@openhealth/oht-custom-parser-lib 0.5.51 → 0.5.53

package/dist/index.d.ts

@@ -7,11 +7,10 @@ export { aggregateMessages, aggregateBiMessages, publishToTopic, generateBIMessa
 export { applyRules as applyTransformationRules, validateJsonataExpression as validateTransformationRuleExpression, } from './service/transformationRules.service';
 export { LabToOhtContract, LabToOhtMapper, UnknownMeasurementExtraction, ReferenceAsAnnotation, UnitExtraction, RangeExtraction, RangeExtractionResponse, ValueExtraction, unitSynonyms, ValueExtractionResponse, SynonymUnit, UnknownUnits, TransformationRulesChains, } from './types/custom-parser.types';
 export { AcfBiomarkerRangeAnnotationCheck, AcfBiomarkerGenericDisclaimerLogic, ManualCheck, BiomarkerCompatibility, ReferenceRangeType, AcfReferenceRange, VisualRange, NameAlias, AlternativeUnit, BiomarkerAcf, Biomarker, PipelineStep, DigitizationStatus, MeasurementValueComparator, BiomarkerValueType, DataImportFileUploadStatus, Sex, Digitization, PatientInfo, UnknownMeasurement, UnmappedLabKey, Measurement, DataImportFileUpload, MessagePayload, SignedUpload, ReportStyleConfig, LanguageCode, BiomarkerCustomisation, PartnerCustomPanel, ReportDisplaySettings, ReportCustomisation, OHTPartner, UploadType, PartnerCustomization, RejectReason, AnnotationLabKey, ExtractionPath, AnnotationConfig, OhtReport, OhtMetadata, OhtPatient, Exam, OhtExam, ExamKind, OhtRange, OriginalExam, } from './types/oht.types';
-export { ErrorMessage, ErrorCode, ERROR_CATALOG, ERROR_MESSAGES, getErrorMessage, getRejectReason, ParsingErrorType, ParsingErrorSeverity, PARSING_ERROR_CATALOG, LocalParsingError, ErrorProfilePayload, RecordParsingErrorDetails, } from './types/error.types';
+export { ErrorMessage, ErrorCode, ERROR_CATALOG, ERROR_MESSAGES, getErrorMessage, getRejectReason, } from './types/error.types';
 export { handleError, ValidationError, JSON_VALIDATION_ERROR_NAME, 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, getRequestIdFromContext, getCurrentRequestId, getRequestScopedFilename, runWithContext, runWithContextAsync, } from './service/processingLogger.service';
-export { parsingErrorService, initParsingErrorRequestState, clearParsingErrorRequestState, } from './service/parsingErrorService.service';
+export { processingLogger, ProcessingContext, StageDuration, getRequestIdFromContext, getRequestScopedFilename, 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

