@openhealth/oht-custom-parser-lib 0.3.10 → 0.3.13

package/dist/index.d.ts

@@ -10,7 +10,7 @@ export { AcfBiomarkerRangeAnnotationCheck, AcfBiomarkerGenericDisclaimerLogic, M
 export { ErrorMessage, ErrorCode, ERROR_CATALOG, ERROR_MESSAGES, getErrorMessage, getRejectReason, } from './types/error.types';
 export { handleError, ValidationError, shouldSendSlackNotification, extractFormattedRejectReason, mapErrorToRejectReason, } from './service/fileUploadErrorHandler.service';
 export type { TransformationRule, TransformationContext, ApplyRulesResult as TransformationApplyRulesResult, ApplyRulesOptions as TransformationApplyRulesOptions, ValidationResult as TransformationValidationResult, } from './types/transformationRules.types';
-export { processingLogger, ProcessingContext, StageDuration, runWithContext, runWithContextAsync, } from './service/processingLogger.service';
+export { processingLogger, ProcessingContext, StageDuration, getRequestIdFromContext, runWithContext, runWithContextAsync, } from './service/processingLogger.service';
 export { makeApiCallWithRetry, parseErrorObj } from './util-ts/apiUtils';
 export { extractValue, isBiomarkerValueNumerical, isBiomarkerExternalNoVisualRange, processAppendedMappings, fetchSynonymUnits, resolveUnitFromSynonyms, extractFromPath, applyFormat } from './util-ts/dataUtils';
 export { readFileFromBucket, uploadFileBufferToGCS } from './util-ts/googleStorageUtils';

package/dist/index.js

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.processingLogger = exports.mapErrorToRejectReason = exports.extractFormattedRejectReason = exports.shouldSendSlackNotification = exports.ValidationError = exports.handleError = exports.getRejectReason = exports.getErrorMessage = exports.ERROR_MESSAGES = exports.ERROR_CATALOG = exports.ErrorCode = exports.RejectReason = exports.UploadType = exports.Sex = exports.DataImportFileUploadStatus = exports.BiomarkerValueType = exports.MeasurementValueComparator = exports.DigitizationStatus = exports.PipelineStep = exports.ReferenceRangeType = exports.BiomarkerCompatibility = exports.ManualCheck = exports.AcfBiomarkerGenericDisclaimerLogic = exports.AcfBiomarkerRangeAnnotationCheck = exports.unitSynonyms = exports.validateTransformationRuleExpression = exports.applyTransformationRules = exports.generateBIMessages = exports.publishToTopic = exports.aggregateBiMessages = exports.aggregateMessages = exports.sendMessageToSlack = exports.getSlackFileIssueNotificationMessage = exports.extractValueFromGreaterLowerThan = exports.extractUnit = exports.getRangeFromPositionAndRegex = exports.parseExamValue = exports.extractReferenceAnnotation = exports.extractReferenceRanges = exports.checkValueForPlausibleValues = exports.ohtMeasurementsExtractor = exports.ohtReportMeasurementsExtractor = exports.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.postReportPreviewToCore = exports.postDataImportFileUploadToCore = void 0;
-exports.parseRange = exports.getMappedBiomarkersLatest = exports.getMappedBiomarkers = exports.getLowerThanPatterns = exports.getGreaterThanPatterns = exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = exports.applyFormat = exports.extractFromPath = exports.resolveUnitFromSynonyms = exports.fetchSynonymUnits = exports.processAppendedMappings = exports.isBiomarkerExternalNoVisualRange = exports.isBiomarkerValueNumerical = exports.extractValue = exports.parseErrorObj = exports.makeApiCallWithRetry = exports.runWithContextAsync = exports.runWithContext = void 0;
+exports.parseRange = exports.getMappedBiomarkersLatest = exports.getMappedBiomarkers = exports.getLowerThanPatterns = exports.getGreaterThanPatterns = exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = exports.applyFormat = exports.extractFromPath = exports.resolveUnitFromSynonyms = exports.fetchSynonymUnits = exports.processAppendedMappings = exports.isBiomarkerExternalNoVisualRange = exports.isBiomarkerValueNumerical = exports.extractValue = exports.parseErrorObj = exports.makeApiCallWithRetry = exports.runWithContextAsync = exports.runWithContext = exports.getRequestIdFromContext = void 0;
 // ### SERVICES ###
 var reportCreator_service_1 = require("./service/reportCreator.service");
 Object.defineProperty(exports, "postDataImportFileUploadToCore", { enumerable: true, get: function () { return reportCreator_service_1.postDataImportFileUploadToCore; } });
@@ -70,6 +70,7 @@ Object.defineProperty(exports, "mapErrorToRejectReason", { enumerable: true, get
 // ### PROCESSING LOGGER ###
 var processingLogger_service_1 = require("./service/processingLogger.service");
 Object.defineProperty(exports, "processingLogger", { enumerable: true, get: function () { return processingLogger_service_1.processingLogger; } });
+Object.defineProperty(exports, "getRequestIdFromContext", { enumerable: true, get: function () { return processingLogger_service_1.getRequestIdFromContext; } });
 Object.defineProperty(exports, "runWithContext", { enumerable: true, get: function () { return processingLogger_service_1.runWithContext; } });
 Object.defineProperty(exports, "runWithContextAsync", { enumerable: true, get: function () { return processingLogger_service_1.runWithContextAsync; } });
 // ### UTIL-TS ###

