@openhealth/oht-custom-parser-lib 0.5.49 → 0.5.50

package/dist/index.d.ts

@@ -7,10 +7,11 @@ 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, } from './types/error.types';
+export { ErrorMessage, ErrorCode, ERROR_CATALOG, ERROR_MESSAGES, getErrorMessage, getRejectReason, ParsingErrorType, ParsingErrorSeverity, PARSING_ERROR_CATALOG, LocalParsingError, ErrorProfilePayload, RecordParsingErrorDetails, } 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, getRequestScopedFilename, runWithContext, runWithContextAsync, } from './service/processingLogger.service';
+export { processingLogger, ProcessingContext, StageDuration, getRequestIdFromContext, getCurrentRequestId, getRequestScopedFilename, runWithContext, runWithContextAsync, } from './service/processingLogger.service';
+export { parsingErrorService, initParsingErrorRequestState, clearParsingErrorRequestState, } from './service/parsingErrorService.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.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;
+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;
 // ### SERVICES ###
 var reportCreator_service_1 = require("./service/reportCreator.service");
 Object.defineProperty(exports, "postDataImportFileUploadToCore", { enumerable: true, get: function () { return reportCreator_service_1.postDataImportFileUploadToCore; } });
@@ -63,6 +63,8 @@ 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; } });
@@ -74,9 +76,14 @@ 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

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package/dist/service/auxiliaryFunctions.service.d.ts

@@ -1,4 +1,3 @@
-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";
@@ -12,14 +11,8 @@ 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, errorMessages: ErrorMessage[], notifySlack?: boolean, notifyNotes?: boolean, notifyBi?: boolean): {
+declare function handleRejection(parseType: string, 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

@@ -14,6 +14,8 @@ 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"));
@@ -57,14 +59,8 @@ 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, errorMessages, notifySlack = true, notifyNotes = false, notifyBi = false) {
+function handleRejection(parseType, notifySlack = true, notifyNotes = false, notifyBi = false) {
     const rejectedStatus = 'REJECTED';
     const lowerParseType = parseType.toLowerCase();
     // Priority-based mapping: check most specific cases first
@@ -138,12 +134,45 @@ function handleRejection(parseType, errorMessages, notifySlack = true, notifyNot
     else {
         rejectReason = oht_types_1.RejectReason.INVALID_DATA_NO_BIOMARKER_DATA;
     }
-    errorMessages.push({
-        destination: { slack: notifySlack, notes: notifyNotes, bi: notifyBi },
-        message: `File rejected: ${parseType} parsing failed. Reason: ${rejectReason}`,
-    });
+    const errorType = resolveRejectionParsingErrorType(lowerParseType, rejectReason);
+    const messageSuffix = errorType === error_types_1.ParsingErrorType.FATAL_VALIDATION
+        ? `File rejected: ${parseType} parsing failed. Reason: ${rejectReason}`
+        : String(rejectReason);
+    parsingErrorService_service_1.parsingErrorService.record(errorType, {
+        messageSuffix,
+        rejectReason,
+    }, { notifySlack, notifyNotes, notifyBi });
     return { rejectedStatus, rejectReason };
 }
+function resolveRejectionParsingErrorType(lowerParseType, rejectReason) {
+    if (lowerParseType === 'patientage' || lowerParseType === 'patient age') {
+        return error_types_1.ParsingErrorType.REJECTED_UNDERAGE_PATIENT;
+    }
+    if (lowerParseType === 'patientexternalid' ||
+        lowerParseType === 'patient external id' ||
+        lowerParseType === 'patient externalid') {
+        return error_types_1.ParsingErrorType.REJECTED_MISSING_PATIENT_ID;
+    }
+    if (lowerParseType === 'patientsex' || lowerParseType === 'patient sex') {
+        return error_types_1.ParsingErrorType.REJECTED_MISSING_PATIENT_SEX;
+    }
+    if (lowerParseType.includes('biomarker')) {
+        return error_types_1.ParsingErrorType.REJECTED_NO_BIOMARKERS;
+    }
+    if (rejectReason === oht_types_1.RejectReason.UNDERAGE_PERSON) {
+        return error_types_1.ParsingErrorType.REJECTED_UNDERAGE_PATIENT;
+    }
+    if (rejectReason === oht_types_1.RejectReason.MISSING_EXTERNAL_PATIENT_ID) {
+        return error_types_1.ParsingErrorType.REJECTED_MISSING_PATIENT_ID;
+    }
+    if (rejectReason === oht_types_1.RejectReason.MISSING_PATIENT_SEX) {
+        return error_types_1.ParsingErrorType.REJECTED_MISSING_PATIENT_SEX;
+    }
+    if (rejectReason === oht_types_1.RejectReason.NO_IN_PANEL_BIOMARKER) {
+        return error_types_1.ParsingErrorType.REJECTED_NO_BIOMARKERS;
+    }
+    return error_types_1.ParsingErrorType.FATAL_VALIDATION;
+}
 async function queryFileUploadsWithFilters(filters, ohtCoreApiKey) {
     const OHT_CORE_URL = process.env.OHT_CORE_URL;
     const ohtCoreUrl = `${OHT_CORE_URL}/v1/file-uploads/query`;