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ValidationError = exports.handleError = exports.PARSING_ERROR_CATALOG = exports.ParsingErrorType = 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.getPartnerTransformationRules = exports.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.getPatientAge = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.postReportPreviewToCore = exports.postDataImportFileUploadToCore = void 0;
-exports.mapToOhtReport = exports.fetchActiveMappingRules = exports.lisXmlToJson = exports.lisCsvToExamRows = 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.clearParsingErrorRequestState = exports.initParsingErrorRequestState = exports.parsingErrorService = exports.runWithContextAsync = exports.runWithContext = exports.getRequestScopedFilename = exports.getCurrentRequestId = exports.getRequestIdFromContext = exports.processingLogger = exports.mapErrorToRejectReason = exports.extractFormattedRejectReason = exports.shouldSendSlackNotification = exports.JSON_VALIDATION_ERROR_NAME = void 0;
+exports.shouldSendSlackNotification = exports.JSON_VALIDATION_ERROR_NAME = 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.getPartnerTransformationRules = exports.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.getPatientAge = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.postReportPreviewToCore = exports.postDataImportFileUploadToCore = void 0;
+exports.mapToOhtReport = exports.fetchActiveMappingRules = exports.lisXmlToJson = exports.lisCsvToExamRows = 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.getRequestScopedFilename = exports.getRequestIdFromContext = exports.processingLogger = exports.mapErrorToRejectReason = exports.extractFormattedRejectReason = void 0;
 // ### SERVICES ###
 var reportCreator_service_1 = require("./service/reportCreator.service");
 Object.defineProperty(exports, "postDataImportFileUploadToCore", { enumerable: true, get: function () { return reportCreator_service_1.postDataImportFileUploadToCore; } });
@@ -63,8 +63,6 @@ Object.defineProperty(exports, "ERROR_CATALOG", { enumerable: true, get: functio
 Object.defineProperty(exports, "ERROR_MESSAGES", { enumerable: true, get: function () { return error_types_1.ERROR_MESSAGES; } });
 Object.defineProperty(exports, "getErrorMessage", { enumerable: true, get: function () { return error_types_1.getErrorMessage; } });
 Object.defineProperty(exports, "getRejectReason", { enumerable: true, get: function () { return error_types_1.getRejectReason; } });
-Object.defineProperty(exports, "ParsingErrorType", { enumerable: true, get: function () { return error_types_1.ParsingErrorType; } });
-Object.defineProperty(exports, "PARSING_ERROR_CATALOG", { enumerable: true, get: function () { return error_types_1.PARSING_ERROR_CATALOG; } });
 var fileUploadErrorHandler_service_1 = require("./service/fileUploadErrorHandler.service");
 Object.defineProperty(exports, "handleError", { enumerable: true, get: function () { return fileUploadErrorHandler_service_1.handleError; } });
 Object.defineProperty(exports, "ValidationError", { enumerable: true, get: function () { return fileUploadErrorHandler_service_1.ValidationError; } });
@@ -76,14 +74,9 @@ Object.defineProperty(exports, "mapErrorToRejectReason", { enumerable: true, get
 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, "getCurrentRequestId", { enumerable: true, get: function () { return processingLogger_service_1.getCurrentRequestId; } });
 Object.defineProperty(exports, "getRequestScopedFilename", { enumerable: true, get: function () { return processingLogger_service_1.getRequestScopedFilename; } });
 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; } });
-var parsingErrorService_service_1 = require("./service/parsingErrorService.service");
-Object.defineProperty(exports, "parsingErrorService", { enumerable: true, get: function () { return parsingErrorService_service_1.parsingErrorService; } });
-Object.defineProperty(exports, "initParsingErrorRequestState", { enumerable: true, get: function () { return parsingErrorService_service_1.initParsingErrorRequestState; } });
-Object.defineProperty(exports, "clearParsingErrorRequestState", { enumerable: true, get: function () { return parsingErrorService_service_1.clearParsingErrorRequestState; } });
 // ### UTIL-TS ###
 var apiUtils_1 = require("./util-ts/apiUtils");
 Object.defineProperty(exports, "makeApiCallWithRetry", { enumerable: true, get: function () { return apiUtils_1.makeApiCallWithRetry; } });

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/service/auxiliaryFunctions.service.d.ts

@@ -1,3 +1,4 @@
+import { ErrorMessage } from '../types/error.types';
 import { DataImportFileUpload, DataImportFileUploadStatus, DigitizationStatus, PipelineStep, RejectReason, Sex } from "../types/oht.types";
 import dayjs from 'dayjs';
 import { TransformationRulesChains } from "../types/custom-parser.types";
@@ -11,8 +12,14 @@ declare function parseGender(patientGender?: string): {
 /**
  * Maps parse type and error context to appropriate rejection reason
  * Uses a priority-based approach to ensure the most specific reason is selected
+ *
+ * @param parseType - The type of parsing that failed (e.g., "age", "exam date", "units")
+ * @param errorMessages - Array to append error messages to
+ * @param notifySlack - notifySlack
+ * @param notifyNotes - notifyNotes
+ * @returns Object containing rejectedStatus and rejectReason
  */
-declare function handleRejection(parseType: string, notifySlack?: boolean, notifyNotes?: boolean, notifyBi?: boolean): {
+declare function handleRejection(parseType: string, errorMessages: ErrorMessage[], notifySlack?: boolean, notifyNotes?: boolean, notifyBi?: boolean): {
     rejectedStatus: string;
     rejectReason: RejectReason.INVALID_DATA_NO_BIOMARKER_DATA | RejectReason.LOW_IMAGE_QUALITY | RejectReason.NO_IN_PANEL_BIOMARKER | RejectReason.UNDERAGE_PERSON | RejectReason.LANGUAGE_NOT_SUPPORTED | RejectReason.IMPLAUSIBLE_DATA | RejectReason.MISSING_EXAM_DATE | RejectReason.MISSING_LAB_ORDER_ID | RejectReason.MISSING_EXTERNAL_PATIENT_ID | RejectReason.MISSING_PATIENT_SEX | RejectReason.MISSING_PATIENT_BIRTHDATE | RejectReason.UNSUPPORTED_UPLOAD | RejectReason.INCOMPLETE_DATA | RejectReason.NOT_AN_OFFICIAL_REPORT;
 };