package/dist/index.js.map

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package/dist/service/processingLogger.service.d.ts

@@ -1,4 +1,9 @@
 import pino from 'pino';
+/**
+ * Returns a stable request id for the given context. Same id must be used for the whole request.
+ * Used to key the registry so each request has isolated state.
+ */
+export declare function getRequestIdFromContext(context: ProcessingContext): string;
 /**
  * Processing context interface - contains all context information for a processing cycle
  */
@@ -69,39 +74,41 @@ interface ProcessingState {
     metadata?: Record<string, any>;
 }
 /**
- * ProcessingLoggerService - Singleton service for tracking processing state and logging
+ * ProcessingLoggerService - Singleton facade for request-scoped processing state and logging.
+ *
+ * State is keyed by request id (fileUploadId ?? messageId ?? cloudEventId) in a registry.
+ * AsyncLocalStorage holds only the current request id; getMutableState() resolves state via
+ * registry.get(id). When registry.get(id) is undefined (no context or stale id), a transient
+ * empty state is used so one request never overwrites another's context.
  *
- * Provides simplified API for logging processing progress with automatic stage timing,
- * measurement tracking, and comprehensive summary logging. Use logInfo, logWarn, logError,
- * logDebug for all application logs so they include the same context (file_name, file_upload_id, etc.)
- * and are searchable by fileUploadId/filename.
+ * Entry point: runWithContextAsync(context, fn). Creates registry entry, runs fn with id in ALS,
+ * removes entry in finally. Use logInfo, logWarn, logError, logDebug for application logs so they
+ * include the same context and are searchable by fileUploadId/filename.
  *
  * Usage:
  * ```typescript
- * processingLogger.clear();
- * processingLogger.setContext({ fileName: 'test.json', partnerId: 'partner_123' });
- * processingLogger.logStart();
- * processingLogger.logProgress(20, 'get_transformation_rules');
- * processingLogger.logInfo('Step completed', { count: 5 });
- * processingLogger.addMeasurement(15, 'measurements');
- * processingLogger.logEnd(true);
+ * await runWithContextAsync(context, async () => {
+ *   processingLogger.logStart();
+ *   processingLogger.logProgress(20, 'get_transformation_rules');
+ *   processingLogger.logEnd(true);
+ * });
  * ```
+ * Initial state is set from context by runWithContextAsync; clear() and setContext() are optional if you need to reset/override.
  */
 declare class ProcessingLoggerService {
     private static instance;
-    private state;
     private logger;
     private constructor();
     static getInstance(): ProcessingLoggerService;
-    private initializeState;
     /**
-     * Current state: request-scoped store when inside runWithContext, else singleton state.
-     * All reads/writes go through this so parallel requests do not mix state.
+     * Resolves state from registry by current request id. When registry.get(id) is undefined
+     * (no context or stale id), returns a transient clear state so one request never overwrites another's context.
      */
     private getMutableState;
     /**
      * Reset all state for a new processing cycle. Call at the start of each Cloud Event / request
      * so that context and metrics from a previous request never leak.
+     * Clears both context fields and run state; call setContext(context) after clear() in handlers.
      */
     clear(): void;
     /**
@@ -109,7 +116,7 @@ declare class ProcessingLoggerService {
      * Call after clear() for each new request.
      */
     setContext(context: ProcessingContext): void;
-    /** Public getter for tests / inspection; returns a copy. Use file_upload_id when filtering logs. */
+    /** Public getter for tests / inspection; returns a deep copy so callers cannot mutate internal state. */
     getState(): ProcessingState;
     /**
      * Replace the underlying logger (for testing only).
@@ -137,14 +144,15 @@ declare class ProcessingLoggerService {
 }
 export declare const processingLogger: ProcessingLoggerService;
 /**
- * Run handler logic inside a request-scoped context so all logs (getLogContext) use this
- * context even when many requests run in parallel on the same instance. Call at the start
- * of each Cloud Event / request after building the context from the message.
+ * Run handler logic inside a request-scoped context. State is keyed by request id in the registry;
+ * ALS holds only the id. Call at the start of each Cloud Event / request after building the context.
+ * @deprecated Prefer runWithContextAsync for async handlers.
  */
 export declare function runWithContext<T>(context: ProcessingContext, fn: () => T): T;
 /**
- * Async variant: run handler logic inside a request-scoped context.
- * Each request gets its own state (context, stages, errors); use fileUploadId as unique identifier.
+ * Async variant: run handler logic inside a request-scoped context. Each request gets its own state
+ * in the registry keyed by request id; ALS holds only the id. Entry is removed in finally so one
+ * request never overwrites another's context.
  */
 export declare function runWithContextAsync<T>(context: ProcessingContext, fn: () => Promise<T>): Promise<T>;
 export {};