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

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

@@ -1,6 +1,5 @@
 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.
@@ -121,7 +120,7 @@ import { ErrorMessage } from "../types/error.types";
  *   - `isReportCorrectlyParsed`: Boolean indicating if all measurements were parsed correctly
  *
  * ## Error Handling:
- * - All errors are added to the `errorMessages` array passed as parameter
+ * - All errors are recorded via `parsingErrorService.record()`
  * - Errors are categorized by destination (slack, notes, bi)
  * - Processing continues even if individual exams fail
  * - Errors are logged with context (filename, labKey, ohtBmId, etc.)
@@ -141,12 +140,11 @@ import { ErrorMessage } from "../types/error.types";
  * @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, errorMessages: ErrorMessage[], partnerCustomization?: PartnerCustomization): Promise<{
+declare function ohtReportMeasurementsExtractor(isReportPreview: boolean, exams: Exam[], sourceFilename: string, patientInfo: PatientInfo, documentDate: Date | undefined, allowMultiMeasurementsPerBiomarker: boolean, ohtCoreApiKey: string, partnerId: string, partnerCustomization?: PartnerCustomization): Promise<{
     measurements: Measurement[];
     unknownMeasurements: UnknownMeasurement[];
     unknownUnits: UnknownUnits[];

package/dist/service/ohtReportMeasurementsExtractor.service.js

@@ -43,6 +43,8 @@ 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
@@ -84,6 +86,10 @@ 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.
@@ -204,7 +210,7 @@ let filename = '';
  *   - `isReportCorrectlyParsed`: Boolean indicating if all measurements were parsed correctly
  *
  * ## Error Handling:
- * - All errors are added to the `errorMessages` array passed as parameter
+ * - All errors are recorded via `parsingErrorService.record()`
  * - Errors are categorized by destination (slack, notes, bi)
  * - Processing continues even if individual exams fail
  * - Errors are logged with context (filename, labKey, ohtBmId, etc.)
@@ -224,12 +230,11 @@ let filename = '';
  * @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, errorMessages, partnerCustomization) {
+async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFilename, patientInfo, documentDate, allowMultiMeasurementsPerBiomarker, ohtCoreApiKey, partnerId, partnerCustomization) {
     filename = sourceFilename;
     const measurements = [];
     const unknownMeasurements = [];
@@ -241,9 +246,8 @@ 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);
-        errorMessages.push({
-            destination: { slack: true, notes: false, bi: false },
-            message: errorMsg,
+        parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.NO_LAB_KEYS, {
+            messageSuffix: (0, processingLogger_service_1.getRequestScopedFilename)(filename),
         });
         return {
             measurements,
@@ -390,16 +394,10 @@ 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)) {
-                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:${transformedExamObj.labKey}`
+                parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.DUPLICATE_BIOMARKER, {
+                    labKey: transformedExamObj.labKey,
+                    biomarkerId: finalOhtBmId,
+                    item: `bmId:${finalOhtBmId}, labKey:${transformedExamObj.labKey}`,
                 });
                 continue;
             }
@@ -409,16 +407,11 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 `name:${ohtBiomarker.acf.shortName}, bmId:${finalOhtBmId}, labKey:${transformedExamObj.labKey}` :
                 `bmId:${finalOhtBmId}, labKey:${transformedExamObj.labKey}`;
             if (!ohtBiomarker) {
-                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}`
+                parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.BIOMARKER_NOT_FOUND, {
+                    labKey: transformedExamObj.labKey,
+                    biomarkerId: finalOhtBmId,
+                    item: `${bmInfo}`,
+                    errorTrace: { ohtBmId: finalOhtBmId, labKey: transformedExamObj.labKey },
                 });
                 continue;
             }
@@ -440,24 +433,26 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 });
             }
             if (!isUnitParsedCorrectly) {
-                processingLogger_service_1.processingLogger.addWarning(`Unit not extracted correctly for "${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:${unit}`
+                parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.UNIT_NOT_EXTRACTED, {
+                    labKey: transformedExamObj.labKey,
+                    biomarkerId: finalOhtBmId,
+                    item: `${bmInfo}, unit:${unit}`,
+                    errorTrace: { unit },
                 });
                 isMeasurementCorrectlyParsed = false;
             }
