From 731ef8432f1d358eb7e303bbd7ca22261cba9f4f Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Tue, 4 Apr 2023 18:48:42 -0700
Subject: [PATCH 1/7] association/qualifiers in meta knowledge graph

---
 .../async_operations_builder_with_reasoner.ts                 | 4 +++-
 .../sync_operations_builder_with_reasoner.ts                  | 4 +++-
 src/parser/endpoint.ts                                        | 1 +
 src/parser/types.ts                                           | 2 ++
 src/types.ts                                                  | 3 ++-
 5 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/operations_builder/async_operations_builder_with_reasoner.ts b/src/operations_builder/async_operations_builder_with_reasoner.ts
index fb6d5e9..165f7c0 100644
--- a/src/operations_builder/async_operations_builder_with_reasoner.ts
+++ b/src/operations_builder/async_operations_builder_with_reasoner.ts
@@ -67,9 +67,11 @@ 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,
+                association_id: typeof(pred) === "string" ? undefined : pred.association_id,
+                qualifiers: typeof(pred) === "string" ? undefined : pred.qualifiers,
                 "x-translator": metadata["x-translator"],
               },
               tags: [...metadata.tags, ...["bte-trapi"]],
diff --git a/src/operations_builder/sync_operations_builder_with_reasoner.ts b/src/operations_builder/sync_operations_builder_with_reasoner.ts
index 8fed28c..c723e86 100644
--- a/src/operations_builder/sync_operations_builder_with_reasoner.ts
+++ b/src/operations_builder/sync_operations_builder_with_reasoner.ts
@@ -48,9 +48,11 @@ 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,
+                association_id: typeof(pred) === "string" ? undefined : pred.association_id,
+                qualifiers: typeof(pred) === "string" ? undefined : pred.qualifiers,
                 "x-translator": metadata.association["x-translator"],
                 "x-trapi": metadata.association["x-trapi"],
               },
diff --git a/src/parser/endpoint.ts b/src/parser/endpoint.ts
index b92a082..82d0a52 100644
--- a/src/parser/endpoint.ts
+++ b/src/parser/endpoint.ts
@@ -84,6 +84,7 @@ export default class Endpoint {
       output_id: this.removeBioLinkPrefix(output.id),
       output_type: this.removeBioLinkPrefix(output.semantic),
       predicate: this.removeBioLinkPrefix(op.predicate),
+      association_id: this.removeBioLinkPrefix(op.association_id),
       qualifiers: op.qualifiers
         ? Object.fromEntries(
             Object.entries(op.qualifiers).map(([qualifierType, qualifier]) => [
diff --git a/src/parser/types.ts b/src/parser/types.ts
index 15cc99b..346eb89 100644
--- a/src/parser/types.ts
+++ b/src/parser/types.ts
@@ -111,6 +111,7 @@ export interface XBTEKGSOperationObject {
   inputs: XBTEKGSOperationBioEntityObject[];
   outputs: XBTEKGSOperationBioEntityObject[];
   predicate: string;
+  association_id: string;
   qualifiers?: { [qualifierType: string]: string; };
   source?: string;
   parameters?: XBTEParametersObject;
@@ -158,6 +159,7 @@ interface KGAssociationObject {
   api_name?: string;
   component?: string;
   smartapi?: SmartAPIRegistryRecordObject;
+  association_id: string;
   "x-translator"?: any;
   "x-trapi"?: XTRAPIObject;
   qualifiers?: {
diff --git a/src/types.ts b/src/types.ts
index 839c17f..aff85f9 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -37,6 +37,7 @@ interface PredicatesQueryOperationInterface {
 interface PredicatesAssociationInterface {
   api_name: string;
   smartapi: SmartAPIRegistryRecordObject;
+  association_id: string;
   "x-translator": any;
   "x-trapi"?: XTRAPIObject;
 }
@@ -58,7 +59,7 @@ interface PredicatesNode {
 }
 
 interface ReasonerSubjectAndPredicate {
-  [propName: string]: string[];
+  [propName: string]: any[];
 }
 
 export interface ReasonerPredicatesResponse {

From 0726f1c5cfa7755af82b03fbd22dad6ac7345223 Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Tue, 4 Apr 2023 18:58:34 -0700
Subject: [PATCH 2/7] association id optional

