TRAPI 1.4 feature merge

src/filter.ts

@@ -57,12 +57,20 @@ export const ft = (ops: SmartAPIKGOperationObject[], criteria: FilterCriteria) =
         return filters[field].has(rec.association["x-translator"][field]) ? true : false;
       } else if (field === "qualifiers") {
         // return true;
-        if (rec.tags?.includes?.("bte-trapi") || criteria[field] === undefined || criteria[field].length < 1) {
+        if (criteria[field] === undefined || criteria[field].length < 1) {
           return true;
         }
         return [...filters[field]].some(qualifierConstraintSet => {
           return Object.entries(qualifierConstraintSet).every(([qualifierType, qualifierValue]) => {
-            return rec.association[field] && rec.association[field][qualifierType] === qualifierValue;
+            if (!rec.association[field]) return false;
+            const qualifierValueArray = Array.isArray(qualifierValue) ? qualifierValue : [qualifierValue];
+            const associationValueArray = Array.isArray(rec.association[field][qualifierType])
+              ? rec.association[field][qualifierType]
+              : [rec.association[field][qualifierType]];
+
+            return qualifierValueArray.some(value => {
+              return associationValueArray.includes(value);
+            });
           });
         });
       } else {

src/operations_builder/async_operations_builder_with_reasoner.ts

@@ -67,9 +67,10 @@ export default class AsyncOperationsBuilderWithReasoner extends AsyncOperationsB
               association: {
                 input_type: this.removeBioLinkPrefix(sbj),
                 output_type: this.removeBioLinkPrefix(obj),
-                predicate: this.removeBioLinkPrefix(pred),
+                predicate: this.removeBioLinkPrefix(typeof(pred) === "string" ? pred : pred.predicate),
                 api_name: metadata.title,
                 smartapi: metadata.smartapi,
+                qualifiers: (typeof(pred) === "string" || !pred.qualifiers) ? undefined : Object.fromEntries(pred.qualifiers.map((q: any) => [this.removeBioLinkPrefix(q.qualifier_type_id), q.applicable_values.map(this.removeBioLinkPrefix)])),
                 "x-translator": metadata["x-translator"],
               },
               tags: [...metadata.tags, ...["bte-trapi"]],

src/operations_builder/sync_builder_factory.ts

@@ -7,18 +7,34 @@ export const syncBuilderFactory = (
   options: BuilderOptions,
   includeReasoner: boolean,
   smartapi_path: string,
-  predicates_path: string
+  predicates_path: string,
 ): SmartAPIKGOperationObject[] => {
   let builder;
   if (includeReasoner === true) {
-    builder = new SyncOperationsBuilderWithReasoner(
-      options,
-      smartapi_path,
-      predicates_path
-    );
+    builder = new SyncOperationsBuilderWithReasoner(options, smartapi_path, predicates_path);
   } else {
     builder = new SyncOperationsBuilder(options, smartapi_path);
   }
   const ops = builder.build();
+
+  const primaryKnowledgeAPIs = new Set();
+  options.apiList?.include.forEach(api => {
+    if (api.primarySource) {
+      if (api.id) primaryKnowledgeAPIs.add(api.id);
+      if (api.infores) primaryKnowledgeAPIs.add(api.infores);
+    }
+  });
+  options.apiList?.exclude.forEach(api => {
+    if (api.primarySource) {
+      if (api.id) primaryKnowledgeAPIs.add(api.id);
+      if (api.infores) primaryKnowledgeAPIs.add(api.infores);
+    }
+  });
+  ops.map(op => {
+    const apiIsPrimaryKnowledgeSource =
+      primaryKnowledgeAPIs.has(op.association.smartapi.id) ||
+      primaryKnowledgeAPIs.has(op.association["x-translator"].infores);
+    op.association.apiIsPrimaryKnowledgeSource = apiIsPrimaryKnowledgeSource ? true : false;
+  });
   return ops;
 };

src/operations_builder/sync_operations_builder_with_reasoner.ts

@@ -48,9 +48,10 @@ export default class SyncOperationsBuilderWithReasoner extends BaseOperationsBui
                 input_id: metadata?.nodes?.[sbj]?.id_prefixes,
                 output_type: this.removeBioLinkPrefix(obj),
                 output_id: metadata?.nodes?.[obj]?.id_prefixes,
-                predicate: this.removeBioLinkPrefix(pred),
+                predicate: this.removeBioLinkPrefix(typeof(pred) === "string" ? pred : pred.predicate),
                 api_name: metadata.association.api_name,
                 smartapi: metadata.association.smartapi,
+                qualifiers: (typeof(pred) === "string" || !pred.qualifiers) ? undefined : Object.fromEntries(pred.qualifiers.map((q: any) => [this.removeBioLinkPrefix(q.qualifier_type_id), q.applicable_values.map(this.removeBioLinkPrefix)])),
                 "x-translator": metadata.association["x-translator"],
                 "x-trapi": metadata.association["x-trapi"],
               },
@@ -78,7 +79,7 @@ export default class SyncOperationsBuilderWithReasoner extends BaseOperationsBui
         const includeInfoRes = this._options.apiList.include.find(api => api.infores === op.association?.["x-translator"]?.infores && api.infores !== undefined)
         const excludeSmartAPI = this._options.apiList.exclude.find(api => api.id === op.association.smartapi.id && api.id !== undefined);
         const excludeInfoRes = this._options.apiList.exclude.find(api => api.infores === op.association?.["x-translator"]?.infores && api.infores !== undefined)
-        
+
         let willBeIncluded;
         let apiValue;
         if (excludeSmartAPI) {

src/parser/types.ts

@@ -1,7 +1,7 @@
 export interface XTranslatorObject {
   component: string;
   team: string[];
-  "infores"?: string;
+  infores?: string;
 }
 
 interface SmartAIPInfoObject {
@@ -111,7 +111,7 @@ export interface XBTEKGSOperationObject {
   inputs: XBTEKGSOperationBioEntityObject[];
   outputs: XBTEKGSOperationBioEntityObject[];
   predicate: string;
-  qualifiers?: { [qualifierType: string]: string; };
+  qualifiers?: { [qualifierType: string]: string };
   source?: string;
   parameters?: XBTEParametersObject;
   requestBody?: any;
@@ -157,11 +157,12 @@ interface KGAssociationObject {
   source?: string;
   api_name?: string;
   component?: string;
+  apiIsPrimaryKnowledgeSource?: boolean;
   smartapi?: SmartAPIRegistryRecordObject;
   "x-translator"?: any;
   "x-trapi"?: XTRAPIObject;
   qualifiers?: {
-    [qualifierType: string]: string;
+    [qualifierType: string]: string | string[];
   }
 }
 

src/types.ts

@@ -5,6 +5,7 @@ export interface SmartAPIQueryResult {
 }
 
 export interface apiListItem {
+  primarySource?: boolean;
   id?: string;
   infores?: string;
   name: string;
@@ -58,7 +59,7 @@ interface PredicatesNode {
 }
 
 interface ReasonerSubjectAndPredicate {
-  [propName: string]: string[];
+  [propName: string]: (string | any)[];
 }
 
 export interface ReasonerPredicatesResponse {