fix PCC and removed GO. filtered the extension relatioship

geneontology · May 3, 2024 · 73c6dce · 73c6dce
1 parent 340a4be
commit 73c6dce
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Showing 8 changed files with 97 additions and 8 deletions.
diff --git a/src/@noctua.form/data/config/data-utils.ts b/src/@noctua.form/data/config/data-utils.ts
@@ -21,13 +21,17 @@ export class DataUtils {
     return result;
   }
 
-  public static getPredicates(shapes: ShexShapeAssociation[], subjectIds?: string[], objectIds?: string[]): string[] {
+  public static getPredicates(shapes: ShexShapeAssociation[], subjectIds?: string[], objectIds?: string[], excludeFromExtension = true): string[] {
     const matchedPredicates = new Set<string>();
 
+    console.log(shapes, subjectIds, objectIds, excludeFromExtension)
+
     // If neither subjectIds nor objectIds is provided, return all predicates
     if (!subjectIds && !objectIds) {
       shapes.forEach((shape) => {
-        matchedPredicates.add(shape.predicate);
+        if (shape.exclude_from_extensions !== excludeFromExtension) {
+          matchedPredicates.add(shape.predicate);
+        }
       });
       return [...matchedPredicates];
     }
@@ -36,7 +40,7 @@ export class DataUtils {
       const subjectMatch = !subjectIds || subjectIds.length === 0 || subjectIds.includes(shape.subject);
       const objectMatch = !objectIds || objectIds.length === 0 || shape.object.some(objId => objectIds.includes(objId));
 
-      if (subjectMatch && objectMatch) {
+      if (subjectMatch && objectMatch && shape.exclude_from_extensions !== excludeFromExtension) {
         matchedPredicates.add(shape.predicate);
       }
     });

diff --git a/src/@noctua.form/data/config/entity-definition.ts b/src/@noctua.form/data/config/entity-definition.ts
@@ -10,6 +10,13 @@ export const ObsoleteTerm = {
     categoryType: 'is_obsolete',
 } as GoCategory;
 
+export const GPProteinContainingComplex = {
+    id: ActivityNodeType.GoProteinContainingComplex,
+    category: 'GO:0032991',
+    categoryType: 'isa_closure',
+    suffix: `OR NOT idspace:"GO"`,
+} as GoCategory;
+
 export const GoProteinContainingComplex = {
     id: ActivityNodeType.GoProteinContainingComplex,
     category: 'GO:0032991',

diff --git a/src/@noctua.form/data/config/model-definition.ts b/src/@noctua.form/data/config/model-definition.ts
@@ -110,7 +110,7 @@ export const simpleAnnotonDescription: ActivityDescription = {
         gp: <ActivityNodeDisplay>{
             id: 'gp',
             type: ActivityNodeType.GoMolecularEntity,
-            category: [EntityDefinition.GoMolecularEntity, EntityDefinition.GoProteinContainingComplex],
+            category: [EntityDefinition.GoMolecularEntity, EntityDefinition.GPProteinContainingComplex],
             label: 'Gene Product',
             displaySection: noctuaFormConfig.displaySection.gp,
             displayGroup: noctuaFormConfig.displayGroup.gp,

diff --git a/src/@noctua.form/data/config/shape-definition.ts b/src/@noctua.form/data/config/shape-definition.ts
@@ -65,7 +65,6 @@ export const getShexJson = (subjectIds: string[], excludeFromExtensions = true)
     subjectIds.forEach((subjectId: string) => {
         const subjectShapes = DataUtils.getSubjectShapes(shapes, subjectId, excludeFromExtensions);
         if (subjectShapes) {
-            const predicates = DataUtils.getPredicates(shapes);
             const entities = DataUtils.getRangeLabels(subjectShapes, lookupTable)
 
             pred.push(...entities)

