identify pathfinder queries. identify templates

biothings · Mar 23, 2024 · 52bc25d · 52bc25d
1 parent 559de80
commit 52bc25d
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Showing 4 changed files with 72 additions and 8 deletions.
diff --git a/src/index.ts b/src/index.ts
@@ -413,7 +413,7 @@ export default class TRAPIQueryHandler {
 
   async _processQueryGraph(queryGraph: TrapiQueryGraph): Promise<QEdge[]> {
     try {
-      const queryGraphHandler = new QueryGraph(queryGraph, this.options.schema);
+      const queryGraphHandler = new QueryGraph(queryGraph, this.options.schema, this._queryIsPathfinder());
       const queryEdges = await queryGraphHandler.calculateEdges();
       this.logs = [...this.logs, ...queryGraphHandler.logs];
       return queryEdges;
@@ -509,6 +509,12 @@ export default class TRAPIQueryHandler {
     }
   }
 
+  _queryIsPathfinder(): boolean {
+    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 != null ? 1 : 0), 0);
+    return inferredEdgeCount === 3 && pinnedNodes == 2 && Object.keys(this.queryGraph.edges).length === 3 && Object.keys(this.queryGraph.nodes).length === 3;
+  }
+
   _queryUsesInferredMode(): boolean {
     const inferredEdge = Object.values(this.queryGraph.edges).some((edge) => edge.knowledge_type === 'inferred');
     return inferredEdge;
@@ -519,7 +525,50 @@ export default class TRAPIQueryHandler {
     return oneHop;
   }
 
-  async _handleInferredEdges(): Promise<void> {
+  async _handlePathfinder(): Promise<void> {
+    const [unpinnedNodeId, unpinnedNode] = Object.entries(this.queryGraph.nodes).find(([_, node]) => !node.ids);
+    // 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);
+
+    // intermediateEdges should be in order of n0 -> un & un -> n1
+    if (intermediateEdges[0][1].subject === unpinnedNodeId) {
+        let temp = intermediateEdges[0];
+        intermediateEdges[0] = intermediateEdges[1];
+        intermediateEdges[1] = temp;
+    }
+
+    // remove intermediates for creative execution
+    intermediateEdges.forEach(([edgeId, _]) => delete this.queryGraph.edges[edgeId]);
+
+    if (Object.keys(this.queryGraph.edges).length !== 1) {
+        const message = 'Pathfinder Mode needs exactly one edge between nodes with IDs. Your query terminates.';
+        debug(message);
+        this.logs.push(new LogEntry('WARNING', null, message).getLog());
+        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) {
+        const message = 'Intermediate edges for Pathfinder are incorrect. Your query terminates.';
+        debug(message);
+        this.logs.push(new LogEntry('WARNING', null, message).getLog());
+        return;
+    }
+
+    // test
+    console.log("recognized pathfinder");
+
+    // run creative mode
+    await this._handleInferredEdges(true);
+    const creativeResponse = this.getResponse();
+
+    // restore query graph
+    this.queryGraph.nodes[unpinnedNodeId] = unpinnedNode;
+    intermediateEdges.forEach(([edgeId, edge]) => this.queryGraph.edges[edgeId] = edge);
+  }
+
+  async _handleInferredEdges(pathfinder = false): Promise<void> {
     if (!this._queryIsOneHop()) {
       const message = 'Inferred Mode edges are only supported in single-edge queries. Your query terminates.';
       debug(message);
@@ -534,6 +583,7 @@ export default class TRAPIQueryHandler {
       this.path,
       this.predicatePath,
       this.includeReasoner,
+      pathfinder
     );
     const inferredQueryResponse = await inferredQueryHandler.query();
     if (inferredQueryResponse) {
@@ -668,6 +718,13 @@ export default class TRAPIQueryHandler {
     }
     debug(`(3) All edges created ${JSON.stringify(queryEdges)} `);
 
