: <http://purl.org/dc/elements/1.1/>
@@ -23,6 +24,9 @@ WHERE {
       OPTIONAL { <$uri> sbol2:persistentIdentity ?persistentIdentity . }
       OPTIONAL { <$uri> sbol2:displayId ?displayId . }
       OPTIONAL { <$uri> sbol2:version ?version . }
+      OPTIONAL { <$uri> sbol3:persistentIdentity ?persistentIdentity . }
+      OPTIONAL { <$uri> sbol3:displayId ?displayId . }
+      OPTIONAL { <$uri> sbol3:version ?version . }
       OPTIONAL { <$uri> dcterms:title ?name . }
       OPTIONAL { <$uri> dcterms:description ?description . }
       OPTIONAL { <$uri> dc:creator ?creator . }