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Merge branch 'subclassing-fix' of https://github.com/biothings/bte_tr…
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…api_query_graph_handler into dev
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@tokebe
tokebe committed Aug 19, 2024
2 parents a497bc0 + 7d5d1db commit 654fffc
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Showing 3 changed files with 120 additions and 73 deletions.
24 changes: 20 additions & 4 deletions src/edge_manager.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ import QEdge from './query_edge';
import MetaKG from '@biothings-explorer/smartapi-kg';
import { QueryHandlerOptions } from '@biothings-explorer/types';
import { Record } from '@biothings-explorer/api-response-transform';
import { UnavailableAPITracker } from './types';
import { SubclassEdges, UnavailableAPITracker } from './types';
import { RecordsByQEdgeID } from './results_assembly/query_results';
import path from 'path';
import { promises as fs } from 'fs';
Expand All @@ -22,7 +22,8 @@ export default class QueryEdgeManager {
private _records: Record[];
options: QueryHandlerOptions;
private _organizedRecords: RecordsByQEdgeID;
constructor(edges: QEdge[], metaKG: MetaKG, options: QueryHandlerOptions) {
private _subclassEdges: SubclassEdges;
constructor(edges: QEdge[], metaKG: MetaKG, subclassEdges: SubclassEdges, options: QueryHandlerOptions) {
// flatten list of all edges available
this._qEdges = _.flatten(edges);
this._metaKG = metaKG;
Expand All @@ -31,6 +32,7 @@ export default class QueryEdgeManager {
//organized by edge with refs to connected edges
this._organizedRecords = {};
this.options = options;
this._subclassEdges = subclassEdges;
this.init();
}

Expand Down Expand Up @@ -203,8 +205,22 @@ export default class QueryEdgeManager {

records.forEach((record) => {
// check against original, primaryID, and equivalent ids
const subjectIDs = [record.subject.original, record.subject.curie, ...record.subject.equivalentCuries];
const objectIDs = [record.object.original, record.object.curie, ...record.object.equivalentCuries];
let subjectIDs = [record.subject.original, record.subject.curie, ...record.subject.equivalentCuries];
let objectIDs = [record.object.original, record.object.curie, ...record.object.equivalentCuries];

// check if IDs will be resolved to a parent
subjectIDs = [...subjectIDs, ...subjectIDs.reduce((set, subjectID) => {
Object.entries(this._subclassEdges[subjectID] ?? {}).forEach(([id, qNodes]) => {
if (qNodes.includes(qEdge.reverse ? qEdge.object.id : qEdge.subject.id)) set.add(id);
});
return set;
}, new Set<string>())];
objectIDs = [...objectIDs, ...objectIDs.reduce((set, objectID) => {
Object.entries(this._subclassEdges[objectID] ?? {}).forEach(([id, qNodes]) => {
if (qNodes.includes(qEdge.reverse ? qEdge.subject.id : qEdge.object.id)) set.add(id);
});
return set;
}, new Set<string>())];

// there must be at least a minimal intersection
const subjectMatch = subjectIDs.some((curie) => execSubjectCuries.includes(curie));
Expand Down
163 changes: 94 additions & 69 deletions src/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ import BTEGraph from './graph/graph';
import QEdge from './query_edge';
import { Telemetry } from '@biothings-explorer/utils';
import { enrichTrapiResultsWithPfocrFigures } from './results_assembly/pfocr';
import { SubclassEdges } from './types';

// Exports for external availability
export * from './types';
Expand All @@ -46,7 +47,7 @@ export default class TRAPIQueryHandler {
includeReasoner: boolean;
path: string;
predicatePath: string;
subclassEdges: { [expandedID: string]: string };
subclassEdges: SubclassEdges;
originalQueryGraph: TrapiQueryGraph;
bteGraph: BTEGraph;
knowledgeGraph: KnowledgeGraph;
Expand Down Expand Up @@ -169,14 +170,12 @@ export default class TRAPIQueryHandler {
});

