@openhealth/oht-custom-parser-lib 0.3.13 → 0.4.0

package/{readme.md → README.md}

@@ -33,22 +33,6 @@ After installing, you can import and use the library in your cloud functions:
 const { connectToMongoDB } = require('oht-custom-parser-lib');
 ```
 
-## Logging
-
-- **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

package/dist/index.d.ts

@@ -7,10 +7,8 @@ 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, } 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, RejectReason, AnnotationLabKey, ExtractionPath, AnnotationConfig, } from './types/oht.types';
-export { ErrorMessage, ErrorCode, ERROR_CATALOG, ERROR_MESSAGES, getErrorMessage, getRejectReason, } from './types/error.types';
-export { handleError, ValidationError, shouldSendSlackNotification, extractFormattedRejectReason, mapErrorToRejectReason, } from './service/fileUploadErrorHandler.service';
+export { ErrorMessage } from './types/error.types';
 export type { TransformationRule, TransformationContext, ApplyRulesResult as TransformationApplyRulesResult, ApplyRulesOptions as TransformationApplyRulesOptions, ValidationResult as TransformationValidationResult, } from './types/transformationRules.types';
-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

@@ -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.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 = exports.getRequestIdFromContext = void 0;
+exports.readFileFromBucket = exports.applyFormat = exports.extractFromPath = exports.resolveUnitFromSynonyms = exports.fetchSynonymUnits = exports.processAppendedMappings = exports.isBiomarkerExternalNoVisualRange = exports.isBiomarkerValueNumerical = exports.extractValue = exports.parseErrorObj = exports.makeApiCallWithRetry = 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 = void 0;
 // ### SERVICES ###
 var reportCreator_service_1 = require("./service/reportCreator.service");
 Object.defineProperty(exports, "postDataImportFileUploadToCore", { enumerable: true, get: function () { return reportCreator_service_1.postDataImportFileUploadToCore; } });
@@ -55,24 +55,6 @@ Object.defineProperty(exports, "DataImportFileUploadStatus", { enumerable: true,
 Object.defineProperty(exports, "Sex", { enumerable: true, get: function () { return oht_types_1.Sex; } });
 Object.defineProperty(exports, "UploadType", { enumerable: true, get: function () { return oht_types_1.UploadType; } });
 Object.defineProperty(exports, "RejectReason", { enumerable: true, get: function () { return oht_types_1.RejectReason; } });
-var error_types_1 = require("./types/error.types");
-Object.defineProperty(exports, "ErrorCode", { enumerable: true, get: function () { return error_types_1.ErrorCode; } });
-Object.defineProperty(exports, "ERROR_CATALOG", { enumerable: true, get: function () { return error_types_1.ERROR_CATALOG; } });
-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; } });
-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; } });
-Object.defineProperty(exports, "shouldSendSlackNotification", { enumerable: true, get: function () { return fileUploadErrorHandler_service_1.shouldSendSlackNotification; } });
-Object.defineProperty(exports, "extractFormattedRejectReason", { enumerable: true, get: function () { return fileUploadErrorHandler_service_1.extractFormattedRejectReason; } });
-Object.defineProperty(exports, "mapErrorToRejectReason", { enumerable: true, get: function () { return fileUploadErrorHandler_service_1.mapErrorToRejectReason; } });
-// ### 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 ###
 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

@@ -15,8 +15,6 @@ declare function parseGender(patientGender?: string): {
  *
  * @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): {

package/dist/service/auxiliaryFunctions.service.js

@@ -13,13 +13,14 @@ exports.postFileUploadSetStatus = postFileUploadSetStatus;
 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 pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
 const oht_types_1 = require("../types/oht.types");
 const dayjs_1 = __importDefault(require("dayjs"));
 const customParseFormat_1 = __importDefault(require("dayjs/plugin/customParseFormat"));
 const utc_1 = __importDefault(require("dayjs/plugin/utc"));
 dayjs_1.default.extend(customParseFormat_1.default);
 dayjs_1.default.extend(utc_1.default);
+const logger = (0, pinoLogger_1.default)();
 const OHT_CORE_URL = process.env.OHT_CORE_URL;
 function getPatientAge(documentDate, patientBirthdate) {
     if (!patientBirthdate || !documentDate)