---
 src/parser/types.ts | 4 ++--
 src/types.ts        | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/parser/types.ts b/src/parser/types.ts
index 346eb89..7816640 100644
--- a/src/parser/types.ts
+++ b/src/parser/types.ts
@@ -111,7 +111,7 @@ export interface XBTEKGSOperationObject {
   inputs: XBTEKGSOperationBioEntityObject[];
   outputs: XBTEKGSOperationBioEntityObject[];
   predicate: string;
-  association_id: string;
+  association_id?: string;
   qualifiers?: { [qualifierType: string]: string; };
   source?: string;
   parameters?: XBTEParametersObject;
@@ -159,7 +159,7 @@ interface KGAssociationObject {
   api_name?: string;
   component?: string;
   smartapi?: SmartAPIRegistryRecordObject;
-  association_id: string;
+  association_id?: string;
   "x-translator"?: any;
   "x-trapi"?: XTRAPIObject;
   qualifiers?: {
diff --git a/src/types.ts b/src/types.ts
index aff85f9..6150c68 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -37,7 +37,7 @@ interface PredicatesQueryOperationInterface {
 interface PredicatesAssociationInterface {
   api_name: string;
   smartapi: SmartAPIRegistryRecordObject;
-  association_id: string;
+  association_id?: string;
   "x-translator": any;
   "x-trapi"?: XTRAPIObject;
 }

From f95b5ad70d701625ee8376d7c79b53bd5352799e Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Wed, 12 Apr 2023 13:45:04 -0700
Subject: [PATCH 3/7] move association to its own branch

---
 .../async_operations_builder_with_reasoner.ts                   | 1 -
 src/operations_builder/sync_operations_builder_with_reasoner.ts | 1 -
 src/parser/endpoint.ts                                          | 1 -
 src/parser/types.ts                                             | 2 --
 src/types.ts                                                    | 1 -
 5 files changed, 6 deletions(-)

