add template to creative debug

biothings · Nov 1, 2024 · edadf52 · edadf52
1 parent 9eabfa1
commit edadf52
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Showing 16 changed files with 18 additions and 17 deletions.
diff --git a/src/batch_edge_query.ts b/src/batch_edge_query.ts
@@ -2,7 +2,7 @@ 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';
+import { Debug } from "@biothings-explorer/utils";
 const debug = Debug('bte:biothings-explorer-trapi:batch_edge_query');
 import CacheHandler from './cache_handler';
 import { threadId } from 'worker_threads';

diff --git a/src/cache_handler.ts b/src/cache_handler.ts
@@ -1,5 +1,5 @@
 import { redisClient } from '@biothings-explorer/utils';
-import Debug from 'debug';
+import { Debug } from "@biothings-explorer/utils";
 const debug = Debug('bte:biothings-explorer-trapi:cache_handler');
 import { LogEntry, StampedLog } from '@biothings-explorer/utils';
 import async from 'async';

diff --git a/src/edge_manager.ts b/src/edge_manager.ts
@@ -1,7 +1,7 @@
 import _ from 'lodash';
 import { LogEntry, StampedLog } from '@biothings-explorer/utils';
 import BTEError from './exceptions/bte_error';
-import Debug from 'debug';
+import { Debug } from "@biothings-explorer/utils";
 const debug = Debug('bte:biothings-explorer-trapi:edge-manager');
 import * as config from './config';
 import BatchEdgeQueryHandler, { BatchEdgeQueryOptions } from './batch_edge_query';

diff --git a/src/graph/graph.ts b/src/graph/graph.ts
@@ -1,6 +1,6 @@
 import kg_edge from './kg_edge';
 import kg_node from './kg_node';
-import Debug from 'debug';
+import { Debug } from "@biothings-explorer/utils";
 import { LogEntry, StampedLog } from '@biothings-explorer/utils';
 import KGNode from './kg_node';
 import KGEdge from './kg_edge';

diff --git a/src/graph/knowledge_graph.ts b/src/graph/knowledge_graph.ts
@@ -1,4 +1,4 @@
-import Debug from 'debug';
+import { Debug } from "@biothings-explorer/utils";
 import {
   TrapiAttribute,
   TrapiKnowledgeGraph,

diff --git a/src/index.ts b/src/index.ts
@@ -4,7 +4,7 @@ import QueryGraph from './query_graph';
 import KnowledgeGraph from './graph/knowledge_graph';
 import TrapiResultsAssembler from './results_assembly/query_results';
 import InvalidQueryGraphError from './exceptions/invalid_query_graph_error';
-import Debug from 'debug';
+import { Debug } from "@biothings-explorer/utils";
 const debug = Debug('bte:biothings-explorer-trapi:main');
 import Graph from './graph/graph';
 import EdgeManager from './edge_manager';

diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts
@@ -1,4 +1,4 @@
-import Debug from 'debug';
+import { Debug, withDebugContext } from "@biothings-explorer/utils"
 import {
   biolink,
   getUnique,
@@ -648,7 +648,8 @@ export default class InferredQueryHandler {
         handler.setQueryGraph(queryGraph);
         const failedHandlerLogs: { [index: number]: StampedLog[] } = {};
         try {
-          await timeoutPromise(handler.query(AbortSignal.timeout(this.CREATIVE_TIMEOUT)), this.CREATIVE_TIMEOUT);
+          const query = withDebugContext(` Template-${i + 1}`, handler.query.bind(handler));
+          await timeoutPromise(query(AbortSignal.timeout(this.CREATIVE_TIMEOUT)), this.CREATIVE_TIMEOUT);
         } catch (error) {
           handler.logs.forEach((log) => {
             log.message = `[Template-${i + 1}]: ${log.message}`;

diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts
@@ -13,7 +13,7 @@ import InferredQueryHandler from './inferred_mode';
 import { scaled_sigmoid, inverse_scaled_sigmoid } from '../results_assembly/score';
 import * as utils from '@biothings-explorer/utils';
 import { LogEntry, StampedLog, Telemetry, removeBioLinkPrefix } from '@biothings-explorer/utils';
-import Debug from 'debug';
+import { Debug } from "@biothings-explorer/utils";
 import generateTemplates from './pf_template_generator';
 import { enrichTrapiResultsWithPfocrFigures } from '../results_assembly/pfocr';
 const debug = Debug('bte:biothings-explorer-trapi:pathfinder');