package/dist/service/auxiliaryFunctions.service.js

@@ -14,8 +14,6 @@ exports.getPartnerTransformationRules = getPartnerTransformationRules;
 const moment_1 = __importDefault(require("moment/moment"));
 const apiUtils_1 = require("../util-ts/apiUtils");
 const processingLogger_service_1 = require("./processingLogger.service");
-const parsingErrorService_service_1 = require("./parsingErrorService.service");
-const error_types_1 = require("../types/error.types");
 const oht_types_1 = require("../types/oht.types");
 const dayjs_1 = __importDefault(require("dayjs"));
 const customParseFormat_1 = __importDefault(require("dayjs/plugin/customParseFormat"));
@@ -59,8 +57,14 @@ function parseGender(patientGender) {
 /**
  * Maps parse type and error context to appropriate rejection reason
  * Uses a priority-based approach to ensure the most specific reason is selected
+ *
+ * @param parseType - The type of parsing that failed (e.g., "age", "exam date", "units")
+ * @param errorMessages - Array to append error messages to
+ * @param notifySlack - notifySlack
+ * @param notifyNotes - notifyNotes
+ * @returns Object containing rejectedStatus and rejectReason
  */
-function handleRejection(parseType, notifySlack = true, notifyNotes = false, notifyBi = false) {
+function handleRejection(parseType, errorMessages, notifySlack = true, notifyNotes = false, notifyBi = false) {
     const rejectedStatus = 'REJECTED';
     const lowerParseType = parseType.toLowerCase();
     // Priority-based mapping: check most specific cases first
@@ -134,45 +138,12 @@ function handleRejection(parseType, notifySlack = true, notifyNotes = false, not
     else {
         rejectReason = oht_types_1.RejectReason.INVALID_DATA_NO_BIOMARKER_DATA;
     }
-    const errorType = resolveRejectionParsingErrorType(lowerParseType, rejectReason);
-    const messageSuffix = errorType === error_types_1.ParsingErrorType.FATAL_VALIDATION
-        ? `File rejected: ${parseType} parsing failed. Reason: ${rejectReason}`
-        : String(rejectReason);
-    parsingErrorService_service_1.parsingErrorService.record(errorType, {
-        messageSuffix,
-        rejectReason,
-    }, { notifySlack, notifyNotes, notifyBi });
+    errorMessages.push({
+        destination: { slack: notifySlack, notes: notifyNotes, bi: notifyBi },
+        message: `File rejected: ${parseType} parsing failed. Reason: ${rejectReason}`,
+    });
     return { rejectedStatus, rejectReason };
 }
-function resolveRejectionParsingErrorType(lowerParseType, rejectReason) {
-    if (lowerParseType === 'patientage' || lowerParseType === 'patient age') {
-        return error_types_1.ParsingErrorType.REJECTED_UNDERAGE_PATIENT;
-    }
-    if (lowerParseType === 'patientexternalid' ||
-        lowerParseType === 'patient external id' ||
-        lowerParseType === 'patient externalid') {
-        return error_types_1.ParsingErrorType.REJECTED_MISSING_PATIENT_ID;
-    }
-    if (lowerParseType === 'patientsex' || lowerParseType === 'patient sex') {
-        return error_types_1.ParsingErrorType.REJECTED_MISSING_PATIENT_SEX;
-    }
-    if (lowerParseType.includes('biomarker')) {
-        return error_types_1.ParsingErrorType.REJECTED_NO_BIOMARKERS;
-    }
-    if (rejectReason === oht_types_1.RejectReason.UNDERAGE_PERSON) {
-        return error_types_1.ParsingErrorType.REJECTED_UNDERAGE_PATIENT;
-    }
-    if (rejectReason === oht_types_1.RejectReason.MISSING_EXTERNAL_PATIENT_ID) {
-        return error_types_1.ParsingErrorType.REJECTED_MISSING_PATIENT_ID;
-    }
-    if (rejectReason === oht_types_1.RejectReason.MISSING_PATIENT_SEX) {
-        return error_types_1.ParsingErrorType.REJECTED_MISSING_PATIENT_SEX;
-    }
-    if (rejectReason === oht_types_1.RejectReason.NO_IN_PANEL_BIOMARKER) {
-        return error_types_1.ParsingErrorType.REJECTED_NO_BIOMARKERS;
-    }
-    return error_types_1.ParsingErrorType.FATAL_VALIDATION;
-}
 async function queryFileUploadsWithFilters(filters, ohtCoreApiKey) {
     const OHT_CORE_URL = process.env.OHT_CORE_URL;
     const ohtCoreUrl = `${OHT_CORE_URL}/v1/file-uploads/query`;

