fix: typings, imports

jest.config.js

@@ -1,4 +1,4 @@
 module.exports = {
-    transform: { "\\.ts$": ['ts-jest'] },
-    setupFilesAfterEnv: ['./jest.setup.js', './jest.setup.redis-mock.js']
-};
+  preset: 'ts-jest',
+  testEnvironment: 'node',
+};

package.json

@@ -38,6 +38,7 @@
     "coveralls": "^3.1.0",
     "ioredis-mock": "^8.2.2",
     "jest": "^26.6.3",
+    "jest-util": "^26.6.2",
     "prettier": "^2.2.1",
     "standard-version": "^9.1.1",
     "ts-jest": "^26.5.4",

src/batch_edge_query.ts

@@ -10,7 +10,7 @@ import { StampedLog } from './log_entry';
 import { QueryHandlerOptions } from '.';
 import QEdge from './query_edge';
 import { UnavailableAPITracker } from './types';
-import { Record } from '../../api-response-transform/built';
+import { Record } from '@biothings-explorer/api-response-transform';
 
 export interface BatchEdgeQueryOptions extends QueryHandlerOptions {
   recordHashEdgeAttributes: string[];
@@ -24,7 +24,7 @@ export default class BatchEdgeQueryHandler {
   options: QueryHandlerOptions;
   resolveOutputIDs: boolean;
   qEdges: QEdge | QEdge[];
-  constructor(metaKG: MetaKG, resolveOutputIDs = true, options: BatchEdgeQueryOptions) {
+  constructor(metaKG: MetaKG, resolveOutputIDs = true, options?: BatchEdgeQueryOptions) {
     this.metaKG = metaKG;
     this.subscribers = [];
     this.logs = [];

src/graph/knowledge_graph.ts

@@ -26,8 +26,8 @@ export default class KnowledgeGraph {
     [edgeID: string]: TrapiKGEdge;
   };
   kg: TrapiKnowledgeGraph;
-  apiList: APIDefinition[];
-  constructor(apiList: APIDefinition[]) {
+  apiList?: APIDefinition[];
+  constructor(apiList?: APIDefinition[]) {
     this.nodes = {};
     this.edges = {};
     this.kg = {
@@ -84,7 +84,7 @@ export default class KnowledgeGraph {
     for (const key in kgNode.nodeAttributes) {
       node.attributes.push({
         attribute_type_id: key,
-        value: kgNode.nodeAttributes[key],
+        value: kgNode.nodeAttributes[key] as string[],
         //value_type_id: 'bts:' + key,
       });
     }

src/index.ts

@@ -11,10 +11,8 @@ import EdgeManager from './edge_manager';
 import _ from 'lodash';
 import QEdge2APIEdgeHandler from './qedge2apiedge';
 import LogEntry, { StampedLog } from './log_entry';
-import { redisClient, getNewRedisClient } from './redis-client';
 import { promises as fs } from 'fs';
 import { getDescendants } from '@biothings-explorer/node-expansion';
-import { getTemplates, supportedLookups } from './inferred_mode/template_lookup';
 import { resolveSRI, SRIResolverFailiure } from 'biomedical_id_resolver';
 import InferredQueryHandler from './inferred_mode/inferred_mode';
 import KGNode from './graph/kg_node';
@@ -32,7 +30,15 @@ import {
 import BTEGraph from './graph/graph';
 import QEdge from './query_edge';
 
-export { InvalidQueryGraphError, redisClient, getNewRedisClient, LogEntry, getTemplates, supportedLookups };
+// Exports for external availability
+export * from './types';
+export { redisClient, getNewRedisClient } from './redis-client';
+export { getTemplates, supportedLookups } from './inferred_mode/template_lookup';
+export { default as QEdge } from './query_edge';
+export { default as QNode } from './query_node';
+export { default as InvalidQueryGraphError } from './exceptions/invalid_query_graph_error';
+export { default as LogEntry } from './log_entry';
+export * from './qedge2apiedge';
 