package/dist/service/processingLogger.service.js

@@ -4,16 +4,40 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.processingLogger = void 0;
+exports.getRequestIdFromContext = getRequestIdFromContext;
 exports.runWithContext = runWithContext;
 exports.runWithContextAsync = runWithContextAsync;
 const async_hooks_1 = require("async_hooks");
+const crypto_1 = __importDefault(require("crypto"));
 const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
 /**
- * Request-scoped full state so parallel requests (e.g. up to 100 messages per instance)
- * do not overwrite each other. Each request gets its own state (context, stages, errors, etc.)
- * keyed by runWithContext(context, fn). Use fileUploadId (or fileName) as the unique identifier.
+ * Registry: one ProcessingState per request, keyed by request id.
+ * When registry.get(id) is undefined we use a transient empty state so one request never overwrites another's context.
  */
-const processingStateStorage = new async_hooks_1.AsyncLocalStorage();
+const processingStateRegistry = new Map();
+/**
+ * AsyncLocalStorage holds only the current request id (not the full state).
+ * State is resolved via processingStateRegistry.get(id).
+ */
+const requestIdStorage = new async_hooks_1.AsyncLocalStorage();
+/** One-time dev warning when logging/state update happens with no registry entry (transient state). */
+let hasWarnedNoContext = false;
+function warnOnceNoContext() {
+    if (process.env.NODE_ENV === 'production' || hasWarnedNoContext)
+        return;
+    hasWarnedNoContext = true;
+    (0, pinoLogger_1.default)().warn({ msg: 'ProcessingLogger used outside runWithContextAsync; using transient state. Ensure handlers run inside runWithContextAsync(context, fn).' });
+}
+/**
+ * Returns a stable request id for the given context. Same id must be used for the whole request.
+ * Used to key the registry so each request has isolated state.
+ */
+function getRequestIdFromContext(context) {
+    return (context.fileUploadId ??
+        context.messageId ??
+        context.cloudEventId ??
+        crypto_1.default.randomUUID());
+}
 function buildInitialStateFromContext(context) {
     return {
         fileName: context.fileName ?? undefined,
@@ -46,28 +70,65 @@ function buildInitialStateFromContext(context) {
     };
 }
 /**
- * ProcessingLoggerService - Singleton service for tracking processing state and logging
+ * Creates a fresh empty state. Used as transient state when registry.get(id) is undefined
+ * so one request never overwrites another's context. This state is never stored in the registry.
+ */
+function createEmptyState() {
+    return {
+        fileName: undefined,
+        fileUploadId: undefined,
+        partnerId: undefined,
+        partnerName: undefined,
+        signedUploadId: undefined,
+        cloudEventId: undefined,
+        messageId: undefined,
+        publishTime: undefined,
+        fileMimeType: undefined,
+        normalizerName: undefined,
+        isPreview: false,
+        reportPreviewId: undefined,
+        startTime: undefined,
+        endTime: undefined,
+        totalDurationMs: undefined,
+        stages: [],
+        currentStageStartTime: undefined,
+        currentStep: undefined,
+        progressPercentage: undefined,
+        measurementsCount: undefined,
+        unknownMeasurementsCount: undefined,
+        unknownUnitsCount: undefined,
+        unmappedLabKeysCount: undefined,
+        errors: [],
+        warnings: [],
+        success: undefined,
+        metadata: undefined,
+    };
+}
+/**
+ * ProcessingLoggerService - Singleton facade for request-scoped processing state and logging.
+ *
+ * State is keyed by request id (fileUploadId ?? messageId ?? cloudEventId) in a registry.
+ * AsyncLocalStorage holds only the current request id; getMutableState() resolves state via
+ * registry.get(id). When registry.get(id) is undefined (no context or stale id), a transient
+ * empty state is used so one request never overwrites another's context.
  *
- * Provides simplified API for logging processing progress with automatic stage timing,
- * measurement tracking, and comprehensive summary logging. Use logInfo, logWarn, logError,
- * logDebug for all application logs so they include the same context (file_name, file_upload_id, etc.)
- * and are searchable by fileUploadId/filename.
+ * Entry point: runWithContextAsync(context, fn). Creates registry entry, runs fn with id in ALS,
+ * removes entry in finally. Use logInfo, logWarn, logError, logDebug for application logs so they
+ * include the same context and are searchable by fileUploadId/filename.
  *
  * Usage:
  * ```typescript
- * processingLogger.clear();
- * processingLogger.setContext({ fileName: 'test.json', partnerId: 'partner_123' });
- * processingLogger.logStart();
- * processingLogger.logProgress(20, 'get_transformation_rules');
- * processingLogger.logInfo('Step completed', { count: 5 });
- * processingLogger.addMeasurement(15, 'measurements');
- * processingLogger.logEnd(true);
+ * await runWithContextAsync(context, async () => {
+ *   processingLogger.logStart();
+ *   processingLogger.logProgress(20, 'get_transformation_rules');
+ *   processingLogger.logEnd(true);
+ * });
  * ```
+ * Initial state is set from context by runWithContextAsync; clear() and setContext() are optional if you need to reset/override.
  */
 class ProcessingLoggerService {
     constructor() {
         this.logger = (0, pinoLogger_1.default)();
-        this.state = this.initializeState();
     }
     static getInstance() {
         if (!ProcessingLoggerService.instance) {
@@ -75,50 +136,42 @@ class ProcessingLoggerService {
         }
         return ProcessingLoggerService.instance;
     }