package/dist/service/auxiliaryFunctions.service.js.map

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package/dist/service/ohtReportMeasurementsExtractor.service.d.ts

@@ -1,5 +1,6 @@
 import { UnknownUnits } from "../types/custom-parser.types";
 import { Measurement, PatientInfo, UnknownMeasurement, Exam, UnmappedLabKey, PartnerCustomization } from "../types/oht.types";
+import { ErrorMessage } from "../types/error.types";
 /**
  * Extracts measurements from OHT report exams by processing each exam through biomarker mapping,
  * transformation rules, and value extraction.
@@ -120,7 +121,7 @@ import { Measurement, PatientInfo, UnknownMeasurement, Exam, UnmappedLabKey, Par
  *   - `isReportCorrectlyParsed`: Boolean indicating if all measurements were parsed correctly
  *
  * ## Error Handling:
- * - All errors are recorded via `parsingErrorService.record()`
+ * - All errors are added to the `errorMessages` array passed as parameter
  * - Errors are categorized by destination (slack, notes, bi)
  * - Processing continues even if individual exams fail
  * - Errors are logged with context (filename, labKey, ohtBmId, etc.)
@@ -140,11 +141,12 @@ import { Measurement, PatientInfo, UnknownMeasurement, Exam, UnmappedLabKey, Par
  * @param allowMultiMeasurementsPerBiomarker - Whether to allow multiple measurements per biomarker ID
  * @param ohtCoreApiKey - API key for OHT Core API calls
  * @param partnerId - Partner ID for fetching biomarker mappings and synonym units
+ * @param errorMessages - Array to accumulate error messages (modified in-place)
  * @param isReportPreview - isReportPreview Report Simulator
  * @param partnerCustomization - `panelCustomisation` and `reportCustomisation` coming from `partnerConfig`.
  * @returns Promise resolving to extraction result with measurements, unknownMeasurements, unknownUnits, unmappedLabKeys, and parsing status
  */
-declare function ohtReportMeasurementsExtractor(isReportPreview: boolean, exams: Exam[], sourceFilename: string, patientInfo: PatientInfo, documentDate: Date | undefined, allowMultiMeasurementsPerBiomarker: boolean, ohtCoreApiKey: string, partnerId: string, partnerCustomization?: PartnerCustomization): Promise<{
+declare function ohtReportMeasurementsExtractor(isReportPreview: boolean, exams: Exam[], sourceFilename: string, patientInfo: PatientInfo, documentDate: Date | undefined, allowMultiMeasurementsPerBiomarker: boolean, ohtCoreApiKey: string, partnerId: string, errorMessages: ErrorMessage[], partnerCustomization?: PartnerCustomization): Promise<{
     measurements: Measurement[];
     unknownMeasurements: UnknownMeasurement[];
     unknownUnits: UnknownUnits[];