 export interface QueryHandlerOptions {
   provenanceUsesServiceProvider?: boolean;
@@ -48,7 +54,7 @@ export interface QueryHandlerOptions {
   caching?: boolean; // from request url query values
   EDGE_ATTRIBUTES_USED_IN_RECORD_HASH?: string[];
 }
-export class TRAPIQueryHandler {
+export default class TRAPIQueryHandler {
   logs: StampedLog[];
   options: QueryHandlerOptions;
   includeReasoner: boolean;
@@ -62,7 +68,12 @@ export class TRAPIQueryHandler {
   auxGraphs: TrapiAuxGraphCollection;
   finalizedResults: TrapiResult[];
   queryGraph: TrapiQueryGraph;
-  constructor(options = {}, smartAPIPath = undefined, predicatesPath = undefined, includeReasoner = true) {
+  constructor(
+    options: QueryHandlerOptions = {},
+    smartAPIPath: string = undefined,
+    predicatesPath: string = undefined,
+    includeReasoner = true,
+  ) {
     this.logs = [];
     this.options = options;
     this.options.provenanceUsesServiceProvider = this.options.smartAPIID || this.options.teamName ? true : false;
@@ -173,8 +184,8 @@ export class TRAPIQueryHandler {
           subject,
           object,
         });
-        const source = Object.keys(ontologyKnowledgeSourceMapping).find(([prefix]) => {
-          if (expanded.includes(prefix)) return true;
+        const source = Object.entries(ontologyKnowledgeSourceMapping).find(([prefix]) => {
+          return expanded.includes(prefix);
         })[1];
         subclassEdge.addSource([
           { resource_id: source, resource_role: 'primary_knowledge_source' },
@@ -599,9 +610,9 @@ export class TRAPIQueryHandler {
       new LogEntry(
         'INFO',
         null,
-        `execution Summary: (${KGNodes}) nodes / (${kgEdges}) edges / (${results}) results; (${resultQueries}/${queries}) queries${
+        `Execution Summary: (${KGNodes}) nodes / (${kgEdges}) edges / (${results}) results; (${resultQueries}/${queries}) queries${
           cached ? ` (${cached} cached qEdges)` : ''
-        } returned results from(${sources.length}) unique APIs ${sources.length === 1 ? 's' : ''} `,
+        } returned results from(${sources.length}) unique API${sources.length === 1 ? 's' : ''}`,
       ).getLog(),
       new LogEntry('INFO', null, `APIs: ${sources.join(', ')} `).getLog(),
     ];
@@ -640,7 +651,7 @@ export class TRAPIQueryHandler {
           null,
           `The following APIs were unavailable at the time of execution: ${global.missingAPIs
             .map((spec) => spec.info.title)
-            .join(', ')} `,
+            .join(', ')}`,
         ).getLog(),
       );
     }

src/inferred_mode/inferred_mode.ts

@@ -5,7 +5,7 @@ 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 { QueryHandlerOptions, TRAPIQueryHandler } from '..';
+import TRAPIQueryHandler, { QueryHandlerOptions } from '../index';
 import {
   CompactQualifiers,
   TrapiAuxGraphCollection,
@@ -20,11 +20,12 @@ import {
 const debug = Debug('bte:biothings-explorer-trapi:inferred-mode');
 
 export interface CombinedResponse {
-  workflow: { id: string }[];
+  description?: string;
+  workflow?: { id: string }[];
   message: {
     query_graph: TrapiQueryGraph;
     knowledge_graph: TrapiKnowledgeGraph;
-    auxiliary_graphs: TrapiAuxGraphCollection;
+    auxiliary_graphs?: TrapiAuxGraphCollection;
     results: {
       [resultID: string]: TrapiResult;
     };
@@ -488,6 +489,8 @@ export default class InferredQueryHandler {
     const { qEdgeID, qEdge, qSubject, qObject } = this.getQueryParts();
     const subQueries = await this.createQueries(qEdge, qSubject, qObject);
     const combinedResponse = {
+      status: 'Success',
+      description: '',
       schema_version: global.SCHEMA_VERSION,
       biolink_version: global.BIOLINK_VERSION,
       workflow: [{ id: 'lookup' }],

src/qedge2apiedge.ts

@@ -5,8 +5,8 @@ const CURIE_WITH_PREFIXES = ['MONDO', 'DOID', 'UBERON', 'EFO', 'HP', 'CHEBI', 'C
 import Debug from 'debug';
 import QEdge from './query_edge';
 import MetaKG from '@biothings-explorer/smartapi-kg';
-import { SmartAPIKGOperationObject } from '../../smartapi-kg/built/parser/types';
-import { SRIBioEntity } from '../../../biomedical_id_resolver/built/common/types';
+import { SmartAPIKGOperationObject } from '@biothings-explorer/smartapi-kg';
+import { SRIBioEntity } from 'biomedical_id_resolver';
 const debug = Debug('bte:biothings-explorer-trapi:qedge2btedge');
 
 export interface MetaXEdge extends SmartAPIKGOperationObject {

src/query_edge.ts

@@ -7,7 +7,6 @@ import QNode from './query_node';
 import { QNodeInfo } from './query_node';
 import { StampedLog } from './log_entry';
 import { TrapiAttributeConstraint, TrapiQualifierConstraint } from './types';
-// import { FrozenRecord } from '../../api-response-transform/built/record';
 
 const debug = Debug('bte:biothings-explorer-trapi:QEdge');
 

