From e1ab1497b4ccfad7dd4794af33644934b429f66c Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Wed, 17 Apr 2024 19:56:05 -0700 Subject: [PATCH 1/4] make aux graphs more efficient --- src/inferred_mode/pathfinder.ts | 49 +++++++++++++++++---------------- 1 file changed, 26 insertions(+), 23 deletions(-) diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts index 4591bf77..c842dde1 100644 --- a/src/inferred_mode/pathfinder.ts +++ b/src/inferred_mode/pathfinder.ts @@ -156,7 +156,7 @@ export default class PathfinderQueryHandler { debug(message1); this.logs.push(new LogEntry('INFO', null, message1).getLog()); - const { results: newResultObject, graphs: newAuxGraphs } = this._searchForIntermediates(creativeResponse, dfsGraph, supportGraphsPerNode, kgSrc, kgDst, kgEdge); + const { results: newResultObject, graphs: newAuxGraphs } = this._searchForIntermediates(creativeResponse, dfsGraph, supportGraphsPerNode, kgSrc, kgDst); creativeResponse.message.results = Object.values(newResultObject).sort((a, b) => (b.analyses[0].score ?? 0) - (a.analyses[0].score ?? 0)).slice(0, this.CREATIVE_LIMIT); creativeResponse.description = `Query processed successfully, retrieved ${creativeResponse.message.results.length} results.` @@ -166,7 +166,11 @@ export default class PathfinderQueryHandler { for (const eb of Object.values(creativeResponse.message.results[res].analyses[0].edge_bindings)) { for (const edge of eb) { const auxGraph = creativeResponse.message.knowledge_graph.edges[edge.id].attributes.find(attr => attr.attribute_type_id === 'biolink:support_graphs')?.value[0]; - finalNewAuxGraphs[auxGraph] = { edges: Array.from(newAuxGraphs[auxGraph].edges) }; + finalNewAuxGraphs[auxGraph] = { edges: [] }; + for (const ed of newAuxGraphs[auxGraph].edges) { + const [st, en] = ed.split('-'); + finalNewAuxGraphs[auxGraph].edges.push.apply(finalNewAuxGraphs[auxGraph].edges, dfsGraph[st][en]); + } } } } @@ -182,15 +186,18 @@ export default class PathfinderQueryHandler { return creativeResponse; } - _searchForIntermediates(creativeResponse: TrapiResponse, dfsGraph: DfsGraph, supportGraphsPerNode: { [node: string]: Set }, kgSrc: string, kgDst: string, kgEdge: string): ResultAuxObject { + _searchForIntermediates(creativeResponse: TrapiResponse, dfsGraph: DfsGraph, supportGraphsPerNode: { [node: string]: Set }, kgSrc: string, kgDst: string): ResultAuxObject { const span = Telemetry.startSpan({ description: 'pathfinderIntermediateSearch' }); // perform dfs const stack = [{ node: kgSrc, path: [kgSrc] }]; const newResultObject: ResultObject = {}; const newAuxGraphs: AuxGraphObject = {}; + let a= 0; + let b=0; while (stack.length !== 0) { const { node, path } = stack.pop()!; + a++; // continue creating path if we haven't reached end yet if (node !== kgDst) { @@ -206,30 +213,29 @@ export default class PathfinderQueryHandler { if (path.length <= 2) { continue; } - +b++; // loop through all intermediate nodes in path to dest for (let i = 1; i < path.length - 1; i++) { const intermediateNode = path[i]; - const firstEdges: string[] = []; - const secondEdges: string[] = []; + + if (!(`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject)) { + newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`] = { edges: new Set() }; + newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`] = { edges: new Set() }; + newAuxGraphs[`pathfinder-${intermediateNode}-support`] = { edges: new Set() }; + } + + // add "edges" to aux graphs (kg edges will be added later) for (let j = 0; j < i; j++) { - firstEdges.push.apply(firstEdges, dfsGraph[path[j]][path[j+1]]); + newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`].edges.add(`${[path[j]]}-${[path[j+1]]}`); + newAuxGraphs[`pathfinder-${intermediateNode}-support`].edges.add(`${[path[j]]}-${[path[j+1]]}`); } for (let j = i; j < path.length - 1; j++) { - secondEdges.push.apply(secondEdges, dfsGraph[path[j]][path[j+1]]); - } + newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`].edges.add(`${[path[j]]}-${[path[j+1]]}`); + newAuxGraphs[`pathfinder-${intermediateNode}-support`].edges.add(`${[path[j]]}-${[path[j+1]]}`); + } - if (`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject) { - firstEdges.forEach(edge => { - newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`].edges.add(edge); - newAuxGraphs[`pathfinder-${intermediateNode}-support`].edges.add(edge) - }); - secondEdges.forEach(edge => { - newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`].edges.add(edge); - newAuxGraphs[`pathfinder-${intermediateNode}-support`].edges.add(edge); - }); - continue; - } + // code