Merge pull request #745 from SynBioHub/sequencesbol3

added sequence for sbol3, added a different variation of encoding for…
SynBioHub · Sep 2, 2024 · a77cfaa · a77cfaa
2 parents ae16727 + 43ef2d7
commit a77cfaa
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Showing 3 changed files with 39 additions and 21 deletions.
diff --git a/frontend/components/Viewing/PageJSON/Rendering/SectionRenderer.js b/frontend/components/Viewing/PageJSON/Rendering/SectionRenderer.js
@@ -80,6 +80,7 @@ export default function SectionRenderer({ section, metadata }) {
         }
       })
     }
+    console.log(section.text);
     if (/SO:\s*(\d{7})/.test(section.text)) {
       for (let key in sequenceOntology) {
         if (section.text === key) {
@@ -96,7 +97,13 @@ export default function SectionRenderer({ section, metadata }) {
         }
       }
     }
-    if (/http:\/\/edamontology\.org\/format_\d{4}/.test(section.text)) {
+    if (/^(http:\/\/edamontology\.org\/format_\d{4}|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');
+      }
+
+      // Now proceed with checking against the keys in edamOntology
       for (let key in edamOntology) {
         if (section.text === key) {
           section.text = edamOntology[key];

diff --git a/frontend/components/Viewing/PageJSON/Types/Sequence.json b/frontend/components/Viewing/PageJSON/Types/Sequence.json
@@ -20,7 +20,6 @@
             {
                "title": "Encoding",
                "stripAfter": "/",
-               "text": "Encoding",
                "predicates": [
                ],
                "link": "$<encodingLink>"

diff --git a/frontend/components/Viewing/PageJSON/Types/Sequence3.json b/frontend/components/Viewing/PageJSON/Types/Sequence3.json
@@ -11,27 +11,39 @@
        "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>",
        "PREFIX purl: <http://purl.obolibrary.org/obo/>"
     ],
-    "metadata": [],
+    "metadata": [
+      {
+         "title": "Encoding",
+         "rootPredicate": "sbol:encoding",
+         "icon": "faCode",
+         "sections": [
+            {
+               "title": "Encoding",
+               "stripAfter": "/",
+               "predicates": [
+               ],
+               "link": "$<encodingLink>"
+            },
+            {
+               "title": "encodingLink",
+               "predicates": [],
+               "hide": true
+            }
+         ]
+      }
+    ],
     "tables": [
       {
-        "icon": "faDna",
-        "title": "Sequence",
-        "rootPredicate": "sbol:elements",
-        "sections": [ 
-          {
-             "title": "Sequence",
-             "infoLink": "$<Encoding>",
-             "predicates": []
-          },
-          {
-             "title": "Encoding",
-             "rootPredicateOverride": "sbol:encoding",
-             "predicates": [
-                "rdf:resource"
-             ],
-             "hide": true
-          }
-       ]
+         "icon": "faDna",
+         "title": "Sequence",
+         "rootPredicate": "sbol:elements",
+         "sections": [
+            {
+               "title": "Sequence",
+               "infoLink": "https://sbols.org/v3#sequence",
+               "predicates": []
+            }
+         ]
       }
     ],
     "pages": [