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create pathfinder intermediate aux graphs & results
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@rjawesome
rjawesome committed Mar 26, 2024
1 parent 52bc25d commit 60dc949
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Showing 3 changed files with 92 additions and 3 deletions.
77 changes: 75 additions & 2 deletions src/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -530,7 +530,7 @@ export default class TRAPIQueryHandler {
// remove unpinned node & all edges involving unpinned node for now
delete this.queryGraph.nodes[unpinnedNodeId];
const intermediateEdges = Object.entries(this.queryGraph.edges).filter(([_, edge]) => edge.subject === unpinnedNodeId || edge.object === unpinnedNodeId);
const mainEdge = Object.entries(this.queryGraph.edges).find(([_, edge]) => edge.subject !== unpinnedNodeId && edge.object !== unpinnedNodeId);
const [mainEdgeID, mainEdge] = Object.entries(this.queryGraph.edges).find(([_, edge]) => edge.subject !== unpinnedNodeId && edge.object !== unpinnedNodeId);

// intermediateEdges should be in order of n0 -> un & un -> n1
if (intermediateEdges[0][1].subject === unpinnedNodeId) {
Expand All @@ -549,7 +549,7 @@ export default class TRAPIQueryHandler {
return;
}

if (intermediateEdges[0][1].subject !== mainEdge[1].subject || intermediateEdges[1][1].object !== mainEdge[1].object || intermediateEdges[0][1].object !== unpinnedNodeId || intermediateEdges[1][1].subject !== unpinnedNodeId) {
if (intermediateEdges[0][1].subject !== mainEdge.subject || intermediateEdges[1][1].object !== mainEdge.object || intermediateEdges[0][1].object !== unpinnedNodeId || intermediateEdges[1][1].subject !== unpinnedNodeId) {
const message = 'Intermediate edges for Pathfinder are incorrect. Your query terminates.';
debug(message);
this.logs.push(new LogEntry('WARNING', null, message).getLog());
Expand All @@ -562,10 +562,83 @@ export default class TRAPIQueryHandler {
// run creative mode
await this._handleInferredEdges(true);
const creativeResponse = this.getResponse();
const originalAnalyses = (creativeResponse as any).original_analyses;
delete (creativeResponse as any).original_analyses;

// restore query graph
this.queryGraph.nodes[unpinnedNodeId] = unpinnedNode;
intermediateEdges.forEach(([edgeId, edge]) => this.queryGraph.edges[edgeId] = edge);

// set up a graph structure
const kgEdge = creativeResponse.message.results[0].analyses[0].edge_bindings[mainEdgeID][0].id;
const kgSrc = creativeResponse.message.results[0].node_bindings[mainEdge.subject][0].id;
const kgDst = creativeResponse.message.results[0].node_bindings[mainEdge.object][0].id;
const dfsNodes: {[node: string]: {dst: string, edge: string}[]} = {};
for (const supportGraph of creativeResponse.message.knowledge_graph.edges[kgEdge].attributes.find(attr => attr.attribute_type_id === 'biolink:support_graphs').value as string[]) {
const auxGraph = creativeResponse.message.auxiliary_graphs[supportGraph];
for (const subEdge of auxGraph.edges) {
const kgSubEdge = creativeResponse.message.knowledge_graph.edges[subEdge];
if (!dfsNodes[kgSubEdge.subject]) {
dfsNodes[kgSubEdge.subject] = [];
}
dfsNodes[kgSubEdge.subject].push({ dst: kgSubEdge.object, edge: subEdge });
}
}