below is only for new results + if (`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject) continue; // create new edges & aux graph newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`] = { @@ -290,9 +296,6 @@ export default class PathfinderQueryHandler { ], attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-support`] }], }; - newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`] = { edges: new Set(firstEdges) }; - newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`] = { edges: new Set(secondEdges) }; - newAuxGraphs[`pathfinder-${intermediateNode}-support`] = { edges: new Set([...firstEdges, ...secondEdges]) }; // calculate score if (supportGraphsPerNode[intermediateNode]?.size > 0) { From 715c1c98e82394796aaadfcd1be90b014fa91c7e Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Thu, 18 Apr 2024 17:37:56 -0700 Subject: [PATCH 2/4] Analyze aux graphs individually --- src/inferred_mode/inferred_mode.ts | 2 +- src/inferred_mode/pathfinder.ts | 255 +++++++++++++++-------------- 2 files changed, 136 insertions(+), 121 deletions(-) diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts index 44830c5f..498eb2f2 100644 --- a/src/inferred_mode/inferred_mode.ts +++ b/src/inferred_mode/inferred_mode.ts @@ -379,7 +379,7 @@ export default class InferredQueryHandler { }; if (this.pathfinder) { - combinedResponse.original_analyses[auxGraphID] = translatedResult.analyses[0]; + combinedResponse.original_analyses[auxGraphID] = result.analyses[0]; } } diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts index c842dde1..716e020f 100644 --- a/src/inferred_mode/pathfinder.ts +++ b/src/inferred_mode/pathfinder.ts @@ -19,8 +19,12 @@ interface AuxGraphObject { [id: string]: { edges: Set } } +interface FullGraph { + [node: string]: { [dst: string]: Set } +} + interface DfsGraph { - [node: string]: { [dst: string]: string[] } + [node: string]: { [dst: string]: boolean }; } export default class PathfinderQueryHandler { @@ -130,20 +134,20 @@ export default class PathfinderQueryHandler { const kgEdge = creativeResponse.message.results[0].analyses[0].edge_bindings[this.mainEdgeId][0].id; const kgSrc = creativeResponse.message.results[0].node_bindings[this.mainEdge.subject][0].id; const kgDst = creativeResponse.message.results[0].node_bindings[this.mainEdge.object][0].id; - const dfsGraph: DfsGraph = {}; + const fullGraph: FullGraph = {}; const supportGraphsPerNode: { [node: string]: Set } = {}; const supportGraphs = (creativeResponse.message.knowledge_graph.edges[kgEdge]?.attributes?.find(attr => attr.attribute_type_id === 'biolink:support_graphs')?.value ?? []) as string[]; for (const supportGraph of supportGraphs) { const auxGraph = (creativeResponse.message.auxiliary_graphs ?? {})[supportGraph]; for (const subEdge of auxGraph.edges) { const kgSubEdge = creativeResponse.message.knowledge_graph.edges[subEdge]; - if (!dfsGraph[kgSubEdge.subject]) { - dfsGraph[kgSubEdge.subject] = {}; + if (!fullGraph[kgSubEdge.subject]) { + fullGraph[kgSubEdge.subject] = {}; } - if (!dfsGraph[kgSubEdge.subject][kgSubEdge.object]) { - dfsGraph[kgSubEdge.subject][kgSubEdge.object] = []; + if (!fullGraph[kgSubEdge.subject][kgSubEdge.object]) { + fullGraph[kgSubEdge.subject][kgSubEdge.object] = new Set(); } - dfsGraph[kgSubEdge.subject][kgSubEdge.object].push(subEdge); + fullGraph[kgSubEdge.subject][kgSubEdge.object].add(subEdge); if (!supportGraphsPerNode[kgSubEdge.subject]) { supportGraphsPerNode[kgSubEdge.subject] = new Set(); @@ -156,7 +160,7 @@ export default class PathfinderQueryHandler { debug(message1); this.logs.push(new LogEntry('INFO', null, message1).getLog()); - const { results: newResultObject, graphs: newAuxGraphs } = this._searchForIntermediates(creativeResponse, dfsGraph, supportGraphsPerNode, kgSrc, kgDst); + const { results: newResultObject, graphs: newAuxGraphs } = this._searchForIntermediates(creativeResponse, supportGraphsPerNode, kgSrc, kgDst); creativeResponse.message.results = Object.values(newResultObject).sort((a, b) => (b.analyses[0].score ?? 0) - (a.analyses[0].score ?? 0)).slice(0, this.CREATIVE_LIMIT); creativeResponse.description = `Query processed successfully, retrieved ${creativeResponse.message.results.length} results.