-    initializeState() {
-        return {
-            fileName: undefined,
-            fileUploadId: undefined,
-            partnerId: undefined,
-            partnerName: undefined,
-            signedUploadId: undefined,
-            cloudEventId: undefined,
-            messageId: undefined,
-            publishTime: undefined,
-            fileMimeType: undefined,
-            normalizerName: undefined,
-            isPreview: undefined,
-            reportPreviewId: undefined,
-            startTime: undefined,
-            endTime: undefined,
-            totalDurationMs: undefined,
-            stages: [],
-            currentStageStartTime: undefined,
-            currentStep: undefined,
-            progressPercentage: undefined,
-            measurementsCount: undefined,
-            unknownMeasurementsCount: undefined,
-            unknownUnitsCount: undefined,
-            unmappedLabKeysCount: undefined,
-            errors: [],
-            warnings: [],
-            success: undefined,
-            metadata: undefined,
-        };
-    }
     /**
-     * Current state: request-scoped store when inside runWithContext, else singleton state.
-     * All reads/writes go through this so parallel requests do not mix state.
+     * Resolves state from registry by current request id. When registry.get(id) is undefined
+     * (no context or stale id), returns a transient clear state so one request never overwrites another's context.
      */
     getMutableState() {
-        return processingStateStorage.getStore() ?? this.state;
+        const id = requestIdStorage.getStore();
+        if (id == null) {
+            warnOnceNoContext();
+            return createEmptyState();
+        }
+        const state = processingStateRegistry.get(id);
+        if (state === undefined) {
+            warnOnceNoContext();
+            return createEmptyState();
+        }
+        return state;
     }
     /**
      * Reset all state for a new processing cycle. Call at the start of each Cloud Event / request
      * so that context and metrics from a previous request never leak.
+     * Clears both context fields and run state; call setContext(context) after clear() in handlers.
      */
     clear() {
         const state = this.getMutableState();
+        state.fileName = undefined;
+        state.fileUploadId = undefined;
+        state.partnerId = undefined;
+        state.partnerName = undefined;
+        state.signedUploadId = undefined;
+        state.cloudEventId = undefined;
+        state.messageId = undefined;
+        state.publishTime = undefined;
+        state.fileMimeType = undefined;
+        state.normalizerName = undefined;
+        state.isPreview = false;
+        state.reportPreviewId = undefined;
         state.stages = [];
         state.errors = [];
         state.warnings = [];
@@ -154,9 +207,15 @@ class ProcessingLoggerService {
         state.isPreview = context.isPreview ?? false;
         state.reportPreviewId = context.reportPreviewId ?? undefined;
     }
-    /** Public getter for tests / inspection; returns a copy. Use file_upload_id when filtering logs. */
+    /** Public getter for tests / inspection; returns a deep copy so callers cannot mutate internal state. */
     getState() {
-        return { ...this.getMutableState() };
+        const src = this.getMutableState();
+        return {
+            ...src,
+            stages: src.stages.map((s) => ({ ...s })),
+            errors: src.errors.map((e) => ({ ...e, timestamp: e.timestamp })),
+            warnings: src.warnings.map((w) => ({ ...w, timestamp: w.timestamp })),
+        };
     }
     /**
      * Replace the underlying logger (for testing only).
@@ -452,20 +511,35 @@ class ProcessingLoggerService {
 }
 exports.processingLogger = ProcessingLoggerService.getInstance();
 /**
- * Run handler logic inside a request-scoped context so all logs (getLogContext) use this
- * context even when many requests run in parallel on the same instance. Call at the start
- * of each Cloud Event / request after building the context from the message.
+ * Run handler logic inside a request-scoped context. State is keyed by request id in the registry;
+ * ALS holds only the id. Call at the start of each Cloud Event / request after building the context.
+ * @deprecated Prefer runWithContextAsync for async handlers.
  */
 function runWithContext(context, fn) {
+    const requestId = getRequestIdFromContext(context);
     const initialState = buildInitialStateFromContext(context);
-    return processingStateStorage.run(initialState, fn);
+    processingStateRegistry.set(requestId, initialState);
+    try {
+        return requestIdStorage.run(requestId, fn);
+    }
+    finally {
+        processingStateRegistry.delete(requestId);
+    }
 }
 /**
- * Async variant: run handler logic inside a request-scoped context.
- * Each request gets its own state (context, stages, errors); use fileUploadId as unique identifier.
+ * Async variant: run handler logic inside a request-scoped context. Each request gets its own state
+ * in the registry keyed by request id; ALS holds only the id. Entry is removed in finally so one
+ * request never overwrites another's context.
  */
 async function runWithContextAsync(context, fn) {
+    const requestId = getRequestIdFromContext(context);
     const initialState = buildInitialStateFromContext(context);
-    return processingStateStorage.run(initialState, fn);
+    processingStateRegistry.set(requestId, initialState);
+    try {
+        return await requestIdStorage.run(requestId, () => fn());
+    }
+    finally {
+        processingStateRegistry.delete(requestId);
+    }
 }
 //# sourceMappingURL=processingLogger.service.js.map