@@ -60,8 +61,6 @@ function parseGender(patientGender) {
  *
  * @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) {
@@ -189,7 +188,7 @@ async function postFileUploadSetStatus(payload, fileUploadId, filename, ohtCoreA
         formattedPayload.digitalization = digitalization;
     }
     const processingResponse = await (0, apiUtils_1.makeApiCallWithRetry)('post', ohtCoreFileUploadSetStatusUrl, formattedPayload, ohtCoreApiKey);
-    processingLogger_service_1.processingLogger.logInfo(`Resp: POST status: ${payload.status} /file-uploads/${fileUploadId}, filename: ${filename}`, { resp: processingResponse?.data });
+    logger.info({ resp: processingResponse?.data }, `Resp: POST status: ${payload.status} /file-uploads/${fileUploadId}, filename: ${filename}`);
     return processingResponse?.data;
 }
 // getPartnerTransformationRules fetches all the available partner transformation rules

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

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

@@ -1,5 +1,8 @@
 import { LabToOhtContract, LabToOhtMapper, RangeExtraction, RangeExtractionResponse, UnitExtraction, ValueExtraction, SynonymUnit, UnknownUnits, TransformationRulesChains } from "../types/custom-parser.types";
 import { Biomarker, BiomarkerValueType, Measurement, MeasurementValueComparator, PatientInfo, UnknownMeasurement, Exam } from "../types/oht.types";
+type ExamWithSyntheticId = Exam & {
+    _syntheticId: string;
+};
 declare function extractUnit(unitExtraction: UnitExtraction | undefined, rawData: any, ohtBiomarker: Biomarker, synonymUnits?: SynonymUnit[] | null, partnerId?: string | null | undefined): {
     unit: string;
     isUnitParsedCorrectly: boolean;
@@ -27,7 +30,7 @@ declare function parseExamValue(rawExamObj: any, valueExtraction: ValueExtractio
 };
 declare function checkValueForPlausibleValues(labToOhtMapper: LabToOhtMapper, ohtBiomarker: Biomarker, unit: string, value: number, isUnitParsedCorrectly: boolean): boolean;
 type ApplyTransformationRulesResult = {
-    transformedExams: Exam[];
+    transformedExams: ExamWithSyntheticId[];
     applicationErrorMessages: string[];
 };
 declare function ohtMeasurementsExtractor(labToOhtContract: LabToOhtContract, exams: Exam[], transformationRules: TransformationRulesChains, ohtCoreApiKey: string, partnerId?: string | null | undefined): Promise<{

package/dist/service/ohtMeasurementsExtractor.service.js

@@ -1,4 +1,7 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getRangeFromPositionAndRegex = void 0;
 exports.ohtMeasurementsExtractor = ohtMeasurementsExtractor;
@@ -8,13 +11,15 @@ exports.extractReferenceAnnotation = extractReferenceAnnotation;
 exports.parseExamValue = parseExamValue;
 exports.extractUnit = extractUnit;
 exports.extractValueFromGreaterLowerThan = extractValueFromGreaterLowerThan;
+const crypto_1 = __importDefault(require("crypto"));
 const dataUtils_1 = require("../util-ts/dataUtils");
 const regexUtils_1 = require("../util-ts/regexUtils");
-const processingLogger_service_1 = require("./processingLogger.service");
+const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
 const apiUtils_1 = require("../util-ts/apiUtils");
 const oht_types_1 = require("../types/oht.types");
 const transformationRules_service_1 = require("./transformationRules.service");
 const auxiliaryFunctions_service_1 = require("./auxiliaryFunctions.service");
+const logger = (0, pinoLogger_1.default)();
 const OHT_CORE_URL = process.env.OHT_CORE_URL;
 let filename = '';
 function extractUnit(unitExtraction, rawData, ohtBiomarker, synonymUnits = null, partnerId = null) {
@@ -292,7 +297,7 @@ function checkValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, value,
     const isPlausibleValue = value >= plausibleLowerValue && value <= plausibleUpperValue;
     // Log if the value is not plausible
     if (!isPlausibleValue) {
-        processingLogger_service_1.processingLogger.logWarn(`Value "${value} ${standardUnit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${labToOhtMapper.ohtBmId}" | "${labToOhtMapper.labKey}", filename: ${filename}`, { labToOhtMapper, value, standardUnit, plausibleLowerValue, plausibleUpperValue, filename });
+        logger.warn({ labToOhtMapper, value, standardUnit, plausibleLowerValue, plausibleUpperValue, filename }, `Value "${value} ${standardUnit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${labToOhtMapper.ohtBmId}" | "${labToOhtMapper.labKey}", filename: ${filename}`);
     }
     return isPlausibleValue;
 }
@@ -300,12 +305,11 @@ function checkValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, value,