` @@ -168,8 +172,8 @@ export default class PathfinderQueryHandler { const auxGraph = creativeResponse.message.knowledge_graph.edges[edge.id].attributes.find(attr => attr.attribute_type_id === 'biolink:support_graphs')?.value[0]; finalNewAuxGraphs[auxGraph] = { edges: [] }; for (const ed of newAuxGraphs[auxGraph].edges) { - const [st, en] = ed.split('-'); - finalNewAuxGraphs[auxGraph].edges.push.apply(finalNewAuxGraphs[auxGraph].edges, dfsGraph[st][en]); + const [st, en] = ed.split('\n'); + finalNewAuxGraphs[auxGraph].edges.push.apply(finalNewAuxGraphs[auxGraph].edges, Array.from(fullGraph[st][en])); } } } @@ -186,127 +190,138 @@ export default class PathfinderQueryHandler { return creativeResponse; } - _searchForIntermediates(creativeResponse: TrapiResponse, dfsGraph: DfsGraph, supportGraphsPerNode: { [node: string]: Set }, kgSrc: string, kgDst: string): ResultAuxObject { + _searchForIntermediates(creativeResponse: TrapiResponse, supportGraphsPerNode: { [node: string]: Set }, kgSrc: string, kgDst: string): ResultAuxObject { const span = Telemetry.startSpan({ description: 'pathfinderIntermediateSearch' }); - // perform dfs - const stack = [{ node: kgSrc, path: [kgSrc] }]; const newResultObject: ResultObject = {}; const newAuxGraphs: AuxGraphObject = {}; - let a= 0; - let b=0; - while (stack.length !== 0) { - const { node, path } = stack.pop()!; - a++; - - // continue creating path if we haven't reached end yet - if (node !== kgDst) { - for (const neighbor in dfsGraph[node]) { - if (!path.includes(neighbor)) { - stack.push({ node: neighbor, path: [...path, neighbor] }); - } + for (let analysis of Object.values(this.originalAnalyses)) { + const dfsGraph: DfsGraph = {}; + for (const subEdge of Object.values(analysis.edge_bindings).map(eb => eb[0].id)) { + const kgSubEdge = creativeResponse.message.knowledge_graph.edges[subEdge]; + if (!dfsGraph[kgSubEdge.subject]) { + dfsGraph[kgSubEdge.subject] = {}; + } + if (!dfsGraph[kgSubEdge.subject][kgSubEdge.object]) { + dfsGraph[kgSubEdge.subject][kgSubEdge.object] = true; } - continue; } - // path to dest too short - if (path.length <= 2) { - continue; - } -b++; - // loop through all intermediate nodes in path to dest - for (let i = 1; i < path.length - 1; i++) { - const intermediateNode = path[i]; - - if (!(`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject)) { - newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`] = { edges: new Set() }; - newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`] = { edges: new Set() }; - newAuxGraphs[`pathfinder-${intermediateNode}-support`] = { edges: new Set() }; - } + // perform dfs + const stack = [{ node: kgSrc, path: [kgSrc] }]; - // add "edges" to aux graphs (kg edges will be added later) - for (let j = 0; j < i; j++) { - newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`].edges.add(`${[path[j]]}-${[path[j+1]]}`); - newAuxGraphs[`pathfinder-${intermediateNode}-support`].edges.add(`${[path[j]]}-${[path[j+1]]}`); + while (stack.length !== 0) { + const { node, path } = stack.pop()!; + + // continue creating path if we haven't reached end yet + if (node !== kgDst) { + for (const neighbor in dfsGraph[node]) { + if (!path.includes(neighbor)) { + stack.push({ node: neighbor, path: [...path, neighbor] }); + } + } + continue; } - for (let j = i; j < path.length - 1; j++) { - newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`].edges.add(`${[path[j]]}-${[path[j+1]]}`); - newAuxGraphs[`pathfinder-${intermediateNode}-support`].edges.add(`${[path[j]]}-${[path[j+1]]}`); - } - - // code below is only for new results - if (`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject) continue; - - // create new edges & aux graph - newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`] = { - node_bindings: { - [this.mainEdge.subject]: [{ id: kgSrc }], - [this.mainEdge.object]: [{ id: kgDst }], - [this.unpinnedNodeId]: [{ id: intermediateNode }] - }, - analyses: [{ - resource_id: "infores:biothings-explorer", - edge_bindings: { - [this.mainEdgeId]: [{ id: `pathfinder-${intermediateNode}` }], - [this.intermediateEdges[0][0]]: [{ id: `pathfinder-${kgSrc}-${intermediateNode}` }], - [this.intermediateEdges[1][0]]: [{ id: `pathfinder-${intermediateNode}-${kgDst}` }], - }, - score: undefined - }], - }; - creativeResponse.message.knowledge_graph.edges[`pathfinder-${kgSrc}-${intermediateNode}`] = { - predicate: 'biolink:related_to', - subject: kgSrc, - object: intermediateNode, - sources: [ - { - resource_id: this.options.provenanceUsesServiceProvider - ? 'infores:service-provider-trapi' - : 'infores:biothings-explorer', - resource_role: 'primary_knowledge_source', - }, - ], - attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${kgSrc}-${intermediateNode}-support`] }], - }; - creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}-${kgDst}`] = { - predicate: 'biolink:related_to', - subject: intermediateNode, - object: kgDst, - sources: [ - { - resource_id: this.options.provenanceUsesServiceProvider - ? 