chore: move biolink methods to utils

biothings · Sep 26, 2024 · ae2fcfc · ae2fcfc
1 parent 9bc677d
commit ae2fcfc
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Showing 11 changed files with 54 additions and 175 deletions.
diff --git a/src/biolink.ts b/src/biolink.ts
diff --git a/src/graph/knowledge_graph.ts b/src/graph/knowledge_graph.ts
@@ -1,4 +1,3 @@
-import { toArray } from '../utils';
 import Debug from 'debug';
 import {
   TrapiAttribute,
@@ -14,7 +13,7 @@ import KGNode from './kg_node';
 import KGEdge from './kg_edge';
 import { BTEGraphUpdate } from './graph';
 import { APIDefinition } from '@biothings-explorer/types';
-import { Telemetry } from '@biothings-explorer/utils';
+import { toArray, Telemetry } from '@biothings-explorer/utils';
 
 const debug = Debug('bte:biothings-explorer-trapi:KnowledgeGraph');
 

diff --git a/src/index.ts b/src/index.ts
@@ -192,7 +192,8 @@ export default class TRAPIQueryHandler {
           subject,
           object,
         });
-        const source = ontologyKnowledgeSourceMapping[this.subclassEdges[expanded][original].source] ?? 'error-not-provided';
+        const source =
+          ontologyKnowledgeSourceMapping[this.subclassEdges[expanded][original].source] ?? 'error-not-provided';
         subclassEdge.addAdditionalAttributes('biolink:knowledge_level', 'knowledge_assertion');
         subclassEdge.addAdditionalAttributes('biolink:agent_type', 'manual_agent');
         subclassEdge.addSource([
@@ -430,7 +431,9 @@ export default class TRAPIQueryHandler {
         const descendantsByCurie: { [curie: string]: { [descendants: string]: string } } = getDescendants(
           queryGraph.nodes[nodeId].ids,
         );
-        let expanded = Object.values(descendantsByCurie).map(descendants => Object.keys(descendants)).flat()
+        let expanded = Object.values(descendantsByCurie)
+          .map((descendants) => Object.keys(descendants))
+          .flat();
 
         expanded = _.uniq([...queryGraph.nodes[nodeId].ids, ...expanded]);
 
@@ -442,10 +445,11 @@ export default class TRAPIQueryHandler {
 
         if (foundExpandedIds) {
           Object.entries(descendantsByCurie).forEach(([curie, descendants]) => {
-            Object.entries(descendants).forEach(([ descendant, source ]) => {
+            Object.entries(descendants).forEach(([descendant, source]) => {
               if (queryGraph.nodes[nodeId].ids.includes(descendant)) return;
               if (!this.subclassEdges[descendant]) this.subclassEdges[descendant] = {};
-              if (!this.subclassEdges[descendant][curie]) this.subclassEdges[descendant][curie] = { source, qNodes: [] };
+              if (!this.subclassEdges[descendant][curie])
+                this.subclassEdges[descendant][curie] = { source, qNodes: [] };
               this.subclassEdges[descendant][curie].qNodes.push(nodeId);
             });
           });
@@ -474,10 +478,10 @@ export default class TRAPIQueryHandler {
   }
 
   async _processQueryGraph(queryGraph: TrapiQueryGraph): Promise<QEdge[]> {
-const queryGraphHandler = new QueryGraph(queryGraph, this.options.schema, this._queryIsPathfinder());
-const queryEdges = await queryGraphHandler.calculateEdges();
-this.logs = [...this.logs, ...queryGraphHandler.logs];
-return queryEdges;
+    const queryGraphHandler = new QueryGraph(queryGraph, this.options.schema, this._queryIsPathfinder());
+    const queryEdges = await queryGraphHandler.calculateEdges();
+    this.logs = [...this.logs, ...queryGraphHandler.logs];
+    return queryEdges;
   }
 
   async _edgesSupported(qEdges: QEdge[], metaKG: MetaKG): Promise<boolean> {
@@ -563,9 +567,17 @@ return queryEdges;
   }
 
