Merge pull request #225 from biothings/fix-896-bte

Add file locking while reading smartapi

Author: tokebe

package.json

@@ -57,12 +57,12 @@
     "@biothings-explorer/call-apis": "workspace:../call-apis",
     "@biothings-explorer/node-expansion": "workspace:../node-expansion",
     "@biothings-explorer/smartapi-kg": "workspace:../smartapi-kg",
-    "@biothings-explorer/utils": "workspace:../utils",
     "@biothings-explorer/types": "workspace:../types",
-    "biolink-model": "workspace:../biolink-model",
-    "biomedical_id_resolver": "workspace:../biomedical_id_resolver",
+    "@biothings-explorer/utils": "workspace:../utils",
     "@sentry/node": "^7.74.1",
     "async": "^3.2.4",
+    "biolink-model": "workspace:../biolink-model",
+    "biomedical_id_resolver": "workspace:../biomedical_id_resolver",
     "chi-square-p-value": "^1.0.5",
     "debug": "^4.3.4",
     "ioredis": "^5.3.2",

src/index.ts

@@ -10,7 +10,7 @@ import Graph from './graph/graph';
 import EdgeManager from './edge_manager';
 import _ from 'lodash';
 import QEdge2APIEdgeHandler from './qedge2apiedge';
-import { LogEntry, StampedLog } from '@biothings-explorer/utils';
+import { lockWithActionAsync, LogEntry, StampedLog } from '@biothings-explorer/utils';
 import { promises as fs } from 'fs';
 import { getDescendants } from '@biothings-explorer/node-expansion';
 import { resolveSRI, SRINodeNormFailure } from 'biomedical_id_resolver';
@@ -81,8 +81,11 @@ export default class TRAPIQueryHandler {
     if (this.options.smartapi) {
       smartapiRegistry = this.options.smartapi;
     } else {
-      const file = await fs.readFile(this.path, 'utf-8');
-      smartapiRegistry = JSON.parse(file);
+      smartapiRegistry = await lockWithActionAsync([this.path], async () => {
+        const file = await fs.readFile(this.path, 'utf-8');
+        const hits = JSON.parse(file);
+        return hits;
+      }, debug);
     }
 
     const smartapiIds: string[] = [];
@@ -124,7 +127,7 @@ export default class TRAPIQueryHandler {
 
     const metaKG = new MetaKG(this.path, this.predicatePath);
     debug(`SmartAPI Specs read from path: ${this.path}`);
-    metaKG.constructMetaKGSync(this.includeReasoner, this.options);
+    await metaKG.constructMetaKGWithFileLock(this.includeReasoner, this.options);
     return metaKG;
   }
 
@@ -722,7 +725,6 @@ export default class TRAPIQueryHandler {
       return;
     }
     debug('MetaKG successfully loaded!');
-
     span1?.finish();
 
     if (global.missingAPIs) {