  * Apply transformation rules to exams
  * This function applies transformation rules chain to each exam, passing all exams as context
  *
- * @param exams - Array of original exam objects
+ * @param exams - Array of original exam objects with synthetic IDs
  * @param transformationRules - Mapping of labKey to transformation rule chains
- * @param patientInfo - PatientInfo
- * @param documentDate - Source DocumentDate
- *
- * @returns Promise<ApplyTransformationRulesResult[]> - Array of transformed exams
+ * @param patientInfo - Patient information
+ * @param documentDate - Document date
+ * @returns Promise<ApplyTransformationRulesResult> - Array of transformed exams and error messages
  */
 async function applyTransformationRulesToExams(exams, transformationRules, patientInfo, documentDate) {
     if (transformationRules.size === 0) {
@@ -327,7 +331,7 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
     const ohtReport = {
         exams: exams.map(e => e.ohtExam),
     };
-    processingLogger_service_1.processingLogger.logInfo('Applying transformation rules to exams...', { exams_count: exams.length, chains_count: transformationRules.size, filename });
+    logger.info({ examsCount: exams.length, chainsCount: transformationRules.size, filename }, 'Applying transformation rules to exams...');
     let labKeysWithRulesCount = 0;
     let transformedLabKeysCount = 0;
     const applicationErrorMessages = [];
@@ -345,33 +349,38 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
                 contextJson: reportContext,
             });
             if (result.errors.length > 0) {
-                processingLogger_service_1.processingLogger.logWarn('Errors applying transformation rule(s) for labKey.', { labKey, errors: result.errors, filename });
+                logger.warn({ labKey, errors: result.errors, filename }, 'Errors applying transformation rule(s) for labKey.');
                 applicationErrorMessages.push(`${labKey}: ${result.errors.map(e => `(rule ID ${e.ruleId}) ${e.error}`).join('; ')}`);
+                // Keep original exam when transformation fails
+                transformedExams.push(exam);
             }
             else {
                 if (result.appliedRules.length > 0) {
                     transformedLabKeysCount++;
                 }
-                processingLogger_service_1.processingLogger.logInfo('Done applying transformation rule(s) for labKey.', { labKey, applied_rules: result.appliedRules.length, filename });
-                // Add the transformed exam to the result array only if there are no errors in the chain
+                logger.info({ labKey, appliedRules: result.appliedRules.length, filename }, 'Done applying transformation rule(s) for labKey.');
+                // Preserve the synthetic ID through transformation
                 transformedExams.push({
+                    _syntheticId: exam._syntheticId,
                     ohtExam: result.data,
                     originalExam: exam.originalExam
                 });
             }
         }
         catch (error) {
-            processingLogger_service_1.processingLogger.logError('Failed to apply transformation rules for labKey.', error instanceof Error ? error : undefined, { labKey, filename });
+            logger.error({ labKey, error, filename }, 'Failed to apply transformation rules for labKey.');
             applicationErrorMessages.push(`${labKey}: Unhandled error occurred.`);
+            // Keep original exam when transformation throws
+            transformedExams.push(exam);
         }
     }
-    processingLogger_service_1.processingLogger.logInfo('Done applying the transformation rules to exams.', {
+    logger.info({
         filename,
-        exams_count: exams.length,
-        chains_count: transformationRules.size,
-        transformed_lab_keys_count: transformedLabKeysCount,
-        lab_keys_with_rules_count: labKeysWithRulesCount,
-    });
+        examsCount: exams.length,
+        chainsCount: transformationRules.size,
+        transformedLabKeysCount,
+        labKeysWithRulesCount,
+    }, 'Done applying the transformation rules to exams.');
     return {
         transformedExams,
         applicationErrorMessages
@@ -384,13 +393,28 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
     const unknownUnits = [];
     let isReportCorrectlyParsed = true;
     let transformationRulesErrors = [];
+    // Assign UUIDs to exams and labToOhtList items for tracking through transformation.