+    if (this._queryIsPathfinder()) {
+        const span2 = Telemetry.startSpan({ description: 'pathfinderExecution' });
+        await this._handlePathfinder();
+        span2?.finish();
+        return;
+    }
+
     if (this._queryUsesInferredMode()) {
       const span2 = Telemetry.startSpan({ description: 'creativeExecution' });
       await this._handleInferredEdges();

diff --git a/src/inferred_mode/inferred_mode.ts b/src/inferred_mode/inferred_mode.ts
@@ -51,6 +51,7 @@ export default class InferredQueryHandler {
   path: string;
   predicatePath: string;
   includeReasoner: boolean;
+  pathfinder: boolean;
   CREATIVE_LIMIT: number;
   constructor(
     parent: TRAPIQueryHandler,
@@ -60,6 +61,7 @@ export default class InferredQueryHandler {
     path: string,
     predicatePath: string,
     includeReasoner: boolean,
+    pathfinder: boolean
   ) {
     this.parent = parent;
     this.queryGraph = queryGraph;
@@ -68,6 +70,7 @@ export default class InferredQueryHandler {
     this.path = path;
     this.predicatePath = predicatePath;
     this.includeReasoner = includeReasoner;
+    this.pathfinder = pathfinder;
     this.CREATIVE_LIMIT = process.env.CREATIVE_LIMIT ? parseInt(process.env.CREATIVE_LIMIT) : 500;
   }
 
@@ -107,7 +110,7 @@ export default class InferredQueryHandler {
       Object.values(this.queryGraph.nodes).reduce((sum, node) => {
         return typeof node.ids !== 'undefined' ? sum + node.ids.length : sum;
       }, 0);
-    if (tooManyIDs) {
+    if (tooManyIDs && !this.pathfinder) {
       const message = 'Inferred Mode queries with multiple IDs are not supported. Your query terminates.';
       this.logs.push(new LogEntry('WARNING', null, message).getLog());
       debug(message);
@@ -195,7 +198,7 @@ export default class InferredQueryHandler {
       }, []);
       return [...arr, ...objectCombos];
     }, []);
-    const templates = await getTemplates(lookupObjects);
+    const templates = await getTemplates(lookupObjects, this.pathfinder);
 
     const logMessage = `Got ${templates.length} inferred query templates.`;
     debug(logMessage);

diff --git a/src/inferred_mode/template_lookup.ts b/src/inferred_mode/template_lookup.ts
@@ -25,6 +25,7 @@ export interface TemplateGroup {
   object: string[];
   qualifiers?: CompactQualifiers;
   templates: string[];
+  pathfinder: boolean;
 }
 
 export interface CompactEdge {
@@ -34,7 +35,7 @@ export interface CompactEdge {
   qualifiers: CompactQualifiers;
 }
 
-export async function getTemplates(lookups: TemplateLookup[]): Promise<MatchedTemplate[]> {
+export async function getTemplates(lookups: TemplateLookup[], pathfinder = false): Promise<MatchedTemplate[]> {
   async function getFiles(dir: string): Promise<string[]> {
     const rootFiles = await fs.readdir(path.resolve(dir));
     return await async.reduce(rootFiles, [] as string[], async (arr, fname: string) => {
@@ -57,6 +58,7 @@ export async function getTemplates(lookups: TemplateLookup[]): Promise<MatchedTe
   const matchingTemplatePaths: string[] = templateGroups.reduce((matches: string[], group: TemplateGroup) => {
     const lookupMatch = lookups.some((lookup) => {
       return (
+        group.pathfinder === pathfinder &&
         group.subject.includes(lookup.subject) &&
         group.object.includes(lookup.object) &&
         group.predicate.includes(lookup.predicate) &&

diff --git a/src/query_graph.ts b/src/query_graph.ts
@@ -15,11 +15,13 @@ export default class QueryGraph {
   queryGraph: TrapiQueryGraph;
   schema: any;
   logs: StampedLog[];
+  skipCycleDetection: boolean;
   nodes: { [QNodeID: string]: QNode };
   edges: { [QEdgeID: string]: QEdge };
-  constructor(queryGraph: TrapiQueryGraph, schema: any) {
+  constructor(queryGraph: TrapiQueryGraph, schema: any, skipCycleDetection = false) {
     this.queryGraph = queryGraph;
     this.schema = schema;
+    this.skipCycleDetection = skipCycleDetection;
     this.logs = [];
   }
 
@@ -93,7 +95,7 @@ export default class QueryGraph {
     }
 
     for (const firstNode in nodes) {
-      if (nodes[firstNode].visited === true) continue;
+      if (nodes[firstNode].visited == true) continue;
       const stack: { curNode: string; parent: string | number }[] = [{ curNode: firstNode, parent: -1 }];
       nodes[firstNode].visited = true;
       while (stack.length !== 0) {
@@ -191,7 +193,7 @@ export default class QueryGraph {
     this._validateNodeProperties(queryGraph);
     this._validateEdgeProperties(queryGraph);
     this._validateBatchSize(queryGraph);
-    this._validateCycles(queryGraph);
+    !this.skipCycleDetection && this._validateCycles(queryGraph);
     this._validateNoDuplicateQualifierTypes(queryGraph);
   }