Merge branch 'main' of https://github.com/biothings/biothings_explorer …

…into retriever-backport
biothings · Sep 20, 2024 · 710d5bc · 710d5bc
2 parents 1dfd7a9 + 69a3023
commit 710d5bc
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Showing 8 changed files with 66 additions and 27 deletions.
diff --git a/deploy/values.yaml b/deploy/values.yaml
@@ -78,8 +78,8 @@ affinity:
       topologyKey: "kubernetes.io/hostname"
 resources:
   requests:
-    memory: 50Gi
-    cpu: 10000m
+    memory: 25Gi
+    cpu: 8000m
   limits:
-    memory: 58Gi
-    cpu: 14000m 
+    memory: 35Gi
+    cpu: 10000m 
diff --git a/package.json b/package.json
@@ -79,14 +79,14 @@
     "@sentry/node": "^7.74.1",
     "@sentry/profiling-node": "^1.2.1",
     "axios": "^0.28.0",
-    "body-parser": "^1.20.2",
+    "body-parser": "^1.20.3",
     "bull": "^4.11.4",
     "compression": "^1.7.4",
     "connect-history-api-fallback": "^2.0.0",
     "cors": "^2.8.5",
     "debug": "^4.3.4",
     "dotenv": "^8.6.0",
-    "express": "^4.18.2",
+    "express": "^4.20.0",
     "express-rate-limit": "^5.5.1",
     "express-winston": "^4.2.0",
     "helmet": "^4.6.0",

diff --git a/packages/types/src/exceptions.ts b/packages/types/src/exceptions.ts
@@ -28,4 +28,21 @@ export class InvalidQueryGraphError extends Error {
     this.message = message;
     this.statusCode = 400;
   }
+}
+
+export class NotImplementedError extends Error {
+  statusCode: number;
+  constructor(message = 'Feature not implemented', ...params: string[]) {
+    super(...params);
+
+    Object.setPrototypeOf(this, NotImplementedError.prototype);
+
+    if (Error.captureStackTrace) {
+      Error.captureStackTrace(this, NotImplementedError);
+    }
+
+    this.name = 'NotImplementedError';
+    this.message = message;
+    this.statusCode = 501;
+  }
 }
diff --git a/packages/types/src/query_graph.ts b/packages/types/src/query_graph.ts
@@ -9,6 +9,7 @@ import QNode from "./query_node";
 import { resolveSRI } from "biomedical_id_resolver";
 import _ from "lodash";
 import * as utils from "@biothings-explorer/utils";
+import { NotImplementedError } from "./exceptions";
 
 const debug = Debug("bte:query_graph");
 
@@ -18,9 +19,11 @@ export default class QueryGraph {
   logs: StampedLog[];
   nodes: { [QNodeID: string]: QNode };
   edges: { [QEdgeID: string]: QEdge };
-  constructor(queryGraph: TrapiQueryGraph, schema: any) {
+  skipCycleDetection: boolean;
+  constructor(queryGraph: TrapiQueryGraph, schema: any, skipCycleDetection = false) {
     this.queryGraph = queryGraph;
     this.schema = schema;
+    this.skipCycleDetection = skipCycleDetection;
     this.logs = [];
   }
 
@@ -110,7 +113,7 @@ 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 },
       ];
@@ -206,6 +209,14 @@ export default class QueryGraph {
       }
     });
   }
+
+  _validateNoMCQ(queryGraph: TrapiQueryGraph): boolean {
+    return Object.values(queryGraph.nodes).some((node) => {
+      if (node.set_interpretation && node.set_interpretation.toLowerCase() === 'many') {
+        throw new NotImplementedError('NotImplementedError', 'Set interpretation is not yet implemented.')
+      }
+    })
+  }
 
   _validate(queryGraph: TrapiQueryGraph): void {
     this._validateEmptyEdges(queryGraph);
@@ -216,8 +227,9 @@ export default class QueryGraph {
     this._validateNodeProperties(queryGraph);
     this._validateEdgeProperties(queryGraph);
     this._validateBatchSize(queryGraph);
-    this._validateCycles(queryGraph);
+    !this.skipCycleDetection && this._validateCycles(queryGraph);
     this._validateNoDuplicateQualifierTypes(queryGraph);
+    this._validateNoMCQ(queryGraph);
   }
 
