Merge branch 'main' of https://github.com/biothings/bte_trapi_query_g…

…raph_handler into kg-refactor

__test__/integration/TRAPIQueryHandler.test.ts

@@ -1,5 +1,6 @@
-import axios from 'axios';
+import axios, { AxiosStatic } from 'axios';
 jest.mock('axios');
+const mockedAxios = axios as jest.Mocked<AxiosStatic>;
 
 import TRAPIQueryHandler from '../../src/index';
 import path from 'path';
@@ -26,7 +27,7 @@ describe('Testing TRAPIQueryHandler Module', () => {
   };
   describe('Testing query function', () => {
     test('test with one query edge', async () => {
-      (axios.get as jest.Mock).mockResolvedValue({
+      (mockedAxios.get as jest.Mock).mockResolvedValue({
         data: {
           message: {
             query_graph: {
@@ -101,7 +102,7 @@ describe('Testing TRAPIQueryHandler Module', () => {
           workflow: [{ id: 'lookup' }],
         },
       });
-      (axios.post as jest.Mock).mockResolvedValue({
+      (mockedAxios.post as jest.Mock).mockResolvedValue({
         data: {
           'MONDO:0005737': {
             id: { identifier: 'MONDO:0005737', label: 'Ebola hemorrhagic fever' },
@@ -139,6 +140,6 @@ describe('Testing TRAPIQueryHandler Module', () => {
       queryHandler.setQueryGraph(OneHopQuery);
       await queryHandler.query();
       expect(queryHandler.knowledgeGraph.kg).toHaveProperty('nodes');
-    }, 15000);
+    }, 30000);
   });
 });

data/templates/Drug-treats-Disease/Chem-treats-DoP.json

@@ -13,7 +13,7 @@
                 "eA": {
                     "subject": "creativeQuerySubject",
                     "object": "creativeQueryObject",
-                    "predicates": ["biolink:treats"]
+                    "predicates": ["biolink:treats_or_applied_or_studied_to_treat"]
                 }
             }
         }

data/templates/Drug-treats-Disease/Chem-treats-PhenoOfDisease.json

@@ -17,7 +17,7 @@
                 "eA": {
                     "subject": "creativeQuerySubject",
                     "object": "nA",
-                    "predicates": ["biolink:treats"]
+                    "predicates": ["biolink:treats_or_applied_or_studied_to_treat"]
                 },
                 "eB": {
                     "subject": "creativeQueryObject",

package.json

@@ -58,10 +58,11 @@
     "@biothings-explorer/node-expansion": "workspace:../node-expansion",
     "@biothings-explorer/smartapi-kg": "workspace:../smartapi-kg",
     "@biothings-explorer/utils": "workspace:../utils",
-    "@sentry/node": "^7.74.1",
-    "async": "^3.2.4",
+    "@biothings-explorer/types": "workspace:../types",
     "biolink-model": "workspace:../biolink-model",
     "biomedical_id_resolver": "workspace:../biomedical_id_resolver",
+    "@sentry/node": "^7.74.1",
+    "async": "^3.2.4",
     "chi-square-p-value": "^1.0.5",
     "debug": "^4.3.4",
     "ioredis": "^5.3.2",

src/batch_edge_query.ts

@@ -1,4 +1,5 @@
-import call_api, { RedisClient } from '@biothings-explorer/call-apis';
+import call_api from '@biothings-explorer/call-apis';
+import { redisClient } from '@biothings-explorer/utils';
 import QEdge2APIEdgeHandler, { APIEdge } from './qedge2apiedge';
 import NodesUpdateHandler from './update_nodes';
 import Debug from 'debug';
@@ -7,26 +8,25 @@ import CacheHandler from './cache_handler';
 import { threadId } from 'worker_threads';
 import MetaKG from '@biothings-explorer/smartapi-kg';
 import { StampedLog } from '@biothings-explorer/utils';
-import { QueryHandlerOptions, redisClient } from '.';
+import { QueryHandlerOptions } from '@biothings-explorer/types';
 import QEdge from './query_edge';
 import { UnavailableAPITracker } from './types';
 import { Record } from '@biothings-explorer/api-response-transform';
 
 export interface BatchEdgeQueryOptions extends QueryHandlerOptions {
   recordHashEdgeAttributes: string[];
+  caching: boolean;
 }
 