src/query_node.ts

@@ -10,7 +10,7 @@ const debug = Debug('bte:biothings-explorer-trapi:QNode');
 export interface QNodeInfo {
   id: string;
   categories?: string[];
-  ids: string[];
+  ids?: string[];
   is_set?: boolean;
   expanded_curie?: ExpandedCuries;
   held_curie?: string[];

src/redis-client.ts

@@ -70,7 +70,6 @@ interface RedisClientInterface {
   usingLock: (
     resources: string[],
     duration: number,
-    settings: unknown,
     routine?: (signal: RedlockAbortSignal) => Promise<unknown>,
   ) => Promise<unknown>;
   incrTimeout: (key: string, callback: Callback<number>) => Promise<number>;
@@ -106,8 +105,8 @@ function addClientFuncs(client: Redis | Cluster, redlock: Redlock): RedisClientI
         ? addPrefixToAll(timeoutFunc((...args: RedisKey[]) => client.del(...args)))
         : timeoutFunc((...args: RedisKey[]) => client.del(...args)),
     usingLock: lockPrefix(
-      (resources: string[], duration: number, settings, routine?: (signal: RedlockAbortSignal) => Promise<unknown>) =>
-        redlock.using(resources, duration, settings, routine),
+      (resources: string[], duration: number, routine?: (signal: RedlockAbortSignal) => Promise<unknown>) =>
+        redlock.using(resources, duration, routine),
     ),
     incrTimeout: decorate((key: string) => client.incr(key)),
     decrTimeout: decorate((key: string) => client.decr(key)),

src/types.ts

@@ -20,19 +20,19 @@ declare global {
 }
 
 export interface TrapiQNode {
-  ids: string[];
-  categories: string[];
-  is_set: boolean;
-  constraints: TrapiAttributeConstraint[];
+  ids?: string[];
+  categories?: string[];
+  is_set?: boolean;
+  constraints?: TrapiAttributeConstraint[];
 }
 
 export interface TrapiQEdge {
-  knowledge_type: string;
-  predicates: string[];
+  knowledge_type?: string;
+  predicates?: string[];
   subject: string;
   object: string;
-  attribute_constraints: TrapiAttributeConstraint[];
-  qualifier_constraints: TrapiQualifierConstraint[];
+  attribute_constraints?: TrapiAttributeConstraint[];
+  qualifier_constraints?: TrapiQualifierConstraint[];
 }
 
 export interface TrapiQueryGraph {
@@ -83,9 +83,10 @@ export interface TrapiAttribute {
   original_attribute_name?: string;
   value: string | string[] | number | number[];
   value_type_id?: string;
-  attribute_source?: string;
-  value_url?: string;
+  attribute_source?: string | null;
+  value_url?: string | null;
   attributes?: TrapiAttribute;
+  [additionalProperties: string]: string | string[] | null | TrapiAttribute | number | number[];
 }
 
 export interface TrapiQualifier {
@@ -117,8 +118,8 @@ export interface TrapiEdgeBinding {
 }
 
 export interface TrapiAnalysis {
-  resource_id: string;
-  score: number;
+  resource_id?: string;
+  score?: number;
   edge_bindings: {
     [qEdgeID: string]: TrapiEdgeBinding[];
   };
@@ -152,14 +153,14 @@ export interface TrapiAuxGraphCollection {
 }
 
 export interface TrapiResponse {
-  description: string;
-  schema_version: string;
-  biolink_version: string;
-  workflow: { id: string }[];
+  description?: string;
+  schema_version?: string;
+  biolink_version?: string;
+  workflow?: { id: string }[];
   message: {
     query_graph: TrapiQueryGraph;
     knowledge_graph: TrapiKnowledgeGraph;
-    auxiliary_graphs: TrapiAuxGraphCollection;
+    auxiliary_graphs?: TrapiAuxGraphCollection;
     results: TrapiResult[];
   };
   logs: TrapiLog[];

src/update_nodes.ts

@@ -3,6 +3,7 @@ import Debug from 'debug';
 import { ResolverInput, SRIResolverOutput } from '../../../biomedical_id_resolver/built/common/types';
 import { Record } from '@biothings-explorer/api-response-transform';
 import QEdge from './query_edge';
+import { NodeNormalizerResultObj } from '../../api-response-transform/built';
 const debug = Debug('bte:biothings-explorer-trapi:nodeUpdateHandler');
 
 export interface CuriesByCategory {
@@ -63,7 +64,7 @@ export default class NodesUpdateHandler {
     return;
   }
 
-  _createEquivalentIDsObject(record: Record) {
+  _createEquivalentIDsObject(record: Record): { [curie: string]: NodeNormalizerResultObj } {
     if (record.object.normalizedInfo !== undefined) {
       return {
         [record.object.curie]: record.object.normalizedInfo,