package/dist/service/ohtReportMeasurementsExtractor.service.js

@@ -43,8 +43,6 @@ const extractionUtils_1 = require("../util-ts/extractionUtils");
 const processingLogger_service_1 = require("./processingLogger.service");
 const apiUtils_1 = require("../util-ts/apiUtils");
 const oht_types_1 = require("../types/oht.types");
-const error_types_1 = require("../types/error.types");
-const parsingErrorService_service_1 = require("./parsingErrorService.service");
 const path = __importStar(require("path"));
 const fs = __importStar(require("fs"));
 // Import version from package.json file
@@ -86,10 +84,6 @@ const OHT_CORE_URL = process.env.OHT_CORE_URL;
  * Current filename being processed (global state for error reporting)
  */
 let filename = '';
-function resolveUnknownMeasurementName(parts, fallback) {
-    const name = parts.filter((part) => part?.trim()).join(':');
-    return name || fallback;
-}
 /**
  * Extracts measurements from OHT report exams by processing each exam through biomarker mapping,
  * transformation rules, and value extraction.
@@ -210,7 +204,7 @@ function resolveUnknownMeasurementName(parts, fallback) {
  *   - `isReportCorrectlyParsed`: Boolean indicating if all measurements were parsed correctly
  *
  * ## Error Handling:
- * - All errors are recorded via `parsingErrorService.record()`
+ * - All errors are added to the `errorMessages` array passed as parameter
  * - Errors are categorized by destination (slack, notes, bi)
  * - Processing continues even if individual exams fail
  * - Errors are logged with context (filename, labKey, ohtBmId, etc.)
@@ -230,11 +224,12 @@ function resolveUnknownMeasurementName(parts, fallback) {
  * @param allowMultiMeasurementsPerBiomarker - Whether to allow multiple measurements per biomarker ID
  * @param ohtCoreApiKey - API key for OHT Core API calls
  * @param partnerId - Partner ID for fetching biomarker mappings and synonym units
+ * @param errorMessages - Array to accumulate error messages (modified in-place)
  * @param isReportPreview - isReportPreview Report Simulator
  * @param partnerCustomization - `panelCustomisation` and `reportCustomisation` coming from `partnerConfig`.
  * @returns Promise resolving to extraction result with measurements, unknownMeasurements, unknownUnits, unmappedLabKeys, and parsing status
  */
-async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFilename, patientInfo, documentDate, allowMultiMeasurementsPerBiomarker, ohtCoreApiKey, partnerId, partnerCustomization) {
+async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFilename, patientInfo, documentDate, allowMultiMeasurementsPerBiomarker, ohtCoreApiKey, partnerId, errorMessages, partnerCustomization) {
     filename = sourceFilename;
     const measurements = [];
     const unknownMeasurements = [];
@@ -246,8 +241,9 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
     if (labKeys.length === 0) {
         const errorMsg = `No lab keys found, filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`;
         processingLogger_service_1.processingLogger.logError(errorMsg);
-        parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.NO_LAB_KEYS, {
-            messageSuffix: (0, processingLogger_service_1.getRequestScopedFilename)(filename),
+        errorMessages.push({
+            destination: { slack: true, notes: false, bi: false },
+            message: errorMsg,
         });
         return {
             measurements,
@@ -394,10 +390,16 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             let isMeasurementCorrectlyParsed = true;
             // if BM is already in measurements and multiple measurements are not allowed, continue to the next one
             if (!allowMultiMeasurementsPerBiomarker && measurements.some(measurement => measurement.biomarkerId === finalOhtBmId)) {
-                parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.DUPLICATE_BIOMARKER, {
-                    labKey: transformedExamObj.labKey,
-                    biomarkerId: finalOhtBmId,
-                    item: `bmId:${finalOhtBmId}, labKey:${transformedExamObj.labKey}`,
+                processingLogger_service_1.processingLogger.addWarning(`Biomarker already in measurements array, should investigate, filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, 'extract_measurements', {
+                    warningType: 'duplicate_biomarker_measurement',
+                    warningCategory: 'measurements',
+                    warningSeverity: 'degraded',
+                    data: { ohtBmId: finalOhtBmId, labKey },
+                });
+                errorMessages.push({
+                    destination: { slack: false, notes: false, bi: true },
+                    message: `Biomarkers Duplicated keys:[PLACEHOLDER]`,
+                    item: `bmId:${finalOhtBmId}, labKey:${transformedExamObj.labKey}`
                 });
                 continue;
             }
@@ -407,11 +409,16 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 `name:${ohtBiomarker.acf.shortName}, bmId:${finalOhtBmId}, labKey:${transformedExamObj.labKey}` :
                 `bmId:${finalOhtBmId}, labKey:${transformedExamObj.labKey}`;
             if (!ohtBiomarker) {
-                parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.BIOMARKER_NOT_FOUND, {
-                    labKey: transformedExamObj.labKey,
-                    biomarkerId: finalOhtBmId,
-                    item: `${bmInfo}`,
-                    errorTrace: { ohtBmId: finalOhtBmId, labKey: transformedExamObj.labKey },
+                processingLogger_service_1.processingLogger.addWarning(`Biomarker not found in API response for ohtBmId: ${finalOhtBmId}, labKey: ${transformedExamObj.labKey}, filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, 'extract_measurements', {
+                    warningType: 'biomarker_not_found',
+                    warningCategory: 'mapping',
+                    warningSeverity: 'critical',
+                    data: { ohtBmId: finalOhtBmId, labKey },
+                });
+                errorMessages.push({
+                    destination: { slack: true, notes: true, bi: true },
+                    message: `Biomarker not found for:[PLACEHOLDER]`,
+                    item: `${bmInfo}`
                 });
                 continue;
             }
@@ -433,26 +440,24 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 });
             }
             if (!isUnitParsedCorrectly) {
-                parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.UNIT_NOT_EXTRACTED, {
-                    labKey: transformedExamObj.labKey,
-                    biomarkerId: finalOhtBmId,
-                    item: `${bmInfo}, unit:${unit}`,
-                    errorTrace: { unit },
+                processingLogger_service_1.processingLogger.addWarning(`Unit not extracted correctly for "${finalOhtBmId}|${transformedExamObj.labKey}", filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, 'extract_measurements', {
