fix: add file locking mechanism

package.json

@@ -31,13 +31,13 @@
   "devDependencies": {
     "@commitlint/cli": "^18.2.0",
     "@commitlint/config-conventional": "^11.0.0",
-    "biolink-model": "workspace:../biolink-model",
     "@types/debug": "^4.1.10",
     "@types/jest": "^29.5.7",
     "@types/lodash": "^4.14.200",
     "@types/node": "^20.8.10",
     "@typescript-eslint/eslint-plugin": "^6.8.0",
     "@typescript-eslint/parser": "^6.8.0",
+    "biolink-model": "workspace:../biolink-model",
     "eslint": "^8.53.0",
     "eslint-config-prettier": "^9.0.0",
     "eslint-plugin-prettier": "^5.0.1",
@@ -59,6 +59,7 @@
     "ioredis": "^5.3.2",
     "ioredis-mock": "^8.9.0",
     "lodash": "^4.17.21",
+    "proper-lockfile": "^4.1.2",
     "redlock": "5.0.0-beta.2"
   }
 }

src/misc.ts

@@ -1,3 +1,6 @@
+import lockfile from "proper-lockfile";
+import { setTimeout as sleep } from "timers/promises";
+
 export function toArray<Type>(input: Type | Type[]): Type[] {
   if (Array.isArray(input)) {
     return input;
@@ -76,3 +79,62 @@ export function timeoutPromise<T>(promise: Promise<T>, timeout: number): Promise
     reject = newReject;
   });
 }
+
+export const LOCKFILE_STALENESS = {stale: 5000}; // lock expiration in milliseconds to prevent deadlocks
+export const LOCKFILE_RETRY_CONFIG = {
+  retries: {
+    retries: 10,
+    factor: 2,
+    minTimeout: 100,
+    maxTimeout: 1000,
+  },
+  stale: LOCKFILE_STALENESS["stale"],
+};
+
+export async function lockWithActionAsync<T>(filePath: string, action: () => Promise<T>, debug?: (message: string) => void): Promise<T> {
+  if (process.env.NODE_ENV !== "production") {
+    debug(`Development mode: Skipping lockfile ${process.env.NODE_ENV}`);
+    const result = await action();
+    return result;
+  }
+
+  let release;
+  try {
+    release = await lockfile.lock(filePath, LOCKFILE_RETRY_CONFIG);
+    const result = await action();
+    return result;
+  } catch (error) {
+    debug(`Lockfile error: ${error}`);
+    // throw error;
+  } finally {
+    if (release) release();
+  }
+}
+
+export function lockWithActionSync<T>(filePath: string, action: () => T, debug?: (message: string) => void): T {
+  if (process.env.NODE_ENV !== "production") {
+    debug(`Development mode: Skipping lockfile ${process.env.NODE_ENV}`);
+    return action();
+  }
+
+  let release;
+  try {
+    const startTime = Date.now();
+
+    while (Date.now() - startTime < LOCKFILE_STALENESS["stale"]) {
+      if (!lockfile.checkSync(filePath)) {
+        release = lockfile.lockSync(filePath, LOCKFILE_STALENESS);
+        const result = action();
+        return result;
+      } else {
+        sleep(LOCKFILE_RETRY_CONFIG["retries"]["minTimeout"]);
+      }
+    }
+    debug("Lockfile timeout: did not read file");
+  } catch (error) {
+    debug(`Lockfile error: ${error}`);
+    // throw error;
+  } finally {
+    if (release) release();
+  }
+}