'infores:service-provider-trapi' - : 'infores:biothings-explorer', - resource_role: 'primary_knowledge_source', - }, - ], - attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-${kgDst}-support`] }], - }; - creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}`] = { - predicate: 'biolink:related_to', - subject: kgSrc, - object: kgDst, - sources: [ - { - resource_id: this.options.provenanceUsesServiceProvider - ? 'infores:service-provider-trapi' - : 'infores:biothings-explorer', - resource_role: 'primary_knowledge_source', + + // path to dest too short + if (path.length <= 2) { + continue; + } + + // loop through all intermediate nodes in path to dest + for (let i = 1; i < path.length - 1; i++) { + const intermediateNode = path[i]; + + if (!(`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject)) { + newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`] = { edges: new Set() }; + newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`] = { edges: new Set() }; + newAuxGraphs[`pathfinder-${intermediateNode}-support`] = { edges: new Set() }; + } + + // add "edges" to aux graphs (kg edges will be added later) + for (let j = 0; j < i; j++) { + newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}-support`].edges.add(`${path[j]}\n${path[j+1]}`); + newAuxGraphs[`pathfinder-${intermediateNode}-support`].edges.add(`${path[j]}\n${path[j+1]}`); + } + for (let j = i; j < path.length - 1; j++) { + newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}-support`].edges.add(`${path[j]}\n${path[j+1]}`); + newAuxGraphs[`pathfinder-${intermediateNode}-support`].edges.add(`${path[j]}\n${path[j+1]}`); + } + + // code below is only for new results + if (`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject) continue; + + // create new edges & aux graph + newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`] = { + node_bindings: { + [this.mainEdge.subject]: [{ id: kgSrc }], + [this.mainEdge.object]: [{ id: kgDst }], + [this.unpinnedNodeId]: [{ id: intermediateNode }] }, - ], - attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-support`] }], - }; - - // calculate score - if (supportGraphsPerNode[intermediateNode]?.size > 0) { - let score: number | undefined = undefined; - for (const supportGraph of supportGraphsPerNode[intermediateNode]) { - score = scaled_sigmoid( - inverse_scaled_sigmoid(score ?? 0) + - inverse_scaled_sigmoid(this.originalAnalyses[supportGraph].score), - ); + analyses: [{ + resource_id: "infores:biothings-explorer", + edge_bindings: { + [this.mainEdgeId]: [{ id: `pathfinder-${intermediateNode}` }], + [this.intermediateEdges[0][0]]: [{ id: `pathfinder-${kgSrc}-${intermediateNode}` }], + [this.intermediateEdges[1][0]]: [{ id: `pathfinder-${intermediateNode}-${kgDst}` }], + }, + score: undefined + }], + }; + creativeResponse.message.knowledge_graph.edges[`pathfinder-${kgSrc}-${intermediateNode}`] = { + predicate: 'biolink:related_to', + subject: kgSrc, + object: intermediateNode, + sources: [ + { + resource_id: this.options.provenanceUsesServiceProvider + ? 'infores:service-provider-trapi' + : 'infores:biothings-explorer', + resource_role: 'primary_knowledge_source', + }, + ], + attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${kgSrc}-${intermediateNode}-support`] }], + }; + creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}-${kgDst}`] = { + predicate: 'biolink:related_to', + subject: intermediateNode, + object: kgDst, + sources: [ + { + resource_id: this.options.provenanceUsesServiceProvider + ? 'infores:service-provider-trapi' + : 'infores:biothings-explorer', + resource_role: 'primary_knowledge_source', + }, + ], + attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-${kgDst}-support`] }], + }; + creativeResponse.message.knowledge_graph.edges[`pathfinder-${intermediateNode}`] = { + predicate: 'biolink:related_to', + subject: kgSrc, + object: kgDst, + sources: [ + { + resource_id: this.options.provenanceUsesServiceProvider + ? 'infores:service-provider-trapi' + : 'infores:biothings-explorer', + resource_role: 'primary_knowledge_source', + }, + ], + attributes: [{ attribute_type_id: 'biolink:support_graphs', value: [`pathfinder-${intermediateNode}-support`] }], + }; + + // calculate score + if (supportGraphsPerNode[intermediateNode]?.size > 0) { + let score: number | undefined = undefined; + for (const supportGraph of supportGraphsPerNode[intermediateNode]) { + score = scaled_sigmoid( + inverse_scaled_sigmoid(score ?? 