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

…into fix-857-bte
biothings · Sep 27, 2024 · 5b826f3 · 5b826f3
2 parents 7be22d4 + eae8ca9
commit 5b826f3
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Showing 7 changed files with 12,953 additions and 10,055 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
@@ -81,14 +81,14 @@
     "@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/misc.ts b/packages/types/src/misc.ts
@@ -4,6 +4,7 @@ export type APIDefinition = {
   name: string; // Must match name on SmartAPI registry
   infores?: string; // infores of API
   primarySource?: boolean;
+  includeFlipped?: boolean; // Automatically generate flipped MetaEdges (TRAPI only)
 } & ({ id: string } | { infores: string });
 
 export interface APIList {

diff --git a/packages/types/src/tasks.ts b/packages/types/src/tasks.ts
@@ -6,7 +6,7 @@ import {
   TrapiSchema,
   TrapiWorkflow,
 } from "./trapi";
-import {
+import MetaKG, {
   SmartAPIKGOperationObject,
   SmartAPIQueryResult,
 } from "@biothings-explorer/smartapi-kg";
@@ -17,6 +17,7 @@ export interface QueryOptions {
   submitter?: string;
   smartAPIID?: string;
   teamName?: string;
+  dryrun_pathfinder?: boolean;
   dryrun?: boolean;
   caching?: boolean; // from request url query values
 }
@@ -31,11 +32,12 @@ export interface QueryHandlerOptions extends QueryOptions {
   resolveOutputIDs?: boolean;
   EDGE_ATTRIBUTES_USED_IN_RECORD_HASH?: string[];
   smartapi?: SmartAPIQueryResult;
+  skipPfocr?: boolean;
 }
 
 export interface QueueData {
   queryGraph: TrapiQueryGraph;
-  options: QueryOptions;
+  options: QueryHandlerOptions;
   workflow?: TrapiWorkflow[];
   callback_url?: string;
   smartAPIID?: string;

diff --git a/packages/types/src/trapi.ts b/packages/types/src/trapi.ts
@@ -67,12 +67,12 @@ export interface TrapiAttribute {
   value_type_id?: string;
   attribute_source?: string | null;
   value_url?: string | null;
-  attributes?: TrapiAttribute;
+  attributes?: TrapiAttribute[];
   [additionalProperties: string]:
   | string
   | string[]
   | null
-  | TrapiAttribute
+  | TrapiAttribute[]
   | number
   | number[];
 }
@@ -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 {