diff --git a/src/@noctua.form/data/gp-to-term.json b/src/@noctua.form/data/gp-to-term.json
@@ -76,6 +76,83 @@
         "GO:0032991"
       ],
       "predicate": "BFO:0000050"
+    },
+    {
+      "subject": "GO:0032991",
+      "object": [
+        "GO:0003674"
+      ],
+      "predicate": "RO:0002327"
+    },
+    {
+      "subject": "GO:0032991",
+      "object": [
+        "GO:0003674"
+      ],
+      "predicate": "RO:0002326"
+    },
+    {
+      "subject": "GO:0032991",
+      "object": [
+        "GO:0008150"
+      ],
+      "predicate": "RO:0002331"
+    },
+    {
+      "subject": "GO:0032991",
+      "object": [
+        "GO:0008150"
+      ],
+      "predicate": "RO:0004034"
+    },
+    {
+      "subject": "GO:0032991",
+      "object": [
+        "GO:0008150"
+      ],
+      "predicate": "RO:0004032"
+    },
+    {
+      "subject": "GO:0032991",
+      "object": [
+        "GO:0008150"
+      ],
+      "predicate": "RO:0004033"
+    },
+    {
+      "subject": "GO:0032991",
+      "object": [
+        "GO:0008150"
+      ],
+      "predicate": "RO:0004034"
+    },
+    {
+      "subject": "GO:0032991",
+      "object": [
+        "GO:0008150"
+      ],
+      "predicate": "RO:0004035"
+    },
+    {
+      "subject": "GO:0032991",
+      "object": [
+        "GO:0005575"
+      ],
+      "predicate": "RO:0002432"
+    },
+    {
+      "subject": "GO:0032991",
+      "object": [
+        "GO:0005575"
+      ],
+      "predicate": "RO:0001025"
+    },
+    {
+      "subject": "GO:0032991",
+      "object": [
+        "GO:0032991"
+      ],
+      "predicate": "BFO:0000050"
     }
   ]
 }
diff --git a/src/@noctua.form/services/config/noctua-form-config.service.ts b/src/@noctua.form/services/config/noctua-form-config.service.ts
@@ -37,7 +37,7 @@ export class NoctuaFormConfigService {
   constructor(private noctuaUserService: NoctuaUserService) {
     this.onSetupReady = new BehaviorSubject(null);
     this.termLookupTable = DataUtils.genTermLookupTable();
-    this.shapePredicates = DataUtils.getPredicates(shexJson.goshapes);
+    this.shapePredicates = DataUtils.getPredicates(shexJson.goshapes, null, null, false);
   }
 
   get edges() {
@@ -445,6 +445,8 @@ export class NoctuaFormConfigService {
     const predicates = DataUtils.getPredicates(
       gpToTerm ? gpToTermJson.goshapes : shexJson.goshapes, subjectIds, objectIds);
 
+
+    console.log('predicates', predicates)
     return predicates.map((predicate) => {
       return this.findEdge(predicate);
     });

diff --git a/workbenches/noctua-standard-annotations/public/inject.tmpl b/workbenches/noctua-standard-annotations/public/inject.tmpl
@@ -214,6 +214,6 @@
     </div>
   </noctua-splash-screen>
   <noctua-root></noctua-root>
-<script src="runtime.38b1f495cb4cd82a.js" type="module"></script><script src="polyfills.a39db01cea6f891e.js" type="module"></script><script src="scripts.c2b224063cd8b44d.js" defer></script><script src="main.b6beb68e913c1597.js" type="module"></script>
+<script src="runtime.38b1f495cb4cd82a.js" type="module"></script><script src="polyfills.a39db01cea6f891e.js" type="module"></script><script src="scripts.c2b224063cd8b44d.js" defer></script><script src="main.90e4a99ea0d23aff.js" type="module"></script>
 
 </body></html>
diff --git a/...notations/public/main.b6beb68e913c1597.js → ...notations/public/main.90e4a99ea0d23aff.js b/...notations/public/main.b6beb68e913c1597.js → ...notations/public/main.90e4a99ea0d23aff.js