 export default class BatchEdgeQueryHandler {
   metaKG: MetaKG;
-  subscribers: any[];
   logs: StampedLog[];
   caching: boolean;
   options: QueryHandlerOptions;
   resolveOutputIDs: boolean;
   qEdges: QEdge | QEdge[];
   constructor(metaKG: MetaKG, resolveOutputIDs = true, options?: BatchEdgeQueryOptions) {
     this.metaKG = metaKG;
-    this.subscribers = [];
     this.logs = [];
     this.caching = options && options.caching;
     this.options = options;
@@ -62,7 +62,7 @@ export default class BatchEdgeQueryHandler {
    * @private
    */
   async _queryAPIEdges(APIEdges: APIEdge[], unavailableAPIs: UnavailableAPITracker = {}): Promise<Record[]> {
-    const executor = new call_api(APIEdges, this.options, redisClient as RedisClient);
+    const executor = new call_api(APIEdges, this.options, redisClient);
     const records: Record[] = await executor.query(this.resolveOutputIDs, unavailableAPIs);
     this.logs = [...this.logs, ...executor.logs];
     return records;
@@ -100,7 +100,7 @@ export default class BatchEdgeQueryHandler {
             const equivalentAlreadyIncluded = qEdge
               .getInputNode()
               .getEquivalentIDs()
-              [curie].equivalentIDs.some((equivalentCurie) => reducedCuries.includes(equivalentCurie));
+            [curie].equivalentIDs.some((equivalentCurie) => reducedCuries.includes(equivalentCurie));
             if (!equivalentAlreadyIncluded) {
               reducedCuries.push(curie);
             } else {
@@ -112,8 +112,7 @@ export default class BatchEdgeQueryHandler {
         strippedCuries.push(...nodeStrippedCuries);
         if (nodeStrippedCuries.length > 0) {
           debug(
-            `stripped (${nodeStrippedCuries.length}) duplicate equivalent curies from ${
-              node.id
+            `stripped (${nodeStrippedCuries.length}) duplicate equivalent curies from ${node.id
             }: ${nodeStrippedCuries.join(',')}`,
           );
         }
@@ -173,31 +172,4 @@ export default class BatchEdgeQueryHandler {
     debug('Update nodes completed!');
     return queryRecords;
   }
-
-  /**
-   * Register subscribers
-   * @param {object} subscriber
-   */
-  subscribe(subscriber): void {
-    this.subscribers.push(subscriber);
-  }
-
-  /**
-   * Unsubscribe a listener
-   * @param {object} subscriber
-   */
-  unsubscribe(subscriber): void {
-    this.subscribers = this.subscribers.filter((fn) => {
-      if (fn != subscriber) return fn;
-    });
-  }
-
-  /**
-   * Nofity all listeners
-   */
-  notify(res): void {
-    this.subscribers.map((subscriber) => {
-      subscriber.update(res);
-    });
-  }
 }

src/cache_handler.ts

@@ -1,4 +1,4 @@
-import { redisClient } from './redis-client';
+import { redisClient } from '@biothings-explorer/utils';
 import Debug from 'debug';
 const debug = Debug('bte:biothings-explorer-trapi:cache_handler');
 import { LogEntry, StampedLog } from '@biothings-explorer/utils';
@@ -9,9 +9,9 @@ import chunker from 'stream-chunker';
 import { Readable, Transform } from 'stream';
 import { Record, RecordPackage } from '@biothings-explorer/api-response-transform';
 import { threadId } from 'worker_threads';
-import MetaKG from '../../smartapi-kg/built';
-import { QueryHandlerOptions } from '.';
+import MetaKG from '@biothings-explorer/smartapi-kg';
 import QEdge from './query_edge';
+import { QueryHandlerOptions } from '@biothings-explorer/types';
 
 export interface RecordPacksByQedgeMetaKGHash {
   [QEdgeHash: string]: RecordPackage;
@@ -113,7 +113,7 @@ export default class CacheHandler {
   }
 
   async categorizeEdges(qEdges: QEdge[]): Promise<{ cachedRecords: Record[]; nonCachedQEdges: QEdge[] }> {
-    if (this.cacheEnabled === false || process.env.INTERNAL_DISABLE_REDIS) {
+    if (this.cacheEnabled === false || process.env.INTERNAL_DISABLE_REDIS === 'true') {
       return {
         cachedRecords: [],
         nonCachedQEdges: qEdges,
@@ -210,7 +210,7 @@ export default class CacheHandler {
   }
 
   async cacheEdges(queryRecords: Record[]): Promise<void> {
-    if (this.cacheEnabled === false || process.env.INTERNAL_DISABLE_REDIS) {
+    if (this.cacheEnabled === false || process.env.INTERNAL_DISABLE_REDIS === 'true') {
       if (global.parentPort) {
         global.parentPort.postMessage({ threadId, cacheDone: true });
       }
@@ -257,7 +257,9 @@ export default class CacheHandler {
                   resolve();
                 });
             });
-            await redisClient.client.expireTimeout(redisID, process.env.REDIS_KEY_EXPIRE_TIME || 1800);
+            if (process.env.QEDGE_CACHE_TIME_S !== '0') {
+              await redisClient.client.expireTimeout(redisID, process.env.QEDGE_CACHE_TIME_S || 1800);
+            }
           } catch (error) {
             failedHashes.push(hash);
             debug(

src/config.ts

@@ -55,7 +55,6 @@ const EDGE_ATTRIBUTES_USED_IN_RECORD_HASH = [
   //"NCIT:C61594",
   // Multiomics BigGIM Drug-Response 2023-05-31: may later change?
   'biolink:context_qualifier',
-  'biolink:primary_knowledge_source',   // added 2024-01-17
   // commenting it out since I haven't tested if it works for this KP or
   //   if it'll cause bugs when processing other KPs.
   //   It is only needed to differentiate records from some operations