+                    warningType: 'unit_extraction_failed',
+                    warningCategory: 'measurements',
+                    warningSeverity: 'degraded',
+                    data: { ohtBmId: finalOhtBmId, labKey },
+                });
+                errorMessages.push({
+                    destination: { slack: true, notes: true, bi: true },
+                    message: `Unit not extracted correctly for:[PLACEHOLDER]`,
+                    item: `${bmInfo}, unit:${unit}`
                 });
                 isMeasurementCorrectlyParsed = false;
             }
             let { valueType, alphanumericalValue, numberValue, valueComparator, isValueParsedCorrectly } = (0, extractionUtils_1.ohtReportParseExamValue)(transformedExamObj, ohtBiomarker);
             if ((0, dataUtils_1.isNumericalWithoutValidResult)(valueType, numberValue, alphanumericalValue)) {
                 const alphanumericalValueTrimmed = alphanumericalValue?.trim() ?? '';
-                parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.NUMERIC_BIOMARKER_ALPHANUMERIC_VALUE, {
-                    labKey: transformedExamObj.labKey,
-                    biomarkerId: finalOhtBmId,
-                    item: `${bmInfo}, value:${alphanumericalValueTrimmed}`,
-                    ohtExam: transformedExamObj,
-                    originalExam: originalExam ?? undefined,
-                });
                 const unknownMeasurement = {
-                    biomarkerName: resolveUnknownMeasurementName([transformedExamObj.description], transformedExamObj.labKey || labKey || '(unmapped measurement)'),
+                    biomarkerName: transformedExamObj.description ?? '',
                     value: alphanumericalValueTrimmed,
                     unit: unit ?? '',
                     annotation: transformedExamObj.annotation ?? '',
@@ -473,11 +478,16 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 continue;
             }
             if (!isValueParsedCorrectly) {
-                parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.VALUE_NOT_EXTRACTED, {
-                    labKey: transformedExamObj.labKey,
-                    biomarkerId: finalOhtBmId,
-                    item: `${bmInfo}, value:${numberValue}${unit}`,
-                    errorTrace: { numberValue, unit },
+                processingLogger_service_1.processingLogger.addWarning(`Value not extracted correctly for "${finalOhtBmId}|${transformedExamObj.labKey}", filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, 'extract_measurements', {
+                    warningType: 'value_extraction_failed',
+                    warningCategory: 'measurements',
+                    warningSeverity: 'degraded',
+                    data: { ohtBmId: finalOhtBmId, labKey },
+                });
+                errorMessages.push({
+                    destination: { slack: true, notes: true, bi: true },
+                    message: `Value not extracted correctly for:[PLACEHOLDER]`,
+                    item: `${bmInfo}, value:${numberValue}${unit}`
                 });
                 isMeasurementCorrectlyParsed = false;
             }
@@ -485,12 +495,10 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             if (isValueParsedCorrectly && valueType === 'NUMERICAL') {
                 const isPlausibleValue = numberValue !== null && (0, extractionUtils_1.ohtReportCheckValueForPlausibleValues)(finalOhtBmId, transformedExamObj.labKey, ohtBiomarker, unit, numberValue, isUnitParsedCorrectly, filename);
                 if (!isPlausibleValue) {
-                    parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.VALUE_NOT_PLAUSIBLE, {
-                        labKey: transformedExamObj.labKey,
-                        biomarkerId: finalOhtBmId,
-                        item: `${bmInfo}, value:${numberValue}${unit}`,
-                        ohtExam: transformedExamObj,
-                        originalExam: originalExam ?? undefined,
+                    errorMessages.push({
+                        destination: { slack: false, notes: true, bi: true },
+                        message: `Value is not plausible for:[PLACEHOLDER]`,
+                        item: `${bmInfo}, value:${numberValue}${unit}`
                     });
                     // Resolve name with fallbacks
                     const implausibleName = transformedExamObj.examName ||
@@ -539,10 +547,16 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 to = extractedRange.to ?? null;
                 isRangeParsedCorrectly = extractedRange.isRangeParsedCorrectly;
                 if (!isRangeParsedCorrectly) {
-                    parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.RANGE_NOT_EXTRACTED, {
-                        labKey: transformedExamObj.labKey,
-                        biomarkerId: finalOhtBmId,
-                        item: `${bmInfo}`,
+                    processingLogger_service_1.processingLogger.addWarning(`Range not extracted correctly for "${finalOhtBmId}|${transformedExamObj.labKey}", filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`, 'extract_measurements', {
+                        warningType: 'range_extraction_failed',
+                        warningCategory: 'measurements',
+                        warningSeverity: 'degraded',
+                        data: { ohtBmId: finalOhtBmId, labKey },
+                    });
+                    errorMessages.push({
+                        destination: { slack: true, notes: true, bi: true },
+                        message: `Range not extracted correctly for:[PLACEHOLDER]`,
+                        item: `${bmInfo}`
                     });
                     isMeasurementCorrectlyParsed = false;
                 }
@@ -606,7 +620,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 continue;
             }
             // No mapping or ohtBmId === -1: create unknownMeasurement
-            const unknownMeasurementName = resolveUnknownMeasurementName([transformedExamObj.mnemonic, transformedExamObj.examName], labKey || '(unmapped measurement)');
+            const unknownMeasurementName = `${transformedExamObj.mnemonic}:${transformedExamObj.examName}`;
             const originalName = labKey.split(':')[1] || transformedExamObj.examName;
             const annotation = `${transformedExamObj.annotation || ''}`;
             const dataOrigin = {
@@ -642,7 +656,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
         backend_mapped_biomarkers: backendMappedCount,
         unmapped_biomarkers: unmappedCount,
         total_processed: exams.length,
-        errors: parsingErrorService_service_1.parsingErrorService.getLocalErrors().length,
+        errors: errorMessages.length,
     });
     return {
         measurements,

