Merge pull request #15 from geneontology/issue-13-pcc

Issue 13 pcc
geneontology · May 3, 2024 · f2a33eb · f2a33eb
2 parents 826b786 + 73c6dce
commit f2a33eb
Show file tree

Hide file tree

Showing 20 changed files with 1,281 additions and 59 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"
     }
   ]
 }