package/dist/service/processingLogger.service.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.3.10",
+  "version": "0.3.13",
   "description": "Shared nodejs lib with with reusable functions",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -8,6 +8,7 @@
     "/dist"
   ],
   "scripts": {
+    "build": "tsc",
     "test": "jest"
   },
   "keywords": [],
@@ -30,6 +31,7 @@
     "@types/jest": "^29.5.14",
     "axios-mock-adapter": "^2.1.0",
     "jest": "^29.7.0",
-    "ts-jest": "^29.2.5"
+    "ts-jest": "^29.2.5",
+    "typescript": "^5.0.0"
   }
 }

package/readme.md

@@ -38,6 +38,17 @@ const { connectToMongoDB } = require('oht-custom-parser-lib');
 - **Production / GCP**: Logs are emitted as JSON (one line per log) for Cloud Logging.
 - **Local / development**: When `NODE_ENV !== 'production'`, logs are pretty-printed in the terminal (colors, timestamps, readable structure). You can override: `LOG_PRETTY=true` to force pretty output, or `LOG_PRETTY=false` to force JSON when not in production.
 
+### Processing logger: request-scoped state
+
+The processing logger (`processingLogger`, `runWithContextAsync`, `getRequestIdFromContext`) uses a **registry + facade** so each request has isolated state and logs never leak context between concurrent invocations (e.g. in Cloud Functions).
+
+- **Registry**: One `ProcessingState` per request, keyed by request id (`fileUploadId ?? messageId ?? cloudEventId ?? generatedId`). The same id is used for the whole request.
+- **AsyncLocalStorage**: Holds only the current request id; state is resolved via `registry.get(id)`.
+- **Entry point**: Wrap your handler in `runWithContextAsync(context, async () => { ... })`. The lib creates a registry entry, runs your callback with the id in AsyncLocalStorage, and removes the entry in a `finally` block.
+- **Clear-state rule**: If there is no request id or the id is not in the registry (e.g. logging outside `runWithContextAsync` or after teardown), the logger uses a **transient empty state** for that call only (never stored). That way one request never overwrites another’s context.
+
+Use `processingLogger.logInfo`, `logWarn`, `logError`, `logProgress`, etc. inside the callback so logs include the same context and are searchable by `fileUploadId` / filename.
+
 ## Development
 
 ### Patch Versions