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

@@ -4,8 +4,6 @@ import pino from 'pino';
  * Used to key the registry so each request has isolated state.
  */
 export declare function getRequestIdFromContext(context: ProcessingContext): string;
-/** Returns the current request id from AsyncLocalStorage (set by runWithContextAsync). */
-export declare function getCurrentRequestId(): string | undefined;
 /**
  * Returns the request-scoped filename for use in log messages.
  * Uses processingLogger state (from registry via AsyncLocalStorage) to ensure the filename
@@ -25,7 +23,6 @@ export interface ProcessingContext {
     partnerId?: string;
     partnerName?: string;
     signedUploadId?: string;
-    uploadedByUserId?: string;
     cloudEventId?: string;
     messageId?: string;
     publishTime?: string;
@@ -67,7 +64,6 @@ interface ProcessingState {
     partnerId?: string;
     partnerName?: string;
     signedUploadId?: string;
-    uploadedByUserId?: string;
     cloudEventId?: string;
     messageId?: string;
     publishTime?: string;
@@ -172,7 +168,6 @@ export declare const processingLogger: ProcessingLoggerService;
  * 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.
- * Note: sync variant does not init/flush parsingErrorService Layer 2 profiles.
  */
 export declare function runWithContext<T>(context: ProcessingContext, fn: () => T): T;
 /**