// Create subclass edges for nodes that were expanded
const nodesToRebind: { [nodeID: string]: { newNode: string; subclassEdgeID: string } } = {};
const nodesToRebind: { [nodeID: string]: { [qEdgeID: string]: { newNode: string; subclassEdgeID: string } } } = {};
Object.keys(this.bteGraph.nodes).forEach((nodeID) => {
const subclassCuries = [...(expandedIDsbyPrimaryID[nodeID] ?? [])]?.map((expandedID) => [
this.subclassEdges[expandedID],
expandedID,
]);
const subclassCuries = [];
expandedIDsbyPrimaryID[nodeID]?.forEach((expandedID) => Object.keys(this.subclassEdges[expandedID]).forEach((parentID) => subclassCuries.push({ original: parentID, expanded: expandedID })));
if (!subclassCuries.length) return; // Nothing to rebind
subclassCuries.forEach(([original, expanded]) => {
subclassCuries.forEach(({original, expanded}) => {
const subject = nodeID;
const object = primaryIDsByOriginalID[original];
// Don't keep self-subclass
Expand All @@ -203,77 +202,101 @@ export default class TRAPIQueryHandler {
},
]);
this.bteGraph.edges[subclassEdgeID] = subclassEdge;
nodesToRebind[subject] = { newNode: object, subclassEdgeID };
if (!nodesToRebind[subject]) nodesToRebind[subject] = {};
this.subclassEdges[expanded][original].forEach((qNodeID) => nodesToRebind[subject][qNodeID] = { newNode: object, subclassEdgeID });
});
});

// Create new constructed edges and aux graphs for edges that used subclass edges
let auxGraphs: { [supportGraphID: string]: TrapiAuxiliaryGraph } = {};
const edgesToRebind = {};
const edgesToRebind: { [edgeID: string]: { [originalSubject: string]: { [originalObject: string]: string /* re-bound edge ID */ } } } = {};
const edgesIDsByAuxGraphID = {};
Object.entries(this.bteGraph.edges).forEach(([edgeID, bteEdge]) => {
if (edgeID.includes('expanded')) return;
const supportGraph = [edgeID];
const [subject, object] = [bteEdge.subject, bteEdge.object].map((edgeNodeID) => {
if (!nodesToRebind[edgeNodeID]) {
return edgeNodeID; // nothing to rebind
const combos: {subject: string, object: string, supportGraph: string[]}[] = [];
const subjectToSupportGraphs: {[sbj: string]: Set<string>} = {
[bteEdge.subject]: new Set(),
...Object.values(nodesToRebind[bteEdge.subject] ?? {}).reduce((acc, x) => {
x.newNode in acc ? acc[x.newNode].add(x.subclassEdgeID) : acc[x.newNode] = new Set([x.subclassEdgeID])
return acc;
}, {})
};
const objectToSupportGraphs: {[obj: string]: Set<string>} = {
[bteEdge.object]: new Set(),
...Object.values(nodesToRebind[bteEdge.object] ?? {}).reduce((acc, x) => {
x.newNode in acc ? acc[x.newNode].add(x.subclassEdgeID) : acc[x.newNode] = new Set([x.subclassEdgeID]);
return acc;
}, {})
};
for (const subject in subjectToSupportGraphs) {
for (const object in objectToSupportGraphs) {
if (subject == bteEdge.subject && object == bteEdge.object) continue; // no nodes are rebound
combos.push({ subject, object, supportGraph: [...subjectToSupportGraphs[subject], ...objectToSupportGraphs[object], edgeID] });
}
supportGraph.push(nodesToRebind[edgeNodeID].subclassEdgeID);
return nodesToRebind[edgeNodeID].newNode;
});