diff --git a/src/operations_builder/async_operations_builder_with_reasoner.ts b/src/operations_builder/async_operations_builder_with_reasoner.ts
index 165f7c0..b1c2ec7 100644
--- a/src/operations_builder/async_operations_builder_with_reasoner.ts
+++ b/src/operations_builder/async_operations_builder_with_reasoner.ts
@@ -70,7 +70,6 @@ export default class AsyncOperationsBuilderWithReasoner extends AsyncOperationsB
                 predicate: this.removeBioLinkPrefix(typeof(pred) === "string" ? pred : pred.predicate),
                 api_name: metadata.title,
                 smartapi: metadata.smartapi,
-                association_id: typeof(pred) === "string" ? undefined : pred.association_id,
                 qualifiers: typeof(pred) === "string" ? undefined : pred.qualifiers,
                 "x-translator": metadata["x-translator"],
               },
diff --git a/src/operations_builder/sync_operations_builder_with_reasoner.ts b/src/operations_builder/sync_operations_builder_with_reasoner.ts
index c723e86..63c4ce6 100644
--- a/src/operations_builder/sync_operations_builder_with_reasoner.ts
+++ b/src/operations_builder/sync_operations_builder_with_reasoner.ts
@@ -51,7 +51,6 @@ export default class SyncOperationsBuilderWithReasoner extends BaseOperationsBui
                 predicate: this.removeBioLinkPrefix(typeof(pred) === "string" ? pred : pred.predicate),
                 api_name: metadata.association.api_name,
                 smartapi: metadata.association.smartapi,
-                association_id: typeof(pred) === "string" ? undefined : pred.association_id,
                 qualifiers: typeof(pred) === "string" ? undefined : pred.qualifiers,
                 "x-translator": metadata.association["x-translator"],
                 "x-trapi": metadata.association["x-trapi"],
diff --git a/src/parser/endpoint.ts b/src/parser/endpoint.ts
index 82d0a52..b92a082 100644
--- a/src/parser/endpoint.ts
+++ b/src/parser/endpoint.ts
@@ -84,7 +84,6 @@ export default class Endpoint {
       output_id: this.removeBioLinkPrefix(output.id),
       output_type: this.removeBioLinkPrefix(output.semantic),
       predicate: this.removeBioLinkPrefix(op.predicate),
-      association_id: this.removeBioLinkPrefix(op.association_id),
       qualifiers: op.qualifiers
         ? Object.fromEntries(
             Object.entries(op.qualifiers).map(([qualifierType, qualifier]) => [
diff --git a/src/parser/types.ts b/src/parser/types.ts
index 7816640..15cc99b 100644
--- a/src/parser/types.ts
+++ b/src/parser/types.ts
@@ -111,7 +111,6 @@ export interface XBTEKGSOperationObject {
   inputs: XBTEKGSOperationBioEntityObject[];
   outputs: XBTEKGSOperationBioEntityObject[];
   predicate: string;
-  association_id?: string;
   qualifiers?: { [qualifierType: string]: string; };
   source?: string;
   parameters?: XBTEParametersObject;
@@ -159,7 +158,6 @@ interface KGAssociationObject {
   api_name?: string;
   component?: string;
   smartapi?: SmartAPIRegistryRecordObject;
-  association_id?: string;
   "x-translator"?: any;
   "x-trapi"?: XTRAPIObject;
   qualifiers?: {
diff --git a/src/types.ts b/src/types.ts
index 6150c68..809185f 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -37,7 +37,6 @@ interface PredicatesQueryOperationInterface {
 interface PredicatesAssociationInterface {
   api_name: string;
   smartapi: SmartAPIRegistryRecordObject;
-  association_id?: string;
   "x-translator": any;
   "x-trapi"?: XTRAPIObject;
 }

From 37d79d12ef7b3bd4c8cbcc44d43e99e86d03df1e Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Thu, 13 Apr 2023 15:02:48 -0700
Subject: [PATCH 4/7] handle array qualifiers in filter

---
 src/filter.ts | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/filter.ts b/src/filter.ts
index dfa6bbe..44df46d 100644
--- a/src/filter.ts
+++ b/src/filter.ts
@@ -62,6 +62,9 @@ export const ft = (ops: SmartAPIKGOperationObject[], criteria: FilterCriteria) =
         }
         return [...filters[field]].some(qualifierConstraintSet => {
           return Object.entries(qualifierConstraintSet).every(([qualifierType, qualifierValue]) => {
+            if (Array.isArray(qualifierValue)) {
+                return rec.association[field] && qualifierValue.includes(rec.association[field][qualifierType]);
+            }
             return rec.association[field] && rec.association[field][qualifierType] === qualifierValue;
           });
         });

From 6ed023cd0ddc8a7e234b5a5212c945a64120967e Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Wed, 19 Apr 2023 17:50:04 -0700
Subject: [PATCH 5/7] Filter based on qualifiers for trapi apis