             let { valueType, alphanumericalValue, numberValue, valueComparator, isValueParsedCorrectly } = (0, extractionUtils_1.ohtReportParseExamValue)(transformedExamObj, ohtBiomarker);
             if ((0, dataUtils_1.isNumericalWithoutValidResult)(valueType, numberValue, alphanumericalValue)) {
                 const alphanumericalValueTrimmed = alphanumericalValue?.trim() ?? '';
+                parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.NUMERIC_BIOMARKER_ALPHANUMERIC_VALUE, {
+                    labKey: transformedExamObj.labKey,
+                    biomarkerId: finalOhtBmId,
+                    item: `${bmInfo}, value:${alphanumericalValueTrimmed}`,
+                    ohtExam: transformedExamObj,
+                    originalExam: originalExam ?? undefined,
+                });
                 const unknownMeasurement = {
-                    biomarkerName: transformedExamObj.description ?? '',
+                    biomarkerName: resolveUnknownMeasurementName([transformedExamObj.description], transformedExamObj.labKey || labKey || '(unmapped measurement)'),
                     value: alphanumericalValueTrimmed,
                     unit: unit ?? '',
                     annotation: transformedExamObj.annotation ?? '',
@@ -478,16 +473,11 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 continue;
             }
             if (!isValueParsedCorrectly) {
-                processingLogger_service_1.processingLogger.addWarning(`Value not extracted correctly for "${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}`
+                parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.VALUE_NOT_EXTRACTED, {
+                    labKey: transformedExamObj.labKey,
+                    biomarkerId: finalOhtBmId,
+                    item: `${bmInfo}, value:${numberValue}${unit}`,
+                    errorTrace: { numberValue, unit },
                 });
                 isMeasurementCorrectlyParsed = false;
             }
@@ -495,10 +485,12 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             if (isValueParsedCorrectly && valueType === 'NUMERICAL') {
                 const isPlausibleValue = numberValue !== null && (0, extractionUtils_1.ohtReportCheckValueForPlausibleValues)(finalOhtBmId, transformedExamObj.labKey, ohtBiomarker, unit, numberValue, isUnitParsedCorrectly, filename);
                 if (!isPlausibleValue) {
-                    errorMessages.push({
-                        destination: { slack: false, notes: true, bi: true },
-                        message: `Value is not plausible for:[PLACEHOLDER]`,
-                        item: `${bmInfo}, value:${numberValue}${unit}`
+                    parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.VALUE_NOT_PLAUSIBLE, {
+                        labKey: transformedExamObj.labKey,
+                        biomarkerId: finalOhtBmId,
+                        item: `${bmInfo}, value:${numberValue}${unit}`,
+                        ohtExam: transformedExamObj,
+                        originalExam: originalExam ?? undefined,
                     });
                     // Resolve name with fallbacks
                     const implausibleName = transformedExamObj.examName ||
@@ -547,16 +539,10 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 to = extractedRange.to ?? null;
                 isRangeParsedCorrectly = extractedRange.isRangeParsedCorrectly;
                 if (!isRangeParsedCorrectly) {
-                    processingLogger_service_1.processingLogger.addWarning(`Range not extracted correctly for "${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}`
+                    parsingErrorService_service_1.parsingErrorService.record(error_types_1.ParsingErrorType.RANGE_NOT_EXTRACTED, {
+                        labKey: transformedExamObj.labKey,
+                        biomarkerId: finalOhtBmId,
+                        item: `${bmInfo}`,
                     });
                     isMeasurementCorrectlyParsed = false;
                 }
@@ -620,7 +606,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 continue;
             }
             // No mapping or ohtBmId === -1: create unknownMeasurement
-            const unknownMeasurementName = `${transformedExamObj.mnemonic}:${transformedExamObj.examName}`;
+            const unknownMeasurementName = resolveUnknownMeasurementName([transformedExamObj.mnemonic, transformedExamObj.examName], labKey || '(unmapped measurement)');
             const originalName = labKey.split(':')[1] || transformedExamObj.examName;
             const annotation = `${transformedExamObj.annotation || ''}`;
             const dataOrigin = {
@@ -656,7 +642,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
         backend_mapped_biomarkers: backendMappedCount,
         unmapped_biomarkers: unmappedCount,
         total_processed: exams.length,
-        errors: errorMessages.length,
+        errors: parsingErrorService_service_1.parsingErrorService.getLocalErrors().length,
     });
     return {
         measurements,