diff --git a/src/qedge2apiedge.ts b/src/qedge2apiedge.ts
@@ -2,7 +2,7 @@ import _ from 'lodash';
 import { LogEntry, StampedLog } from '@biothings-explorer/utils';
 import * as config from './config';
 const CURIE_WITH_PREFIXES = ['MONDO', 'DOID', 'UBERON', 'EFO', 'HP', 'CHEBI', 'CL', 'MGI', 'NCIT'];
-import Debug from 'debug';
+import { Debug } from "@biothings-explorer/utils";
 import QEdge from './query_edge';
 import MetaKG from '@biothings-explorer/smartapi-kg';
 import { SmartAPIKGOperationObject } from '@biothings-explorer/smartapi-kg';

diff --git a/src/query_edge.ts b/src/query_edge.ts
@@ -1,5 +1,5 @@
 import helper from './helper';
-import Debug from 'debug';
+import { Debug } from "@biothings-explorer/utils";
 import { Record, RecordNode, FrozenRecord } from '@biothings-explorer/api-response-transform';
 import QNode from './query_node';
 import { QNodeInfo } from './query_node';

diff --git a/src/query_graph.ts b/src/query_graph.ts
@@ -2,7 +2,7 @@ import QEdge from './query_edge';
 import InvalidQueryGraphError from './exceptions/invalid_query_graph_error';
 import * as utils from '@biothings-explorer/utils';
 import { LogEntry, StampedLog } from '@biothings-explorer/utils';
-import Debug from 'debug';
+import { Debug } from "@biothings-explorer/utils";
 import QNode from './query_node';
 import { resolveSRI } from 'biomedical_id_resolver';
 import _ from 'lodash';

diff --git a/src/query_node.ts b/src/query_node.ts
@@ -1,7 +1,7 @@
 /* eslint-disable @typescript-eslint/no-var-requires */
 import _ from 'lodash';
 import * as utils from '@biothings-explorer/utils';
-import Debug from 'debug';
+import { Debug } from "@biothings-explorer/utils";
 import InvalidQueryGraphError from './exceptions/invalid_query_graph_error';
 import { SRIBioEntity } from 'biomedical_id_resolver';
 const debug = Debug('bte:biothings-explorer-trapi:QNode');

diff --git a/src/results_assembly/pfocr.ts b/src/results_assembly/pfocr.ts
@@ -1,5 +1,5 @@
 import axios from 'axios';
-import Debug from 'debug';
+import { Debug } from "@biothings-explorer/utils";
 const debug = Debug('bte:biothings-explorer-trapi:pfocr');
 import _ from 'lodash';
 import { LogEntry, StampedLog, intersection, biolink, toArray, removeBioLinkPrefix } from '@biothings-explorer/utils';

diff --git a/src/results_assembly/query_results.ts b/src/results_assembly/query_results.ts
@@ -1,6 +1,6 @@
 import { LogEntry, StampedLog } from '@biothings-explorer/utils';
 import { TrapiResult } from '@biothings-explorer/types';
-import Debug from 'debug';
+import { Debug } from "@biothings-explorer/utils";
 import { zip } from 'lodash';
 const debug = Debug('bte:biothings-explorer-trapi:QueryResult');
 import { getScores, calculateScore, ScoreCombos } from './score';

diff --git a/src/results_assembly/score.ts b/src/results_assembly/score.ts
@@ -1,4 +1,4 @@
-import Debug from 'debug';
+import { Debug } from "@biothings-explorer/utils";
 import axios from 'axios';
 const debug = Debug('bte:biothings-explorer-trapi:score');
 import os from 'os';

diff --git a/src/update_nodes.ts b/src/update_nodes.ts
@@ -1,5 +1,5 @@
 import { resolveSRI } from 'biomedical_id_resolver';
-import Debug from 'debug';
+import { Debug } from "@biothings-explorer/utils";
 import { ResolverInput, SRIResolverOutput } from 'biomedical_id_resolver';
 import { Record } from '@biothings-explorer/api-response-transform';
 import QEdge from './query_edge';