---
 src/filter.ts                                                 | 4 ++--
 .../async_operations_builder_with_reasoner.ts                 | 3 ++-
 .../sync_operations_builder_with_reasoner.ts                  | 3 ++-
 src/parser/types.ts                                           | 2 +-
 src/types.ts                                                  | 2 +-
 5 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/filter.ts b/src/filter.ts
index dfa6bbe..80d7008 100644
--- a/src/filter.ts
+++ b/src/filter.ts
@@ -57,12 +57,12 @@ 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;
+            return rec.association[field] && (Array.isArray(rec.association[field][qualifierType]) ? rec.association[field][qualifierType].includes(qualifierValue as string) : rec.association[field][qualifierType] === qualifierValue);
           });
         });
       } else {
diff --git a/src/operations_builder/async_operations_builder_with_reasoner.ts b/src/operations_builder/async_operations_builder_with_reasoner.ts
index fb6d5e9..b09fe42 100644
--- a/src/operations_builder/async_operations_builder_with_reasoner.ts
+++ b/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"]],
diff --git a/src/operations_builder/sync_operations_builder_with_reasoner.ts b/src/operations_builder/sync_operations_builder_with_reasoner.ts
index 8fed28c..8fdda71 100644
--- a/src/operations_builder/sync_operations_builder_with_reasoner.ts
+++ b/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"],
               },
diff --git a/src/parser/types.ts b/src/parser/types.ts
index 15cc99b..d091a99 100644
--- a/src/parser/types.ts
+++ b/src/parser/types.ts
@@ -161,7 +161,7 @@ interface KGAssociationObject {
   "x-translator"?: any;
   "x-trapi"?: XTRAPIObject;
   qualifiers?: {
-    [qualifierType: string]: string;
+    [qualifierType: string]: string | string[];
   }
 }
 
diff --git a/src/types.ts b/src/types.ts
index 839c17f..822526d 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -58,7 +58,7 @@ interface PredicatesNode {
 }
 
 interface ReasonerSubjectAndPredicate {
-  [propName: string]: string[];
+  [propName: string]: (string | any)[];
 }
 
 export interface ReasonerPredicatesResponse {

From 2198ece740a42a8edd8a7037ad19e93eb96427dc Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Thu, 27 Apr 2023 12:18:08 -0700
Subject: [PATCH 6/7] feat: support pprovenance refactor (trapi 1.4)

---
 .../sync_builder_factory.ts                   | 28 +++++++++++++++----
 src/parser/types.ts                           |  7 +++--
 src/types.ts                                  |  1 +
 3 files changed, 27 insertions(+), 9 deletions(-)

diff --git a/src/operations_builder/sync_builder_factory.ts b/src/operations_builder/sync_builder_factory.ts
index fd6f44f..b342ad3 100644
--- a/src/operations_builder/sync_builder_factory.ts
+++ b/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;
 };
diff --git a/src/parser/types.ts b/src/parser/types.ts
index 15cc99b..8c51e09 100644
--- a/src/parser/types.ts
+++ b/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;
@@ -157,12 +157,13 @@ interface KGAssociationObject {
   source?: string;
   api_name?: string;
   component?: string;
+  apiIsPrimaryKnowledgeSource?: boolean;
   smartapi?: SmartAPIRegistryRecordObject;
   "x-translator"?: any;
   "x-trapi"?: XTRAPIObject;
   qualifiers?: {
     [qualifierType: string]: string;
-  }
+  };
 }
 
 export interface QueryOperationInterface {
diff --git a/src/types.ts b/src/types.ts
index 839c17f..0fc2e07 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -5,6 +5,7 @@ export interface SmartAPIQueryResult {
 }
 
 export interface apiListItem {
+  primarySource?: boolean;
   id?: string;
   infores?: string;
   name: string;

From cf1f960f31c70095c11f50aa8e98bf536621826c Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Mon, 22 May 2023 12:28:53 -0400
Subject: [PATCH 7/7] fix: merge optional-array behaviors

---
 src/filter.ts | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/filter.ts b/src/filter.ts
index 69dc06c..8b925f9 100644
--- a/src/filter.ts
+++ b/src/filter.ts
@@ -62,10 +62,15 @@ export const ft = (ops: SmartAPIKGOperationObject[], criteria: FilterCriteria) =
         }
         return [...filters[field]].some(qualifierConstraintSet => {
           return Object.entries(qualifierConstraintSet).every(([qualifierType, qualifierValue]) => {
-            if (Array.isArray(qualifierValue)) {
-                return rec.association[field] && qualifierValue.includes(rec.association[field][qualifierType]);
-            }
-            return rec.association[field] && (Array.isArray(rec.association[field][qualifierType]) ? rec.association[field][qualifierType].includes(qualifierValue as string) : 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 {