Merge pull request #514 from SynBioHub/jsonpage5

Jsonpage5
SynBioHub · Aug 18, 2023 · be33433 · be33433
2 parents f6283b3 + ed43639
commit be33433
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Showing 12 changed files with 635 additions and 181 deletions.
diff --git a/frontend/components/Viewing/PageJSON/MasterJSON.js b/frontend/components/Viewing/PageJSON/MasterJSON.js
@@ -18,6 +18,14 @@ import Participation from './Types/Participation.json';
 import SequenceConstraint from './Types/SequenceConstraint.json';
 import Datasheet from './Types/Datasheet.json';
 import Plan from './Types/Plan.json';
+import VariableComponent from './Types/VariableComponent.json';
+import SequenceAnnotation from './Types/SequenceAnnotation.json';
+import Activity from './Types/Activity.json';
+import Usage from './Types/Usage.json';
+import Association from './Types/Association.json';
+import Agent from './Types/Agent.json';
+import GenericLocation from './Types/GenericLocation.json';
+import Cut from './Types/Cut.json';
 
 
 const TypeToJson = {
@@ -39,9 +47,16 @@ const TypeToJson = {
   'http://sbols.org/v2#Interaction': Interaction,
   'http://sbols.org/v2#Participation': Participation,
   'http://sbols.org/v2#SequenceConstraint': SequenceConstraint,
+  'http://sbols.org/v2#VariableComponent': VariableComponent,
+  'http://sbols.org/v2#SequenceAnnotation': SequenceAnnotation,
+  'http://sbols.org/v2#GenericLocation': GenericLocation,
+  'http://sbols.org/v2#Cut': Cut,
   'http://www.myapp.org/Datasheet': Datasheet,
-  'http://www.w3.org/ns/prov#Plan' : Plan
-
+  'http://www.w3.org/ns/prov#Plan' : Plan,
+  'http://www.w3.org/ns/prov#Activity': Activity,
+  'http://www.w3.org/ns/prov#Usage': Usage,
+  'http://www.w3.org/ns/prov#Association': Association,
+  'http://www.w3.org/ns/prov#Agent': Agent
 };
 
 export default TypeToJson;
diff --git a/frontend/components/Viewing/PageJSON/Rendering/SectionRenderer.js b/frontend/components/Viewing/PageJSON/Rendering/SectionRenderer.js
@@ -11,27 +11,31 @@ function loadText(template, args) {
 }
 
 export default function SectionRenderer({ section, metadata }) {
+  console.log(section)
+  const graphPrefix = "https://synbiohub.org/";
+  console.log(section.link);
+  section.link = replaceBeginning("" + section.link, graphPrefix, "/");
+  console.log(section.link);
   if (section.grouped) {
     const items = section.text.split(', ');
     const content = items.map((item, index) => {
       if (section.link && item) {
         return (
           <ColumnLink
             link={loadText(section.link, { This: item })}
-            text={`${item}${
-              index === items.length - 1 ||
+            text={`${item}${index === items.length - 1 ||
               (section.linkType !== 'default' && section.linkType !== undefined)
-                ? ''
-                : ', '
-            }`}
+              ? ''
+              : ', '
+              }`}
             linkType={section.linkType}
             key={index}
           />
         );
       }
       return (
         <span key={index}>
-          {item}
+          "{item}"
           {index === items.length - 1 ? '' : ', '}
         </span>
       );
@@ -58,6 +62,14 @@ export default function SectionRenderer({ section, metadata }) {
   );
 }
 
+function replaceBeginning(original, oldBeginning, newBeginning) {
+  if (original.startsWith(oldBeginning)) {
+    return newBeginning + original.slice(oldBeginning.length);
+  }
+  return original;
+}
+
+
 function ColumnLink({ text, link, linkType }) {
   if (linkType === 'search') {
     const searchStart = link.indexOf('=');