   _queryIsPathfinder(): boolean {
-    const inferredEdgeCount = Object.values(this.queryGraph.edges).reduce((i, edge) => i + (edge.knowledge_type === 'inferred' ? 1 : 0), 0);
+    const inferredEdgeCount = Object.values(this.queryGraph.edges).reduce(
+      (i, edge) => i + (edge.knowledge_type === 'inferred' ? 1 : 0),
+      0,
+    );
     const pinnedNodes = Object.values(this.queryGraph.nodes).reduce((i, node) => i + (node.ids?.length > 0 ? 1 : 0), 0);
-    return inferredEdgeCount === 3 && pinnedNodes == 2 && Object.keys(this.queryGraph.edges).length === 3 && Object.keys(this.queryGraph.nodes).length === 3;
+    return (
+      inferredEdgeCount === 3 &&
+      pinnedNodes == 2 &&
+      Object.keys(this.queryGraph.edges).length === 3 &&
+      Object.keys(this.queryGraph.nodes).length === 3
+    );
   }
 
   _queryUsesInferredMode(): boolean {
@@ -585,7 +597,7 @@ return queryEdges;
     const pathfinderResponse = await pathfinderHandler.query();
 
     if (pathfinderResponse) {
-        this.getResponse = () => pathfinderResponse;
+      this.getResponse = () => pathfinderResponse;
     }
   }
 
@@ -603,7 +615,7 @@ return queryEdges;
       this.options,
       this.path,
       this.predicatePath,
-      this.includeReasoner
+      this.includeReasoner,
     );
     const inferredQueryResponse = await inferredQueryHandler.query();
     if (inferredQueryResponse) {

diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts
@@ -1,8 +1,7 @@
 import Debug from 'debug';
+import * as utils from '@biothings-explorer/utils';
 import { LogEntry, StampedLog, Telemetry } from '@biothings-explorer/utils';
-import * as utils from '../utils';
 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 from '../index';
@@ -164,13 +163,13 @@ export default class InferredQueryHandler {
   async findTemplates(qEdge: TrapiQEdge, qSubject: TrapiQNode, qObject: TrapiQNode): Promise<MatchedTemplate[]> {
     debug('Looking up query Templates');
     const expandedSubject = qSubject.categories.reduce((arr: string[], subjectCategory: string) => {
-      return utils.getUnique([...arr, ...biolink.getDescendantClasses(utils.removeBioLinkPrefix(subjectCategory))]);
+      return utils.getUnique([...arr, ...utils.biolink.getDescendantClasses(utils.removeBioLinkPrefix(subjectCategory))]);
     }, [] as string[]);
     const expandedPredicates = qEdge.predicates.reduce((arr: string[], predicate: string) => {
-      return utils.getUnique([...arr, ...biolink.getDescendantPredicates(utils.removeBioLinkPrefix(predicate))]);
+      return utils.getUnique([...arr, ...utils.biolink.getDescendantPredicates(utils.removeBioLinkPrefix(predicate))]);
     }, [] as string[]);
     const expandedObject = qObject.categories.reduce((arr: string[], objectCategory: string) => {
-      return utils.getUnique([...arr, ...biolink.getDescendantClasses(utils.removeBioLinkPrefix(objectCategory))]);
+      return utils.getUnique([...arr, ...utils.biolink.getDescendantClasses(utils.removeBioLinkPrefix(objectCategory))]);
     }, [] as string[]);
     const qualifierConstraints = (qEdge.qualifier_constraints || []).map((qualifierSetObj) => {
       return Object.fromEntries(
@@ -355,7 +354,7 @@ export default class InferredQueryHandler {
             // Predicate matches or is descendant
             const predicateMatch =
               qEdge.predicates?.some((predicate) => {
-                const descendantMatch = biolink
+                const descendantMatch = utils.biolink
                   .getDescendantPredicates(utils.removeBioLinkPrefix(predicate))
                   .includes(utils.removeBioLinkPrefix(boundEdge.predicate));
                 return predicate === boundEdge.predicate || descendantMatch;
@@ -372,10 +371,10 @@ export default class InferredQueryHandler {
                       let valueMatch: boolean;
                       try {
                         const descendants = queryQualifier.qualifier_value.includes('biolink:')
-                          ? biolink.getDescendantPredicates(
+                          ? utils.biolink.getDescendantPredicates(
                             utils.removeBioLinkPrefix(queryQualifier.qualifier_value as string),
                           )
-                          : biolink.getDescendantQualifiers(
+                          : utils.biolink.getDescendantQualifiers(
                             utils.removeBioLinkPrefix(queryQualifier.qualifier_value as string),
                           );
                         valueMatch =

diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts
@@ -11,11 +11,10 @@ import {
 } from '@biothings-explorer/types';
 import InferredQueryHandler from './inferred_mode';
 import { scaled_sigmoid, inverse_scaled_sigmoid } from '../results_assembly/score';
-import { LogEntry, StampedLog, Telemetry } from '@biothings-explorer/utils';
+import * as utils from '@biothings-explorer/utils';
+import { LogEntry, StampedLog, Telemetry, removeBioLinkPrefix } from '@biothings-explorer/utils';
 import Debug from 'debug';
 import generateTemplates from './pf_template_generator';
-import biolink from '../biolink';
-import { removeBioLinkPrefix } from '../utils';
 const debug = Debug('bte:biothings-explorer-trapi:pathfinder');
 
 interface ResultAuxObject {
@@ -163,7 +162,7 @@ export default class PathfinderQueryHandler {
       const label = [this.mainEdge.subject, this.unpinnedNodeId, this.mainEdge.object];
       const ancestorsToInject = new Set();
       node.categories.forEach((category) => {
-        const ancestors = biolink.getAncestorClasses(removeBioLinkPrefix(category));
+        const ancestors = utils.biolink.getAncestorClasses(removeBioLinkPrefix(category));
         if (!Array.isArray(ancestors)) return;
         ancestors.forEach((ancestor) => {
           if (FALLBACK_ANCESTORS.includes(ancestor)) {
@@ -242,7 +241,7 @@ export default class PathfinderQueryHandler {
     if (this.unpinnedNode.categories && !this.unpinnedNode.categories.includes('biolink:NamedThing')) {
       acceptableTypes = new Set<string>();
       for (const category of this.unpinnedNode.categories) {
-        for (const desc of biolink.getDescendantClasses(removeBioLinkPrefix(category))) {
+        for (const desc of utils.biolink.getDescendantClasses(removeBioLinkPrefix(category))) {
           acceptableTypes.add('biolink:' + desc);
         }
       }

diff --git a/src/inferred_mode/pf_template_generator.ts b/src/inferred_mode/pf_template_generator.ts
@@ -1,7 +1,7 @@
 import path from "path";
 import fs from "fs/promises";
 import yaml2json from "js-yaml";
-import biolink from "../biolink";
+import * as utils from "@biothings-explorer/utils";
 import { TrapiQNode, TrapiQueryGraph } from "@biothings-explorer/types";
 
 interface CategoryTable {
@@ -27,8 +27,8 @@ async function loadTables() {
   for (const table of [categoryTable, predicateTable]) {
     for (const category1 in table) {
       for (const category2 in table[category1]) {
-        for (const descendant1 of biolink.getDescendantClasses(category1)) {
-          for (const descendant2 of biolink.getDescendantClasses(category2)) {
+        for (const descendant1 of utils.biolink.getDescendantClasses(category1)) {
+          for (const descendant2 of utils.biolink.getDescendantClasses(category2)) {
             if (table?.['biolink:'+descendant1]?.['biolink:'+descendant2] !== undefined) continue;
 