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package/dist/service/parsingErrorService.service.d.ts

@@ -0,0 +1,40 @@
+/**
+ * Request-scoped parsing error collector for agnostic-parser.
+ *
+ * Layer 1 (local): in-memory errors → ingestion notes, Slack, processingLogger.
+ * Layer 2 (Core): grouped profiles flushed at end of run via runWithContextAsync finally.
+ *
+ * Call sites use record() only — do not duplicate processingLogger.addWarning/addError.
+ */
+import { LocalParsingError, ErrorProfilePayload, ParsingErrorType, RecordParsingErrorDetails, RecordParsingErrorOptions } from '../types/error.types';
+import { ProcessingContext } from './processingLogger.service';
+declare class ParsingErrorService {
+    /** Called from runWithContextAsync — do not use directly in parsers. */
+    initRequestState(requestId: string): void;
+    clearRequestState(requestId: string): void;
+    /**
+     * Single entry point for parsing issues.
+     * Resolves message/clientMessage from catalog + details, stores Layer 1, syncs logger once.
+     */
+    record(errorType: ParsingErrorType, details?: RecordParsingErrorDetails, options?: RecordParsingErrorOptions): LocalParsingError;
+    getLocalErrors(): LocalParsingError[];
+    getAggregatedNotes(): string;
+    getAggregatedSlack(): string;
+    sendSlackIfNeeded(ohapiUrl: string, partnerName: string, fileUploadId: string): Promise<void>;
+    /**
+     * Groups local errors by (errorType, contextKey).
+     * Technical message → occurrence snapshot; clientMessage → profile message.
+     */
+    buildCorePayloads(ctx: ProcessingContext): ErrorProfilePayload[];
+    /**
+     * POST grouped profiles to Core. Called from runWithContextAsync finally.
+     * No-op when empty, preview, or missing partner/api key. Never throws.
+     */
+    flushToCoreSafe(): Promise<void>;
+    clear(): void;
+}
+export declare const parsingErrorService: ParsingErrorService;
+/** Lifecycle hooks used by processingLogger.runWithContextAsync. */
+export declare function initParsingErrorRequestState(context: ProcessingContext): string;
+export declare function clearParsingErrorRequestState(requestId: string): void;
+export {};