diff --git a/frontend/components/Viewing/PageJSON/Types/Activity.json b/frontend/components/Viewing/PageJSON/Types/Activity.json
@@ -0,0 +1,137 @@
+{
+    "type": "http://www.w3.org/ns/prov#Activity",
+    "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/v2#>",
+        "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": [],
+    "tables": [
+        {
+            "icon": "faVials",
+            "title": "Usages",
+            "rootPredicate": "prov:qualifiedUsage",
+            "sections": [
+                {
+                    "title": "Usage",
+                    "infoLink": "https://www.w3.org/ns/prov#Usage",
+                    "predicates": [
+                        "sbol:displayId"
+                    ],
+                    "stripAfter": "#",
+                    "link": "$<usageLink>"
+                },
+                {
+                    "title": "usageLink",
+                    "predicates": [],
+                    "hide": true
+                },
+                {
+                    "title": "Entity",
+                    "infoLink": "https://www.w3.org/ns/prov#entity",
+                    "predicates": [
+                        "prov:entity"
+                    ],
+                    "link": "$<entityLink>"
+                },
+                {
+                    "title": "entityLink",
+                    "predicates": [],
+                    "hide": true
+                },
+                {
+                    "title": "Roles",
+                    "infoLink": "https://www.w3.org/ns/prov#hasRole",
+                    "predicates": [
+                        "prov:hadRole"
+                    ],
+                    "stripAfter": "#",
+                    "link": "$<roleLink>"
+                },
+                {
+                    "title": "roleLink",
+                    "predicates": [],
+                    "hide": true
+                }
+            ]
+        },
+        {
+            "icon": "faVials",
+            "title": "Associations",
+            "rootPredicate": "prov:qualifiedAssociation",
+            "sections": [
+                {
+                    "title": "Association",
+                    "infoLink": "https://www.w3.org/ns/prov#Association",
+                    "predicates": [
+                        "sbol:displayId"
+                    ],
+                    "stripAfter": "#",
+                    "link": "$<associationLink>"
+                },
+                {
+                    "title": "associationLink",
+                    "predicates": [],
+                    "hide": true
+                },
+                {
+                    "title": "Agent",
+                    "infoLink": "https://www.w3.org/ns/prov#Agent",
+                    "predicates": [
+                        "prov:agent"
+                    ],
+                    "link": "$<agentLink>"
+                },
+                {
+                    "title": "agentLink",
+                    "predicates": [],
+                    "hide": true
+                },
+                {
+                    "title": "Plan",
+                    "infoLink": "https://www.w3.org/ns/prov#Plan",
+                    "predicates": [
+                        "prov:hadPlan"
+                    ],
+                    "link": "$<planLink>"
+                },
+                {
+                    "title": "planLink",
+                    "predicates": [],
+                    "hide": true
+                },
+                {
+                    "title": "Roles",
+                    "infoLink": "https://www.w3.org/ns/prov#hasRole",
+                    "predicates": [
+                        "prov:hadRole"
+                    ],
+                    "link": "$<rolesLink>",
+                    "stripAfter": "#"
+
+                },
+                {
+                    "title": "rolesLink",
+                    "predicates": [
+                        "prov:hadRole"
+                    ],
+                    "hide": true
+                }
+            ]
+        }
+    ],
+    "pages": [
+        "$TABLES[Usages]",
+        "$TABLES[Associations]",
+        "Details",
+        "Other Properties",
+        "Member of these Collections",
+        "Attachments"
+    ]
+}
diff --git a/frontend/components/Viewing/PageJSON/Types/Agent.json b/frontend/components/Viewing/PageJSON/Types/Agent.json
@@ -0,0 +1,23 @@
+{
+    "type": "http://www.w3.org/ns/prov#Agent",
+    "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/v2#>",
+       "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": [],
+    "tables": [
+    ],
+    "pages": [
+      "Details",
+      "Other Properties",
+      "Member of these Collections",
+      "Attachments"
+    ]
+    }
diff --git a/frontend/components/Viewing/PageJSON/Types/Association.json b/frontend/components/Viewing/PageJSON/Types/Association.json
@@ -0,0 +1,57 @@
+{
+    "type": "http://www.w3.org/ns/prov#Association",
+    "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/v2#>",
+        "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": "Roles",
+            "icon": "faVials",
+            "infoLink": "https://sbols.org/v2#role",
+            "rootPredicate": "prov:hadRole",
+            "sections": [
+                {
+                    "title": "name",
+                    "predicates": [
+
+                    ],
+                    "stripAfter":"#",
+                    "link": "$<roleLink>"
+                },
+                {
+                    "title": "roleLink",
+                    "predicates": [],
+                    "hide": true
+                }
+            ]
+        },
+        {
+            "title": "Agent",
+            "icon": "faVials",
+            "infoLink": "https://www.w3.org/ns/prov#agent",
+            "rootPredicate": "prov:agent",
+            "sections": [
+                {
+                    "title": "name",
+                    "predicates": [
+                    ],
+                    "link": "$<This>"
+                }
+            ]
+        }
+    ],
+    "tables": [],
+    "pages": [
+        "Details",
+        "Other Properties",
+        "Attachments"
+    ]
+}
diff --git a/frontend/components/Viewing/PageJSON/Types/CombinatorialDerivation.json b/frontend/components/Viewing/PageJSON/Types/CombinatorialDerivation.json
@@ -20,8 +20,8 @@
                 {
                     "title": "Extra Work",
                     "predicates": [
-                        "sbol:displayId"
-                    ]
+                    ],
+                    "link": "$<This>"
                 }
             ]
         },
@@ -34,7 +34,12 @@
                     "title": "Extra Work",
                     "stripAfter": "#",
                     "predicates": [],
-                    "link": "$<This>"
+                    "link": "$<strategyLink>"
+                },
+                {
+                    "title": "strategyLink",
+                    "predicates": [],
+                    "hide": true
                 }
             ]
         }
@@ -57,38 +62,44 @@
                 {
                     "title": "VariableComponentsLink",
                     "predicates": [
-                        "sbol:persistentIdentity"
                     ],
                     "hide": true
                 },
 
                 {
                     "title": "Variable",
-                    "infoLink": "https://dissys.github.io/sbol-owl/sbol-owl.html#variable",
+                    "infoLink": "https://sbols.org/v2#variable",
                     "predicates": [
                         "sbol:variable"
                     ],
-                    "link": "$<VariableLink>"
+                    "link": "$<This>"
                 },
 
                 {
                     "title": "VariableLink",
                     "predicates": [
-                        "sbol:variable"
                     ],
                     "hide": true
                 },
                 {
                     "title": "Operator",
-                    "infoLink": "https://dissys.github.io/sbol-owl/sbol-owl.html#operator",
+                    "infoLink": "https://sbols.org/v2#operator",
+                    "predicates": [
+                        "sbol:operator"
+                    ],
+                    "stripAfter": "#",
+                    "link": "$<operatorLink>"
+                },
+                {
+                    "title": "operatorLink",
                     "predicates": [
                         "sbol:operator"
                     ],
-                    "stripAfter": "#"
+                    "hide": true
                 },
                 {
                     "title": "Variant",
-                    "infoLink": "https://dissys.github.io/sbol-owl/sbol-owl.html#variant",
+                    "infoLink": "https://sbols.org/v2#variant",
                     "predicates": [
                         "sbol:variant", "sbol:displayId"
                     ],