Merge branch 'move-redisclient' of https://github.com/biothings/bte_t…

…rapi_query_graph_handler into dev
biothings · Mar 22, 2024 · 40313ac · 40313ac
2 parents 9bb68f1 + e62eece
commit 40313ac
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Showing 13 changed files with 51 additions and 516 deletions.
diff --git a/__test__/integration/BatchEdgeQueryHandler.test.ts b/__test__/integration/BatchEdgeQueryHandler.test.ts
diff --git a/__test__/integration/TRAPIQueryHandler.test.ts b/__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);
   });
 });
diff --git a/__test__/unittest/redisClient.test.ts b/__test__/unittest/redisClient.test.ts
diff --git a/package.json b/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",

diff --git a/src/batch_edge_query.ts b/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);
-    });
-  }
 }
diff --git a/src/cache_handler.ts b/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';
@@ -10,8 +10,8 @@ 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 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 });
       }

diff --git a/src/edge_manager.ts b/src/edge_manager.ts
@@ -8,7 +8,7 @@ import BatchEdgeQueryHandler, { BatchEdgeQueryOptions } from './batch_edge_query
 import { Telemetry } from '@biothings-explorer/utils';
 import QEdge from './query_edge';
 import MetaKG from '@biothings-explorer/smartapi-kg';
-import { QueryHandlerOptions } from '.';
+import { QueryHandlerOptions } from '@biothings-explorer/types';
 import { Record } from '@biothings-explorer/api-response-transform';
 import { UnavailableAPITracker } from './types';
 import { RecordsByQEdgeID } from './results_assembly/query_results';
@@ -108,7 +108,7 @@ export default class QueryEdgeManager {
     }
     debug(
       `(5) Sending next edge '${nextQEdge.getID()}' ` +
-        `WITH entity count...(${nextQEdge.subject.entity_count || nextQEdge.object.entity_count})`,
+      `WITH entity count...(${nextQEdge.subject.entity_count || nextQEdge.object.entity_count})`,
     );
     return this.preSendOffCheck(nextQEdge);
   }
@@ -117,19 +117,18 @@ export default class QueryEdgeManager {
     this._qEdges.forEach((qEdge) => {
       debug(
         `'${qEdge.getID()}'` +
-          ` : (${qEdge.subject.entity_count || 0}) ` +
-          `${qEdge.reverse ? '<--' : '-->'}` +
-          ` (${qEdge.object.entity_count || 0})`,
+        ` : (${qEdge.subject.entity_count || 0}) ` +
+        `${qEdge.reverse ? '<--' : '-->'}` +
+        ` (${qEdge.object.entity_count || 0})`,
       );
     });
   }
 
   _logSkippedQueries(unavailableAPIs: UnavailableAPITracker): void {
     Object.entries(unavailableAPIs).forEach(([api, { skippedQueries }]) => {
       if (skippedQueries > 0) {
-        const skipMessage = `${skippedQueries} additional quer${skippedQueries > 1 ? 'ies' : 'y'} to ${api} ${
-          skippedQueries > 1 ? 'were' : 'was'
-        } skipped as the API was unavailable.`;
+        const skipMessage = `${skippedQueries} additional quer${skippedQueries > 1 ? 'ies' : 'y'} to ${api} ${skippedQueries > 1 ? 'were' : 'was'
+          } skipped as the API was unavailable.`;
         debug(skipMessage);
         this.logs.push(new LogEntry('WARNING', null, skipMessage).getLog());
       }
@@ -195,7 +194,7 @@ export default class QueryEdgeManager {
     const objectCuries = qEdge.object.curie;
     debug(
       `'${qEdge.getID()}' Reversed[${qEdge.reverse}] (${JSON.stringify(subjectCuries.length || 0)})` +
-        `--(${JSON.stringify(objectCuries.length || 0)}) entities / (${records.length}) records.`,
+      `--(${JSON.stringify(objectCuries.length || 0)}) entities / (${records.length}) records.`,
     );
     // debug(`IDS SUB ${JSON.stringify(sub_count)}`)
     // debug(`IDS OBJ ${JSON.stringify(obj_count)}`)
@@ -397,8 +396,7 @@ export default class QueryEdgeManager {
         new LogEntry(
           'INFO',
           null,
-          `Executing ${currentQEdge.getID()}${currentQEdge.isReversed() ? ' (reversed)' : ''}: ${
-            currentQEdge.subject.id
+          `Executing ${currentQEdge.getID()}${currentQEdge.isReversed() ? ' (reversed)' : ''}: ${currentQEdge.subject.id
           } ${currentQEdge.isReversed() ? '<--' : '-->'} ${currentQEdge.object.id}`,
         ).getLog(),
       );

diff --git a/src/graph/knowledge_graph.ts b/src/graph/knowledge_graph.ts
@@ -1,7 +1,6 @@
 import { toArray } from '../utils';
 import Debug from 'debug';
 import {
-  APIList,
   TrapiAttribute,
   TrapiKnowledgeGraph,
   TrapiKGEdge,
@@ -10,11 +9,11 @@ import {
   TrapiKGNodes,
   TrapiQualifier,
   TrapiSource,
-  APIDefinition,
 } from '../types';
 import KGNode from './kg_node';
 import KGEdge from './kg_edge';
 import { BTEGraphUpdate } from './graph';
+import { APIDefinition } from '@biothings-explorer/types';
 
 const debug = Debug('bte:biothings-explorer-trapi:KnowledgeGraph');