// perform dfs
const stack = [{ node: kgSrc, path: [kgSrc] }];
const newResultObject: {[id: string]: TrapiResult} = {};
const newAuxGraphs: {[id: string]: {edges: Set<string>}} = {};
while (stack.length !== 0) {
const { node, path } = stack.pop();
if (node === kgDst) {
if (path.length > 3) {
// loop through all intermediate nodes (nodes are even indices)
for (let i = 2; i < path.length - 2; i += 2) {
const intermediateNode = path[i];
if (!(`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}` in newResultObject)) {
newResultObject[`pathfinder-${kgSrc}-${intermediateNode}-${kgDst}`] = {
node_bindings: {
[mainEdge.subject]: [{ id: kgSrc }],
[mainEdge.object]: [{ id: kgDst }],
[unpinnedNodeId]: [{ id: intermediateNode }]
},
analyses: [{
resource_id: "infores:biothings-explorer",
edge_bindings: {
[mainEdgeID]: [{ id: kgEdge }]
},
score: 1
}],
};
newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}`] = { edges: new Set(path.slice(1, i).filter((_, ind) => ind % 2 == 0)) };
newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}`] = { edges: new Set(path.slice(i + 1).filter((_, ind) => ind % 2 == 0)) };
} else {
path.slice(1, i).filter((_, ind) => ind % 2 == 0).forEach(edge => newAuxGraphs[`pathfinder-${kgSrc}-${intermediateNode}`].edges.add(edge));
path.slice(i + 1).filter((_, ind) => ind % 2 == 0).forEach(edge => newAuxGraphs[`pathfinder-${intermediateNode}-${kgDst}`].edges.add(edge));
}
}
}
} else {
for (const neighbor of dfsNodes[node]) {
if (!path.includes(neighbor.dst)) {
stack.push({ node: neighbor.dst, path: [...path, neighbor.edge, neighbor.dst ] });
}
}
}
}

creativeResponse.message.results = Object.values(newResultObject);

const finalNewAuxGraphs: {[id: string]: {edges: string[]}} = newAuxGraphs as any;
for (const auxGraph in finalNewAuxGraphs) {
finalNewAuxGraphs[auxGraph].edges = Array.from(finalNewAuxGraphs[auxGraph].edges);
}
Object.assign(creativeResponse.message.auxiliary_graphs, finalNewAuxGraphs);

// TODO: Add knowledge graph edges & combine scoring information

this.getResponse = () => creativeResponse;
}

async _handleInferredEdges(pathfinder = false): Promise<void> {
Expand Down
14 changes: 13 additions & 1 deletion src/inferred_mode/inferred_mode.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@ import {
TrapiQueryGraph,
TrapiResponse,
TrapiResult,
TrapiAnalysis,
CreativePathfinderResponse
} from '../types';
const debug = Debug('bte:biothings-explorer-trapi:inferred-mode');

Expand All @@ -31,6 +33,9 @@ export interface CombinedResponse {
};
};
logs: StampedLog[];
original_analyses?: {
[graphId: string]: TrapiAnalysis;
}
}

export interface CombinedResponseReport {
Expand Down Expand Up @@ -260,7 +265,7 @@ export default class InferredQueryHandler {
combinedResponse: CombinedResponse,
): CombinedResponseReport {
const span = Telemetry.startSpan({ description: 'creativeCombineResponse' });
const newResponse = handler.getResponse();
const newResponse: CreativePathfinderResponse = handler.getResponse();
const report: CombinedResponseReport = {
querySuccess: 0,
queryHadResults: false,
Expand All @@ -286,6 +291,7 @@ export default class InferredQueryHandler {
combinedResponse.message.auxiliary_graphs[auxGraphID] = auxGraph;
}
});

// add results
newResponse.message.results.forEach((result) => {
const translatedResult: TrapiResult = {
Expand All @@ -302,6 +308,7 @@ export default class InferredQueryHandler {
},
],
};

const resultCreativeSubjectID = translatedResult.node_bindings[qEdge.subject]
.map((binding) => binding.id)
.join(',');
Expand Down Expand Up @@ -356,6 +363,10 @@ export default class InferredQueryHandler {
[] as string[],
),
};

if (this.pathfinder) {
combinedResponse.original_analyses[auxGraphID] = translatedResult.analyses[0];
}
}

if (resultID in combinedResponse.message.results) {
Expand Down Expand Up @@ -511,6 +522,7 @@ export default class InferredQueryHandler {
results: {},
},
logs: this.logs,
...(this.pathfinder && { original_analyses: {} })
} as CombinedResponse;
// add/combine nodes
const resultQueries = [];
Expand Down
4 changes: 4 additions & 0 deletions src/types.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -168,6 +168,10 @@ export interface TrapiResponse {
logs: TrapiLog[];
}

export interface CreativePathfinderResponse extends TrapiResponse {
scores?: { [resID: string]: number };
}

export type APIDefinition = {
// Must have one of id or infores
id?: string; // SmartAPI ID, takes priority over infores
Expand Down

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