+    // This enables support for duplicate labKeys (double-hits).
+    const syntheticIdByLabToOhtMapper = new Map();
+    const examsWithIds = exams.map((exam, index) => {
+        const syntheticId = crypto_1.default.randomUUID();
+        // Link the corresponding labToOhtMapper to this synthetic ID
+        const labToOhtMapper = labToOhtContract.labToOhtList[index];
+        if (labToOhtMapper) {
+            syntheticIdByLabToOhtMapper.set(labToOhtMapper, syntheticId);
+        }
+        return {
+            ...exam,
+            _syntheticId: syntheticId,
+        };
+    });
     // Apply transformation rules to all exams
     let transformedExamsResult = { transformedExams: [], applicationErrorMessages: [] };
     try {
-        transformedExamsResult = await applyTransformationRulesToExams(exams, transformationRules, labToOhtContract.patientInfo, labToOhtContract.documentDate);
+        transformedExamsResult = await applyTransformationRulesToExams(examsWithIds, transformationRules, labToOhtContract.patientInfo, labToOhtContract.documentDate);
     }
     catch (error) {
-        processingLogger_service_1.processingLogger.logError('Unhandled error while applying transformation rules to exams.', error instanceof Error ? error : undefined, { filename });
+        logger.error({ error, filename }, 'Unhandled error while applying transformation rules to exams.');
         labToOhtContract.errorMessages.push({
             destination: { slack: true, notes: true, bi: false },
             message: `Failed applying the transformation rules for filename ${filename}. ${error instanceof Error ? error.message : error}`,
@@ -404,7 +428,8 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
         });
     }
     const transformedExams = transformedExamsResult.transformedExams;
-    const transformedExamsMap = transformedExams.reduce((map, exam) => map.set(exam.ohtExam.labKey, exam), new Map());
+    // Use synthetic UUID as key to support duplicate labKeys (double-hits)
+    const transformedExamsMap = new Map(transformedExams.map(exam => [exam._syntheticId, exam]));
     const allPossibleOHTBmIds = [];
     [
         ...Object.values(labToOhtContract.labToOhtList)
@@ -440,15 +465,18 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
             return;
         }
         let examObj = JSON.parse(labToOhtMapper.rawExam);
-        // Get the transformed exam for this labKey
-        const transformedExam = transformedExamsMap.get(labToOhtMapper.labKey);
-        if (transformedExam) {
-            examObj = transformedExam.ohtExam;
+        // Get the transformed exam by synthetic UUID (supports duplicate labKeys)
+        const syntheticId = syntheticIdByLabToOhtMapper.get(labToOhtMapper);
+        if (syntheticId) {
+            const transformedExam = transformedExamsMap.get(syntheticId);
+            if (transformedExam) {
+                examObj = transformedExam.ohtExam;
+            }
         }
         if (labToOhtMapper?.ohtBmId && labToOhtMapper?.ohtBmId !== -1) {
             // if BM is already in measurements, continue to the next one
             if (measurements.some(measurement => measurement.biomarkerId === labToOhtMapper.ohtBmId)) {
-                processingLogger_service_1.processingLogger.logWarn(`Biomarker already in measurements array, should investigate, filename: ${filename}`, { labToOhtMapper });
+                logger.warn({ labToOhtMapper }, `Biomarker already in measurements array, should investigate, filename: ${filename}`);
                 labToOhtContract.errorMessages.push({
                     destination: { slack: false, notes: false, bi: true },
                     message: `Biomarkers Duplicated keys:[PLACEHOLDER]`,
@@ -475,7 +503,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
                 });
             }
             if (!isUnitParsedCorrectly) {
-                processingLogger_service_1.processingLogger.logWarn(`Unit not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`, { labToOhtMapper });
+                logger.warn({ labToOhtMapper }, `Unit not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
                 labToOhtContract.errorMessages.push({
                     destination: { slack: true, notes: true, bi: true },
                     message: `Unit not extracted correctly for:[PLACEHOLDER]`,