0) + + inverse_scaled_sigmoid(this.originalAnalyses[supportGraph].score), + ); + } + newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`].analyses[0].score = score; } - newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`].analyses[0].score = score; } } } From 88bad1e3715765d8f0bd0b75977885555118477d Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Thu, 2 May 2024 17:27:50 -0700 Subject: [PATCH 3/4] fix: support graph suffixes --- src/inferred_mode/inferred_mode.ts | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts index 498eb2f2..27ab04a9 100644 --- a/src/inferred_mode/inferred_mode.ts +++ b/src/inferred_mode/inferred_mode.ts @@ -261,6 +261,7 @@ export default class InferredQueryHandler { qEdgeID: string, qEdge: TrapiQEdge, combinedResponse: CombinedResponse, + auxGraphSuffixes: {[inferredEdgeID: string]: number} ): CombinedResponseReport { const span = Telemetry.startSpan({ description: 'creativeCombineResponse' }); const newResponse = handler.getResponse(); @@ -293,7 +294,6 @@ export default class InferredQueryHandler { // modified count used for pathfinder const pfIntermediateSet = new Set(); - let auxGraphSuffixes: {[inferredEdgeID: string]: number} = {}; // add results newResponse.message.results.forEach((result) => { const translatedResult: TrapiResult = { @@ -546,6 +546,7 @@ export default class InferredQueryHandler { const mergedResultsCount: { [resultID: string]: number; } = {}; + const auxGraphSuffixes: {[inferredEdgeID: string]: number} = {}; await async.eachOfSeries(subQueries, async ({ template, queryGraph }, i) => { const span = Telemetry.startSpan({ description: 'creativeTemplate' }); @@ -570,6 +571,7 @@ export default class InferredQueryHandler { qEdgeID, qEdge, combinedResponse, + auxGraphSuffixes ); // update values used in logging successfulQueries += querySuccess; From 894bbb0e53148035ab73cd44ca4f22e3af5e6fb1 Mon Sep 17 00:00:00 2001 From: Rohan Juneja Date: Fri, 10 May 2024 19:21:19 -0700 Subject: [PATCH 4/4] add pruning test --- ...hemical_to_disease_pf_creative_result.json | 10570 ++++++++++++++-- __test__/unittest/pathfinder.test.ts | 52 +- src/inferred_mode/pathfinder.ts | 24 +- 3 files changed, 9383 insertions(+), 1263 deletions(-) diff --git a/__test__/data/chemical_to_disease_pf_creative_result.json b/__test__/data/chemical_to_disease_pf_creative_result.json index 8e434d01..d5534205 100644 --- a/__test__/data/chemical_to_disease_pf_creative_result.json +++ b/__test__/data/chemical_to_disease_pf_creative_result.json @@ -192261,20 +192261,138 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support0": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "8f7d23c5eced81998f254d5cc6787907", + "attributes": [] + } + ], + "eA": [ + { + "id": "66cc6748ec77716ffa2f12d4346b8e32", + "attributes": [] + }, + { + "id": "d314ed6dcc558f37425d8908f3f30f4a", + "attributes": [] + }, + { + "id": "973c5ff05df1355650e61e14523f83d1", + "attributes": [] + }, + { + "id": "440d9255d4cd54ba8155bef4da3dc63a", + "attributes": [] + }, + { + "id": "67aba1144edb23d305a10e88afc40319", + "attributes": [] + }, + { + "id": "fdd9e9ef9ba97cd042a2ea3d64c0a764", + "attributes": [] + }, + { + "id": "db91efd3890984c2cd53d8038706fae3", + "attributes": [] + }, + { + "id": "34d605dc5baf9469d9b793abe7f6f2b5", + "attributes": [] + }, + { + "id": "02d5b7e4f5586837c27ac34060f85f0c", + "attributes": [] + }, + { + "id": "f51a8ccbadb7dc8044b9ee439aebc7e0", + "attributes": [] + }, + { + "id": "a616697b583b1697fd45af4649bfd491", + "attributes": [] + }, + { + "id": "4e6dfeb6a4232e289223ae4a2b3b7489", + "attributes": [] + }, + { + "id": "bf5cea28721caa82972436b4b1d2c4f2", + "attributes": [] + }, + { + "id": "bd36a78443ca7549349cf29ec36a5918", + "attributes": [] + }, + { + "id": "2ffa9460f4adc77240f5ee763afd05fe", + "attributes": [] } ] }, - "score": 1 + "score": 0.7151174923382333 }, "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support1": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "dcdbe5c265e19bbca2792c9000230cd8", + "attributes": [] + } + ], + "eA": [ + { + "id": "c33c0debab6bc11d2fff553bcceb8de3", + "attributes": [] + }, + { + "id": "a9777a36ceb16cf854069377722820c4", + "attributes": [] + }, + { 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+ "attributes": [] } ] }, @@ -198861,9 +206709,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support600": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "66758cbb256a0db45826fd13dc36bd03", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "9d3c2413faa083e6bd0639f0e49597ae", + "attributes": [] } ] }, @@ -198872,9 +206727,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support601": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "691e5e09c160dfd35bba027a383436a8", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "7fffdffee29c500aab16e822dd4dbb63", + "attributes": [] } ] }, @@ -198883,9 +206745,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support602": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "cf28b5a8d3388c9701145d8e1e7e1d58", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "c054f8306f0f1fcd77c7d126ee3a66f6", + "attributes": [] } ] }, @@ -198894,9 +206763,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support603": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "31a13b76a84cde380ccb55ca715bf3ad", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "447e0a39b9c6537ce0b610e226ed9f2e", + "attributes": [] } ] }, @@ -198905,9 +206781,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support604": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "a946420055156de441f3ffc62892d19b", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "ef0bdd5c8e035b45a5ab4e5b148f3a59", + "attributes": [] } ] }, @@ -198916,9 +206799,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support605": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "d4712d7456dfa803092cdf68effaa47d", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "3a6de0eb1829b45c46ae4e22e1259e71", + "attributes": [] } ] }, @@ -198927,9 +206817,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support606": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "de755bca957902c27f9d39204118e638", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "f8c276fe9dbb13b0c0fe8d28add2ba68", + "attributes": [] } ] }, @@ -198938,9 +206835,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support607": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "250d668cd9026f7f7ba9e0f4de1a1d65", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "d0d099a0d2dc1b73e59a657c49b8c7ef", + "attributes": [] } ] }, @@ -198949,9 +206853,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support608": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "ee51bd417e126e17ba688123ad4bdd32", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "9e1e89f7b381b5cb427a480864abc7d1", + "attributes": [] } ] }, @@ -198960,9 +206871,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support609": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "b360fccedc3fa3a31a3a65b4839e1daf", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "a967e299ddad817b17f4a5cf0ee562a8", + "attributes": [] } ] }, @@ -198971,9 +206889,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support610": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "02e72033ffdbb8c90caf3ae8021056a2", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "3d6a8614a9ecdd791a44614ae621d9be", + "attributes": [] } ] }, @@ -198982,9 +206907,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support611": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "2f456720f2d925d19040e2e356146099", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "45bb2764a9dec17ee8af40f444b74bc8", + "attributes": [] } ] }, @@ -198993,9 +206925,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support612": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "956023afbbedde2729bc72defc0c75b3", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "ed4ae6b8d898e4da764cada37786a6c5", + "attributes": [] } ] }, @@ -199004,9 +206943,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support613": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "7e0ad8a5e13b6edc1d5cb0b001fb2530", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "98b29d583e6c05204f716e7a9afe09f6", + "attributes": [] } ] }, @@ -199015,9 +206961,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support614": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "3eb4794c1f7a3f56d83c693f9c39a9c5", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "4260e79d6b9488e7a81953a80265950a", + "attributes": [] } ] }, @@ -199026,9 +206979,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support615": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "5765fac9936f8ee34556d3dcb91fc59a", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "0789c0d5a38441f92d3192d251906ad4", + "attributes": [] } ] }, @@ -199037,9 +206997,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support616": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "NCBIGene:1911-gene_associated_with_condition-MONDO:0004979-via_subclass", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "beb5d2a107df336d9310a71ff5d33635", + "attributes": [] } ] }, @@ -199048,9 +207015,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support617": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "NCBIGene:9825-gene_associated_with_condition-MONDO:0004979-via_subclass", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "6728f9ac15ca31ad474c5bcc110c9731", + "attributes": [] } ] }, @@ -199059,9 +207033,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support618": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "NCBIGene:10516-gene_associated_with_condition-MONDO:0004979-via_subclass", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "371eb05a5a12a90df9af10ff64193dcc", + "attributes": [] } ] }, @@ -199070,9 +207051,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support619": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "NCBIGene:26033-gene_associated_with_condition-MONDO:0004979-via_subclass", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "662df3849fb02968bd71507e93fda3fd", + "attributes": [] } ] }, @@ -199081,9 +207069,20 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support620": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "1601a5c7576dcbf6abcaa11b92a07476", + "attributes": [] + } + ], + "eA": [ + { + "id": "2f7ec26c6729bcc473ba0083f34f73d8", + "attributes": [] + }, { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "93feae57f0a1483d9356a13955eb0475", + "attributes": [] } ] }, @@ -199092,9 +207091,20 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support621": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "2bd8c6e8d7ddc76b63885a685c156823", + "attributes": [] + } + ], + "eA": [ + { + "id": "1d0add97904e9639c696179e476839c5", + "attributes": [] + }, + { + "id": "b304ae8d921cd8521278c27852f5b2c5", + "attributes": [] } ] }, @@ -199103,9 +207113,20 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support622": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "d51b00216e0bcb013b1dc5f48a12aa4f", + "attributes": [] + } + ], + "eA": [ + { + "id": "440680dd5bab09ab5991f51ccb0987fa", + "attributes": [] + }, { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "870ee0820b30abd8b393a17c1ad1bc35", + "attributes": [] } ] }, @@ -199114,9 +207135,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support623": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "c07168973f68660eb2c1e3c97b62b957", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "f7e265a66c04e4f39079b422db051f24", + "attributes": [] } ] }, @@ -199125,9 +207153,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support624": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "efd4d55739dbd8d922711bb6d2de2348", + "attributes": [] + } + ], + "eA": [ + { + "id": "1f38a1073329b076c4ddfabf02a825a0", + "attributes": [] } ] }, @@ -199136,9 +207171,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support625": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "29ae3a7724d92a149c3120203d1cbcef", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "785249e5d0dd29665abac557ee52eb7c", + "attributes": [] } ] }, @@ -199147,9 +207189,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support626": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "3e6b78eeb4f34f5912f62a84b194849d", + "attributes": [] + } + ], + "eA": [ + { + "id": "1af8494769f4d7c23c20854199af04f2", + "attributes": [] } ] }, @@ -199158,9 +207207,16 @@ "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979-support627": { "resource_id": "infores:biothings-explorer", "edge_bindings": { - "e2": [ + "eB": [ + { + "id": "e26cf88302d894e044bf4457d43c9bc7", + "attributes": [] + } + ], + "eA": [ { - "id": "inferred-PUBCHEM.COMPOUND:5291-related_to-MONDO:0004979" + "id": "715f922f5c6595b8ac8bdd305ce7fc08", + "attributes": [] } ] }, diff --git a/__test__/unittest/pathfinder.test.ts b/__test__/unittest/pathfinder.test.ts index 4cd9267f..704f67b2 100644 --- a/__test__/unittest/pathfinder.test.ts +++ b/__test__/unittest/pathfinder.test.ts @@ -1,4 +1,5 @@ -import TRAPIQueryHandler, { TrapiQueryGraph, TrapiResponse } from '../../src/index'; +import TRAPIQueryHandler from '../../src/index'; +import { TrapiQueryGraph, TrapiResponse } from '@biothings-explorer/types'; import path from 'path'; import fs from 'fs'; import _ from 'lodash'; @@ -94,5 +95,54 @@ describe('Test Pathfinder', () => { const n0ToN2Aux = pfResponse.message.knowledge_graph.edges[n0ToN2].attributes?.find(s => s.attribute_type_id === 'biolink:support_graphs')?.value as