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

…into dev
biothings · Oct 11, 2024 · ff9e7b1 · ff9e7b1
2 parents 6142684 + f3c7a5b
commit ff9e7b1
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Showing 9 changed files with 361 additions and 1,187 deletions.
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -185,6 +185,57 @@
       ],
       "stopOnEntry": true,
       "console": "integratedTerminal"
-    }
+    },
+    {
+      "name": "Build w/ Cache and Jaeger",
+      "type": "pwa-node",
+      "preLaunchTask": "start redis",
+      "runtimeArgs": [
+        "run",
+        "debug-otel",
+      ],
+      "cwd": "${workspaceFolder}",
+      "runtimeExecutable": "pnpm",
+      "restart": false,
+      "env": {
+        "REDIS_HOST": "localhost",
+        "REDIS_PORT": "6379",
+        "DEBUG": "biomedical-id-resolver,bte*",
+        "SMARTAPI_SYNC": "false",
+        "RESULT_CACHING": "true",
+        "JAEGER_HOST": "localhost",
+        "JAEGER_PORT": "4318",
+      },
+      "request": "launch",
+      "skipFiles": [
+        "<node_internals>/**"
+      ],
+      "stopOnEntry": true,
+      "console": "integratedTerminal"
+    },
+    {
+      "name": "Build w/ Jaeger NO Cache",
+      "type": "pwa-node",
+      "runtimeArgs": [
+        "run",
+        "debug-otel",
+      ],
+      "cwd": "${workspaceFolder}",
+      "runtimeExecutable": "pnpm",
+      "restart": false,
+      "env": {
+        "DEBUG": "biomedical-id-resolver,bte*",
+        "SMARTAPI_SYNC": "false",
+        "RESULT_CACHING": "false",
+        "JAEGER_HOST": "localhost",
+        "JAEGER_PORT": "4318",
+      },
+      "request": "launch",
+      "skipFiles": [
+        "<node_internals>/**"
+      ],
+      "stopOnEntry": true,
+      "console": "integratedTerminal"
+    },
   ]
 }
diff --git a/deploy/values.yaml b/deploy/values.yaml
@@ -79,7 +79,7 @@ affinity:
 resources:
   requests:
     memory: 25Gi
-    cpu: 8000m
+    cpu: 7000m
   limits:
     memory: 35Gi
-    cpu: 10000m 
+    cpu: 8000m 
diff --git a/docs/REFERENCE.md b/docs/REFERENCE.md
@@ -46,6 +46,14 @@ Several environment variables are supported for various purposes, listed below:
 
 **Description:** Run query execution as normal, but do not actually query APIs.
 
+#### `CREATIVE_TIMEOUT_S`
+
+**Default:** `285` (4.75 minutes)
+
+**Docker Default:** `285`
+
+**Description:** Timeout for creative mode template execution (does not include final results merging).
+
 #### `INSTANCE_ENV`
 
 **Default:** `prod`

diff --git a/package.json b/package.json
@@ -26,7 +26,9 @@
     "start": "./scripts/start_server.sh",
     "stop": "./scripts/stop_server.sh",
     "watch": "nodemon -e js,mjs,json,ts --watch './packages/**/src/*' './packages/**/data/*' --exec 'pnpm run build && node .'",
-    "debug": "DEBUG=biomedical-id-resolver,bte* pnpm run watch"
+    "watch-otel": "nodemon -e js,mjs,json,ts --watch './packages/**/src/*' './packages/**/data/*' --exec 'pnpm run build && node --require ./packages/bte-server/built/controllers/opentelemetry.js .'",
+    "debug": "DEBUG=biomedical-id-resolver,bte* pnpm run watch",
+    "debug-otel": "DEBUG=biomedical-id-resolver,bte* pnpm run watch-otel"
   },
   "engines": {
     "node": ">=18.0.0",

diff --git a/packages/types/src/global.ts b/packages/types/src/global.ts
@@ -13,11 +13,15 @@ export interface QueryQueue {
   bte_query_queue_by_team: Queue;
 }
 
+export interface recordCount {
+  [handler_index: number]: number;
+}
+
 export interface QueryInformation {
   queryGraph: TrapiQueryGraph;
   isCreativeMode?: boolean;
   creativeTemplate?: string;
-  totalRecords?: number;
+  totalRecords?: recordCount;
   jobID?: string;
   callback_url?: string;
 }

diff --git a/packages/types/src/misc.ts b/packages/types/src/misc.ts
@@ -5,6 +5,7 @@ export type APIDefinition = {
   infores?: string; // infores of API
   primarySource?: boolean;
   includeFlipped?: boolean; // Automatically generate flipped MetaEdges (TRAPI only)
+  timeout?: number;
 } & ({ id: string } | { infores: string });
 
 export interface APIList {

diff --git a/packages/types/src/tasks.ts b/packages/types/src/tasks.ts
@@ -33,6 +33,7 @@ export interface QueryHandlerOptions extends QueryOptions {
   EDGE_ATTRIBUTES_USED_IN_RECORD_HASH?: string[];
   smartapi?: SmartAPIQueryResult;
   skipPfocr?: boolean;
+  handlerIndex?: number;
 }
 
 export interface QueueData {
@@ -43,6 +44,8 @@ export interface QueueData {
   smartAPIID?: string;
   teamName?: string;
   route: string;
+  traceparent?: string;
+  tracestate?: string;
 }
 
 export interface QueryParams {