             if (!('biolink:'+descendant1 in table)) {
@@ -175,4 +175,4 @@ export default async function generateTemplates(sub: TrapiQNode, un: TrapiQNode,
     queryGraphs.push(queryGraph);
   }
   return queryGraphs;
-}
+}
diff --git a/src/query_edge.ts b/src/query_edge.ts
@@ -1,10 +1,9 @@
 import helper from './helper';
 import Debug from 'debug';
-import * as utils from './utils';
-import biolink from './biolink';
 import { Record, RecordNode, FrozenRecord } from '@biothings-explorer/api-response-transform';
 import QNode from './query_node';
 import { QNodeInfo } from './query_node';
+import * as utils from '@biothings-explorer/utils';
 import { LogEntry, StampedLog } from '@biothings-explorer/utils';
 import { TrapiAttributeConstraint, TrapiQualifierConstraint } from '@biothings-explorer/types';
 
@@ -129,7 +128,7 @@ export default class QEdge {
   }
 
   expandPredicates(predicates: string[]): string[] {
-    return Array.from(new Set(predicates.reduce((acc, cur) => [...acc, ...biolink.getDescendantPredicates(cur)], [])));
+    return Array.from(new Set(predicates.reduce((acc, cur) => [...acc, ...utils.biolink.getDescendantPredicates(cur)], [])));
   }
 
   getPredicate(): string[] {
@@ -141,7 +140,7 @@ export default class QEdge {
     debug(`Expanded edges: ${expandedPredicates}`);
     return expandedPredicates
       .map((predicate) => {
-        return this.isReversed() === true ? biolink.reverse(predicate) : predicate;
+        return this.isReversed() === true ? utils.biolink.reverse(predicate) : predicate;
       })
       .filter((item) => !(typeof item === 'undefined'));
   }
@@ -154,21 +153,21 @@ export default class QEdge {
             ? Array.isArray(qualifier_value)
               ? Array.from(
                   qualifier_value.reduce((set: Set<string>, predicate: string) => {
-                    biolink
+                    utils.biolink
                       .getDescendantPredicates(utils.removeBioLinkPrefix(predicate))
                       .forEach((item) => set.add(`biolink:${utils.removeBioLinkPrefix(item)}`));
                     return set;
                   }, new Set()),
                 )
               : Array.from(
                   new Set(
-                    biolink
+                    utils.biolink
                       .getDescendantPredicates(utils.removeBioLinkPrefix(qualifier_value))
                       .map((item) => `biolink:${utils.removeBioLinkPrefix(item)}`),
                   ),
                 )
             : Array.from(
-                new Set(biolink.getDescendantQualifiers(utils.removeBioLinkPrefix(qualifier_value as string))),
+                new Set(utils.biolink.getDescendantQualifiers(utils.removeBioLinkPrefix(qualifier_value as string))),
               );
 
           return {
@@ -575,6 +574,6 @@ export default class QEdge {
   }
 
   getReversedPredicate(predicate: string): string {
-    return predicate ? biolink.reverse(predicate) : undefined;
+    return predicate ? utils.biolink.reverse(predicate) : undefined;
   }
 }
diff --git a/src/query_graph.ts b/src/query_graph.ts
@@ -1,12 +1,11 @@
 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 QNode from './query_node';
-import biolink from './biolink';
 import { resolveSRI } from 'biomedical_id_resolver';
 import _ from 'lodash';
-import * as utils from './utils';
 import { TrapiQueryGraph } from '@biothings-explorer/types';
 import NotImplementedError from './exceptions/not_implemented_error';
 
@@ -226,7 +225,7 @@ export default class QueryGraph {
     } else {
       try {
         let finalCategories: string[] = [];
-        const tree = biolink.biolink.classTree.objects;
+        const tree = utils.biolink.biolink.classTree.objects;
 
         // get array of all unique categories for all curies
         const allCategories = [