string; expect(pfResponse.message.auxiliary_graphs![n0ToN2Aux].edges.sort()).toEqual([...pfResponse.message.auxiliary_graphs![n0ToUnAux].edges, ...pfResponse.message.auxiliary_graphs![unToN2Aux].edges].sort()); + + // + // check that edges / nodes / aux graphs are properly pruned + // + pfHandler._pruneKg(pfResponse); + const edgeBoundNodes: Set = new Set(); + const resultsBoundEdges: Set = new Set(); + const resultBoundAuxGraphs: Set = new Set(); + + // Handle nodes and edges bound to results directly + pfResponse.message.results.forEach((result) => { + Object.entries(result.analyses[0].edge_bindings).forEach(([, bindings]) => { + bindings.forEach((binding) => resultsBoundEdges.add(binding.id)); + }); + }); + + // Handle edges bound via auxiliary graphs + // This will iterate over new edges as they're added + resultsBoundEdges.forEach((edgeID) => { + edgeBoundNodes.add(pfResponse.message.knowledge_graph.edges[edgeID].subject); + edgeBoundNodes.add(pfResponse.message.knowledge_graph.edges[edgeID].object); + pfResponse.message.knowledge_graph.edges[edgeID].attributes!.find(({ attribute_type_id, value }) => { + if (attribute_type_id === 'biolink:support_graphs') { + (value as string[]).forEach((auxGraphID) => { + resultBoundAuxGraphs.add(auxGraphID); + pfResponse.message.auxiliary_graphs![auxGraphID].edges.forEach((auxGraphEdgeID) => { + edgeBoundNodes.add(pfResponse.message.knowledge_graph.edges[auxGraphEdgeID].subject); + edgeBoundNodes.add(pfResponse.message.knowledge_graph.edges[auxGraphEdgeID].object); + resultsBoundEdges.add(auxGraphEdgeID); + }); + }); + return true; + } + }); + }); + + const extraNodes = Object.keys(pfResponse.message.knowledge_graph.nodes).filter(nodeID => !edgeBoundNodes.has(nodeID)); + expect(extraNodes).toEqual([]); + const extraEdges = Object.keys(pfResponse.message.knowledge_graph.edges).filter(edgeID => !resultsBoundEdges.has(edgeID)); + expect(extraEdges).toEqual([]); + const extraAuxGraphs = Object.keys(pfResponse.message.auxiliary_graphs!).filter(auxGraphID => !resultBoundAuxGraphs.has(auxGraphID)); + expect(extraAuxGraphs).toEqual([]); + + const missingNodes = Array.from(edgeBoundNodes).filter(nodeID => !pfResponse.message.knowledge_graph.nodes[nodeID]); + expect(missingNodes).toEqual([]); + const missingEdges = Array.from(resultsBoundEdges).filter(edgeID => !pfResponse.message.knowledge_graph.edges[edgeID]); + expect(missingEdges).toEqual([]); + const missingAuxGraphs = Array.from(resultBoundAuxGraphs).filter(auxGraphID => !pfResponse.message.auxiliary_graphs![auxGraphID]); + expect(missingAuxGraphs).toEqual([]); }); }); diff --git a/src/inferred_mode/pathfinder.ts b/src/inferred_mode/pathfinder.ts index 716e020f..5fad1393 100644 --- a/src/inferred_mode/pathfinder.ts +++ b/src/inferred_mode/pathfinder.ts @@ -41,6 +41,7 @@ export default class PathfinderQueryHandler { mainEdgeId: string; mainEdge: TrapiQEdge; originalAnalyses: { [id: string]: TrapiAnalysis }; + inferredQueryHandler: InferredQueryHandler; constructor(logs: StampedLog[], queryGraph: TrapiQueryGraph, parent: TRAPIQueryHandler) { this.logs = logs; @@ -70,7 +71,7 @@ export default class PathfinderQueryHandler { this.intermediateEdges.forEach(([edgeId, _]) => delete this.queryGraph.edges[edgeId]); // run creative mode - const inferredQueryHandler = new InferredQueryHandler( + this.inferredQueryHandler = new InferredQueryHandler( this.parent, this.queryGraph, this.logs, @@ -80,7 +81,7 @@ export default class PathfinderQueryHandler { this.parent.includeReasoner, true ); - const creativeResponse = await inferredQueryHandler.query(); + const creativeResponse = await this.inferredQueryHandler.query(); // restore query graph this.queryGraph.nodes[this.unpinnedNodeId] = this.unpinnedNode; @@ -88,9 +89,7 @@ export default class PathfinderQueryHandler { creativeResponse.message.query_graph = this.queryGraph; this.parse(creativeResponse); - - // prune KG - inferredQueryHandler.pruneKnowledgeGraph(creativeResponse); + this._pruneKg(creativeResponse); // logs creativeResponse.logs = this.logs.map(log => log.toJSON()); @@ -118,6 +117,21 @@ export default class PathfinderQueryHandler { } } + _pruneKg(creativeResponse: TrapiResponse) { + if (!this.inferredQueryHandler) { + this.inferredQueryHandler = new InferredQueryHandler( + this.parent, + this.queryGraph, + this.logs, + this.options, + this.parent.path, + this.parent.predicatePath, + this.parent.includeReasoner, + true + ); + } + this.inferredQueryHandler.pruneKnowledgeGraph(creativeResponse); + } parse(creativeResponse: TrapiResponse) { const span = Telemetry.startSpan({ description: 'pathfinderParse' });