feat: use types package

biothings · Mar 22, 2024 · 996370a · 996370a
1 parent 97ddbdc
commit 996370a
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Showing 9 changed files with 42 additions and 123 deletions.
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
@@ -8,26 +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 } 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;
@@ -101,7 +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 {
@@ -113,8 +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(',')}`,
           );
         }
@@ -174,31 +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
@@ -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)}`)
@@ -395,8 +394,7 @@ 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');
 

diff --git a/src/index.ts b/src/index.ts
@@ -18,14 +18,14 @@ import InferredQueryHandler from './inferred_mode/inferred_mode';
 import KGNode from './graph/kg_node';
 import KGEdge from './graph/kg_edge';
 import {
-  APIList,
   TrapiAuxGraphCollection,
   TrapiAuxiliaryGraph,
   TrapiQNode,
   TrapiQueryGraph,
   TrapiResponse,
   TrapiResult,
 } from './types';
+import { QueryHandlerOptions } from '@biothings-explorer/types';
 import BTEGraph from './graph/graph';
 import QEdge from './query_edge';
 import { Telemetry } from '@biothings-explorer/utils';
@@ -38,20 +38,6 @@ export { default as QNode } from './query_node';
 export { default as InvalidQueryGraphError } from './exceptions/invalid_query_graph_error';
 export * from './qedge2apiedge';
 
-export interface QueryHandlerOptions {
-  provenanceUsesServiceProvider?: boolean;
-  smartAPIID?: string;
-  teamName?: string;
-  enableIDResolution?: boolean;
-  // TODO: type instances of `any`
-  apiList?: APIList;
-  schema?: any; // might be hard to type -- it's the entire TRAPI schema IIRC
-  dryrun?: boolean;
-  resolveOutputIDs?: boolean;
-  submitter?: string;
-  caching?: boolean; // from request url query values
-  EDGE_ATTRIBUTES_USED_IN_RECORD_HASH?: string[];
-}
 export default class TRAPIQueryHandler {
   logs: StampedLog[];
   options: QueryHandlerOptions;
@@ -447,13 +433,11 @@ export default class TRAPIQueryHandler {
 
         let log_msg: string;
         if (currentQEdge.reverse) {
-          log_msg = `qEdge ${currentQEdge.id} (reversed): ${currentQEdge.object.categories} > ${
-            currentQEdge.predicate ? `${currentQEdge.predicate} > ` : ''
-          }${currentQEdge.subject.categories}`;
+          log_msg = `qEdge ${currentQEdge.id} (reversed): ${currentQEdge.object.categories} > ${currentQEdge.predicate ? `${currentQEdge.predicate} > ` : ''
+            }${currentQEdge.subject.categories}`;
         } else {
-          log_msg = `qEdge ${currentQEdge.id}: ${currentQEdge.subject.categories} > ${
-            currentQEdge.predicate ? `${currentQEdge.predicate} > ` : ''
-          }${currentQEdge.object.categories}`;
+          log_msg = `qEdge ${currentQEdge.id}: ${currentQEdge.subject.categories} > ${currentQEdge.predicate ? `${currentQEdge.predicate} > ` : ''
+            }${currentQEdge.object.categories}`;
         }
         this.logs.push(new LogEntry('INFO', null, log_msg).getLog());
 
@@ -494,9 +478,8 @@ export default class TRAPIQueryHandler {
     });
     const qEdgesLogStr = qEdgesToLog.length > 1 ? `[${qEdgesToLog.join(', ')}]` : `${qEdgesToLog.join(', ')}`;
     if (len > 0) {
-      const terminateLog = `Query Edge${len !== 1 ? 's' : ''} ${qEdgesLogStr} ${
-        len !== 1 ? 'have' : 'has'
-      } no MetaKG edges. Your query terminates.`;
+      const terminateLog = `Query Edge${len !== 1 ? 's' : ''} ${qEdgesLogStr} ${len !== 1 ? 'have' : 'has'
+        } no MetaKG edges. Your query terminates.`;
       debug(terminateLog);
       this.logs.push(new LogEntry('WARNING', null, terminateLog).getLog());
       return false;
@@ -610,8 +593,7 @@ export default class TRAPIQueryHandler {
       new LogEntry(
         'INFO',
         null,
-        `Execution Summary: (${KGNodes}) nodes / (${kgEdges}) edges / (${results}) results; (${resultQueries}/${queries}) queries${
-          cached ? ` (${cached} cached qEdges)` : ''
+        `Execution Summary: (${KGNodes}) nodes / (${kgEdges}) edges / (${results}) results; (${resultQueries}/${queries}) queries${cached ? ` (${cached} cached qEdges)` : ''
         } returned results from(${sources.length}) unique API${sources.length === 1 ? 's' : ''}`,
       ).getLog(),
       new LogEntry('INFO', null, `APIs: ${sources.join(', ')} `).getLog(),

diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts
@@ -5,7 +5,8 @@ import async from 'async';
 import biolink from '../biolink';
 import { getTemplates, MatchedTemplate, TemplateLookup } from './template_lookup';
 import { scaled_sigmoid, inverse_scaled_sigmoid } from '../results_assembly/score';
-import TRAPIQueryHandler, { QueryHandlerOptions } from '../index';
+import TRAPIQueryHandler from '../index';
+import { QueryHandlerOptions } from '@biothings-explorer/types';
 import {
   CompactQualifiers,
   TrapiAuxGraphCollection,
@@ -384,9 +385,9 @@ export default class InferredQueryHandler {
         if (typeof combinedResponse.message.results[resultID].analyses[0].score !== 'undefined') {
           combinedResponse.message.results[resultID].analyses[0].score = resScore
             ? scaled_sigmoid(
-                inverse_scaled_sigmoid(combinedResponse.message.results[resultID].analyses[0].score) +
-                  inverse_scaled_sigmoid(resScore),
-              )
+              inverse_scaled_sigmoid(combinedResponse.message.results[resultID].analyses[0].score) +
+              inverse_scaled_sigmoid(resScore),
+            )
             : combinedResponse.message.results[resultID].analyses[0].score;
         } else {
           combinedResponse.message.results[resultID].analyses[0].score = resScore;
@@ -554,11 +555,9 @@ export default class InferredQueryHandler {
           const message = [
             `Addition of ${creativeLimitHit} results from Template ${i + 1}`,
             Object.keys(combinedResponse.message.results).length === this.CREATIVE_LIMIT ? ' meets ' : ' exceeds ',
-            `creative result maximum of ${this.CREATIVE_LIMIT} (reaching ${
-              Object.keys(combinedResponse.message.results).length
+            `creative result maximum of ${this.CREATIVE_LIMIT} (reaching ${Object.keys(combinedResponse.message.results).length
             } merged). `,
-            `Response will be truncated to top-scoring ${this.CREATIVE_LIMIT} results. Skipping remaining ${
-              subQueries.length - (i + 1)
+            `Response will be truncated to top-scoring ${this.CREATIVE_LIMIT} results. Skipping remaining ${subQueries.length - (i + 1)
             } `,
             subQueries.length - (i + 1) === 1 ? `template.` : `templates.`,
           ].join('');
@@ -583,9 +582,8 @@ export default class InferredQueryHandler {
       const total =
         Object.values(mergedResultsCount).reduce((sum, count) => sum + count, 0) +
         Object.keys(mergedResultsCount).length;
-      const message = `Merging Summary: (${total}) inferred-template results were merged into (${
-        Object.keys(mergedResultsCount).length
-      }) final results, reducing result count by (${total - Object.keys(mergedResultsCount).length})`;
+      const message = `Merging Summary: (${total}) inferred-template results were merged into (${Object.keys(mergedResultsCount).length
+        }) final results, reducing result count by (${total - Object.keys(mergedResultsCount).length})`;
       debug(message);
       combinedResponse.logs.push(new LogEntry('INFO', null, message).getLog());
     }

diff --git a/src/types.ts b/src/types.ts
@@ -1,26 +1,5 @@
-// TODO change how types are exported on smartapi-kg so this is a normal package import
-import { SmartAPISpec } from '@biothings-explorer/smartapi-kg';
 import { TrapiLog } from '@biothings-explorer/utils';
 
-declare global {
-  var missingAPIs: SmartAPISpec[];
-  var BIOLINK_VERSION: string;
-  var SCHEMA_VERSION: string;
-  var parentPort: MessagePort;
-  var cachingTasks: Promise<void>[];
-  var queryInformation: {
-    queryGraph: TrapiQueryGraph;
-    isCreativeMode: boolean;
-    creativeTemplate?: string;
-    totalRecords: number;
-    jobID?: string;
-    callback_url?: string;
-  };
-  var job: {
-    log: (logString: string) => void;
-  }; // TODO type as Piscina job
-}
-
 export interface TrapiQNode {
   ids?: string[];
   categories?: string[];
@@ -168,19 +147,6 @@ export interface TrapiResponse {
   logs: TrapiLog[];
 }
 
-export type APIDefinition = {
-  // Must have one of id or infores
-  id?: string; // SmartAPI ID, takes priority over infores
-  name: string; // Must match name on SmartAPI registry
-  infores?: string; // infores of API
-  primarySource?: boolean;
-} & ({ id: string } | { infores: string });
-
-export interface APIList {
-  include: APIDefinition[];
-  // takes priority over include, taking into account id/infores prioritization
-  exclude: APIDefinition[];
-}
 
 export interface UnavailableAPITracker {
   [server: string]: { skip: boolean; skippedQueries: number };

diff --git a/tsconfig.json b/tsconfig.json
@@ -9,7 +9,8 @@
       "biolink-model": ["../biolink-model"],
       "biomedical_id_resolver": ["../biomedical_id_resolver"],
       "@biothings-explorer/smartapi-kg": ["../smartapi-kg"],
-      "@biothings-explorer/utils": ["../utils"]
+      "@biothings-explorer/utils": ["../utils"],
+      "@biothings-explorer/types": ["../types"]
     }
   },
   "include": ["./src/**/*", "./src/biolink.json", "./src/smartapi_specs.json", "./src/predicates.json"],
@@ -29,6 +30,9 @@
     },
     {
       "path": "../utils"
+    },
+    {
+      "path": "../types"
     }
   ]
 }