if (supportGraph.length === 1) return; // no subclasses
const boundEdgeID = `${subject}-${bteEdge.predicate.replace('biolink:', '')}-${object}-via_subclass`;
let suffix = 0;
while (Object.keys(auxGraphs).includes(`support${suffix}-${boundEdgeID}`)) {
suffix += 1;
}
const supportGraphID = `support${suffix}-${boundEdgeID}`;
auxGraphs[supportGraphID] = { edges: supportGraph, attributes: [] };
if (!edgesIDsByAuxGraphID[supportGraphID]) {
edgesIDsByAuxGraphID[supportGraphID] = new Set();
}
edgesIDsByAuxGraphID[supportGraphID].add(boundEdgeID);
if (!this.bteGraph.edges[boundEdgeID]) {
const boundEdge = new KGEdge(boundEdgeID, {
predicate: bteEdge.predicate,
subject: subject,
object: object,
});
boundEdge.addAdditionalAttributes('biolink:support_graphs', [supportGraphID]);
boundEdge.addAdditionalAttributes('biolink:knowledge_level', 'logical_entailment')
boundEdge.addAdditionalAttributes('biolink:agent_type', 'automated_agent')
boundEdge.addSource([
{
resource_id: this.options.provenanceUsesServiceProvider
? 'infores:service-provider-trapi'
: 'infores:biothings-explorer',
resource_role: 'primary_knowledge_source',
},
]);
this.bteGraph.edges[boundEdgeID] = boundEdge;
} else {
(this.bteGraph.edges[boundEdgeID].attributes['biolink:support_graphs'] as Set<string>).add(supportGraphID);
}
edgesToRebind[edgeID] = boundEdgeID;

combos.forEach(({subject, object, supportGraph}) => {
const boundEdgeID = `${subject}-${bteEdge.predicate.replace('biolink:', '')}-${object}-via_subclass`;
let suffix = 0;
while (Object.keys(auxGraphs).includes(`support${suffix}-${boundEdgeID}`)) {
suffix += 1;
}
const supportGraphID = `support${suffix}-${boundEdgeID}`;
auxGraphs[supportGraphID] = { edges: supportGraph, attributes: [] };
if (!edgesIDsByAuxGraphID[supportGraphID]) {
edgesIDsByAuxGraphID[supportGraphID] = new Set();
}
edgesIDsByAuxGraphID[supportGraphID].add(boundEdgeID);
if (!this.bteGraph.edges[boundEdgeID]) {
const boundEdge = new KGEdge(boundEdgeID, {
predicate: bteEdge.predicate,
subject: subject,
object: object,
});
boundEdge.addAdditionalAttributes('biolink:support_graphs', [supportGraphID]);
boundEdge.addAdditionalAttributes('biolink:knowledge_level', 'logical_entailment')
boundEdge.addAdditionalAttributes('biolink:agent_type', 'automated_agent')
boundEdge.addSource([
{
resource_id: this.options.provenanceUsesServiceProvider
? 'infores:service-provider-trapi'
: 'infores:biothings-explorer',
resource_role: 'primary_knowledge_source',
},
]);
this.bteGraph.edges[boundEdgeID] = boundEdge;
} else {
(this.bteGraph.edges[boundEdgeID].attributes['biolink:support_graphs'] as Set<string>).add(supportGraphID);
}
if (!edgesToRebind[edgeID]) edgesToRebind[edgeID] = {};
if (!edgesToRebind[edgeID][subject]) edgesToRebind[edgeID][subject] = {};
edgesToRebind[edgeID][subject][object] = boundEdgeID;
})
});

const resultBoundEdgesWithAuxGraphs = new Set();
const fixedResults = this.trapiResultsAssembler.getResults().map((result) => {
result.node_bindings = Object.fromEntries(
Object.entries(result.node_bindings).map(([qNodeID, bindings]) => {
result.analyses[0].edge_bindings = Object.fromEntries(
Object.entries(result.analyses[0].edge_bindings).map(([qEdgeID, bindings]) => {
const subQNode = this.queryGraph.edges[qEdgeID].subject;
const objQNode = this.queryGraph.edges[qEdgeID].object;
return [
qNodeID,
qEdgeID,
bindings.reduce(
({ boundIDs, newBindings }, binding) => {
if (!nodesToRebind[binding.id]) {
const originalSub = this.bteGraph.edges[binding.id].subject;
const originalObj = this.bteGraph.edges[binding.id].object;
const subId = nodesToRebind[originalSub]?.[subQNode]?.newNode ?? originalSub;
const objId = nodesToRebind[originalObj]?.[objQNode]?.newNode ?? originalObj;
if (!edgesToRebind[binding.id]?.[subId]?.[objId]) {
if (!boundIDs.has(binding.id)) {
newBindings.push(binding);
boundIDs.add(binding.id);
}
} else if (!boundIDs.has(nodesToRebind[binding.id].newNode)) {
newBindings.push({ id: nodesToRebind[binding.id].newNode, attributes: [] });
boundIDs.add(nodesToRebind[binding.id].newNode);
} else if (!boundIDs.has(edgesToRebind[binding.id]?.[subId]?.[objId])) {
newBindings.push({ id: edgesToRebind[binding.id]?.[subId]?.[objId], attributes: [] });
boundIDs.add(edgesToRebind[binding.id]?.[subId]?.[objId]);
resultBoundEdgesWithAuxGraphs.add(edgesToRebind[binding.id]?.[subId]?.[objId]);
}
return { boundIDs, newBindings };
},
Expand All @@ -282,21 +305,21 @@ export default class TRAPIQueryHandler {
];
}),
);
result.analyses[0].edge_bindings = Object.fromEntries(
Object.entries(result.analyses[0].edge_bindings).map(([qEdgeID, bindings]) => {