   private async _findNodeCategories(curies: string[]): Promise<string[]> {
@@ -413,6 +425,14 @@ export default class QueryGraph {
         ) {
           nodes[qNodeID].categories.push("biolink:Gene");
         }
+        if (
+          nodes[qNodeID].categories.includes('biolink:Gene') &&
+          !nodes[qNodeID].categories.includes('biolink:Protein')
+        ) {
+          nodes[qNodeID].categories.push('biolink:Protein');
+        }
+        // Ensure categories are rolled into expandedCategories
+        nodes[qNodeID].expandCategories()
       }
     }
     this.logs.push(

diff --git a/packages/types/src/record.ts b/packages/types/src/record.ts
@@ -469,6 +469,8 @@ export class Record {
           sourceA.resource_id.localeCompare(sourceB.resource_id),
         ).map(source => _.omit(source, ["source_record_urls"])),
       ),
+      this.knowledge_level,
+      this.agent_type
     ].join("-");
   }
 
@@ -511,9 +513,9 @@ export class Record {
 
   get apiInforesCurie(): string {
     if (this.association["x-translator"]) {
-      return this.association["x-translator"]["infores"] || undefined;
+      return this.association["x-translator"]["infores"] || "infores:error-not-provided";
     }
-    return undefined;
+    return "infores:error-not-provided";
   }
 
   get metaEdgeSource(): string {

diff --git a/packages/types/src/trapi.ts b/packages/types/src/trapi.ts
@@ -97,12 +97,12 @@ export interface TrapiAttributeConstraint {
 export interface TrapiNodeBinding {
   id: string;
   query_id?: string;
-  attributes?: TrapiAttribute[];
+  attributes: TrapiAttribute[];
 }
 
 export interface TrapiEdgeBinding {
   id: string;
-  attributes?: TrapiAttribute[];
+  attributes: TrapiAttribute[];
 }
 
 export interface TrapiAnalysis {
@@ -118,7 +118,7 @@ export interface TrapiAnalysis {
 
 export interface TrapiAuxiliaryGraph {
   edges: string[];
-  attributes?: TrapiAttribute[];
+  attributes: TrapiAttribute[];
 }
 
 export interface TrapiPfocrFigure {

diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
diff --git a/prod_revisions.txt b/prod_revisions.txt
@@ -2,13 +2,13 @@
 > @biothings-explorer/[email protected] get_rev /Users/jcallaghan/Projects/bte-main
 > ./scripts/get_rev.sh
 
-# Generated from "pnpm run get_rev" on  Fri Aug 30 12:53:17 EDT 2024
-https://github.com/biothings/bte-server.git cdb1b8e cdb1b8e2b7fea8c83852db3542de91c03ca7626f
-https://github.com/biothings/api-respone-transform.js.git f5831b9 f5831b9c54ab974f08c2fb476a61c0e1e4629ebb
-https://github.com/biothings/call-apis.js.git 4c59a93 4c59a930a10024e928e6deffa09725551b9579a3
+# Generated from "pnpm run get_rev" on  Fri Sep 20 12:30:17 EDT 2024
+https://github.com/biothings/bte-server.git b1b8d91 b1b8d91bda0d52bffc6b56b69c86d46843cd2058
+https://github.com/biothings/api-respone-transform.js.git 13c306d 13c306d2accc288d99ade65cb684244498e75013
+https://github.com/biothings/call-apis.js.git 273b866 273b866273056e9e43ab057c25e76758bfa23944
 https://github.com/biothings/smartapi-kg.js.git a328307 a3283077e18145d1865e4a9ba57ef56846d19264
-https://github.com/biothings/bte_trapi_query_graph_handler.git 265360d 265360def22d267d8a621cc4bacd786852e4bcc5
+https://github.com/biothings/bte_trapi_query_graph_handler.git 9bc677d 9bc677dc02ef030bb7debd94b57f0f1f9e38cb7f
 https://github.com/biothings/node-expansion.git d140a26 d140a264e96d71fc20da90891bd37c4f4d0e06a8
 https://github.com/biothings/biolink-model.js.git 24b8192 24b81923c99269185f39b7d5bee02239931a0f1b
 https://github.com/biothings/biomedical_id_resolver.js.git 8c1f094 8c1f094d7525fb1ddc6502a379ae2e23f9dbfbe5
-https://github.com/biothings/bte-utils.git 84708cf 84708cf8bd138ee85b11fdc4564d5faac1f31539
+https://github.com/biothings/bte-utils.git 0e577b6 0e577b6a96a62ada3e393d2d8cddd0b4f6e42c69