result.node_bindings = Object.fromEntries(
Object.entries(result.node_bindings).map(([qNodeID, bindings]) => {
return [
qEdgeID,
qNodeID,
bindings.reduce(
({ boundIDs, newBindings }, binding) => {
if (!edgesToRebind[binding.id]) {
if (!nodesToRebind[binding.id]?.[qNodeID]) {
if (!boundIDs.has(binding.id)) {
newBindings.push(binding);
boundIDs.add(binding.id);
}
} else if (!boundIDs.has(edgesToRebind[binding.id])) {
newBindings.push({ id: edgesToRebind[binding.id], attributes: [] });
boundIDs.add(edgesToRebind[binding.id]);
resultBoundEdgesWithAuxGraphs.add(edgesToRebind[binding.id]);
} else if (!boundIDs.has(nodesToRebind[binding.id][qNodeID].newNode)) {
newBindings.push({ id: nodesToRebind[binding.id][qNodeID].newNode, attributes: [] });
boundIDs.add(nodesToRebind[binding.id][qNodeID].newNode);
}
return { boundIDs, newBindings };
},
Expand All @@ -305,6 +328,7 @@ export default class TRAPIQueryHandler {
];
}),
);

return result;
});

Expand Down Expand Up @@ -404,7 +428,9 @@ export default class TRAPIQueryHandler {
Object.entries(descendantsByCurie).forEach(([curie, descendants]) => {
descendants.forEach((descendant) => {
if (queryGraph.nodes[nodeId].ids.includes(descendant)) return;
this.subclassEdges[descendant] = curie;
if (!this.subclassEdges[descendant]) this.subclassEdges[descendant] = {};
if (!this.subclassEdges[descendant][curie]) this.subclassEdges[descendant][curie] = [];
this.subclassEdges[descendant][curie].push(nodeId);
});
});
}
Expand Down Expand Up @@ -441,7 +467,6 @@ export default class TRAPIQueryHandler {
if (err instanceof InvalidQueryGraphError || err instanceof SRINodeNormFailure) {
throw err;
} else {
console.log(err.stack);
throw new InvalidQueryGraphError();
}
}
Expand All @@ -456,7 +481,7 @@ export default class TRAPIQueryHandler {

// _.cloneDeep() is resource-intensive but only runs once per query
qEdges = _.cloneDeep(qEdges);
const manager = new EdgeManager(qEdges, metaKG, this.options);
const manager = new EdgeManager(qEdges, metaKG, this.subclassEdges, this.options);
const qEdgesMissingOps: { [qEdgeID: string]: boolean } = {};
while (manager.getEdgesNotExecuted()) {
const currentQEdge = manager.getNext();
Expand Down Expand Up @@ -718,7 +743,7 @@ export default class TRAPIQueryHandler {
if (!(await this._edgesSupported(queryEdges, metaKG))) {
return;
}
const manager = new EdgeManager(queryEdges, metaKG, this.options);
const manager = new EdgeManager(queryEdges, metaKG, this.subclassEdges, this.options);

const executionSuccess = await manager.executeEdges();
this.logs = [...this.logs, ...manager.logs];
Expand Down
6 changes: 6 additions & 0 deletions src/types.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,3 +7,9 @@ export interface UnavailableAPITracker {
export interface CompactQualifiers {
[qualifier_type_id: string]: string;
}

export interface SubclassEdges {
[expandedID: string]: {
[parentID: string]: string[] /* QNode IDs */
}
}

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