@@ -485,7 +513,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
             }
             let { valueType, alphanumericalValue, numberValue, valueComparator, isValueParsedCorrectly } = parseExamValue(examObj, labToOhtMapper.valueExtraction, ohtBiomarker);
             if (!isValueParsedCorrectly) {
-                processingLogger_service_1.processingLogger.logWarn(`Value not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`, { labToOhtMapper });
+                logger.warn({ labToOhtMapper }, `Value not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
                 labToOhtContract.errorMessages.push({
                     destination: { slack: true, notes: true, bi: true },
                     message: `Value not extracted correctly for:[PLACEHOLDER]`,
@@ -521,7 +549,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
             if (isValueParsedCorrectly && valueType === 'NUMERICAL') {
                 const isPlausibleValue = numberValue !== null && checkValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, numberValue, isUnitParsedCorrectly);
                 if (!isPlausibleValue) {
-                    processingLogger_service_1.processingLogger.logWarn(`Value [${numberValue} ${unit}] is not plausible for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`, { labToOhtMapper });
+                    logger.warn({ labToOhtMapper }, `Value [${numberValue} ${unit}] is not plausible for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
                     labToOhtContract.errorMessages.push({
                         destination: { slack: true, notes: true, bi: true },
                         message: `Value is not plausible for:[PLACEHOLDER]`,
@@ -539,7 +567,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
                 to = extractedRange.to ?? null;
                 isRangeParsedCorrectly = extractedRange.isRangeParsedCorrectly;
                 if (!isRangeParsedCorrectly) {
-                    processingLogger_service_1.processingLogger.logWarn(`Range not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`, { labToOhtMapper });
+                    logger.warn({ labToOhtMapper }, `Range not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
                     labToOhtContract.errorMessages.push({
                         destination: { slack: true, notes: true, bi: true },
                         message: `Range not extracted correctly for:[PLACEHOLDER]`,
@@ -596,7 +624,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
             measurements.push(measurement);
         }
         else {
-            processingLogger_service_1.processingLogger.logWarn(`Created an ungroupedBiomarker for id: ${labToOhtMapper.labKey}, filename: ${filename}`);
+            logger.warn(`Created an ungroupedBiomarker for id: ${labToOhtMapper.labKey}, filename: ${filename}`);
             labToOhtContract.errorMessages.push({
                 destination: { slack: false, notes: false, bi: true },
                 message: `Created ungroupedBiomarkers for:[PLACEHOLDER]`,

package/dist/service/ohtMeasurementsExtractor.service.js.map

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

@@ -1,8 +1,11 @@
 import { UnknownUnits, TransformationRulesChains } from "../types/custom-parser.types";
 import { Measurement, PatientInfo, UnknownMeasurement, Exam, UnmappedLabKey } from "../types/oht.types";
 import { ErrorMessage } from "../types/error.types";
+type ExamWithSyntheticId = Exam & {
+    _syntheticId: string;
+};
 type ApplyTransformationRulesResult = {
-    transformedExams: Exam[];
+    transformedExams: ExamWithSyntheticId[];
     applicationErrorMessages: string[];
 };
 /**
@@ -141,13 +144,13 @@ type ApplyTransformationRulesResult = {
  * @param patientInfo - Patient information (sex, birthdate) for range extraction
  * @param documentDate - Document date for age calculation and range extraction
  * @param transformationRules - Map of labKey to transformation rule chains to apply
+ * @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
  * @returns Promise resolving to extraction result with measurements, unknownMeasurements, unknownUnits, unmappedLabKeys, parsing status, and transformation errors
  */
-declare function ohtReportMeasurementsExtractor(isReportPreview: boolean, exams: Exam[], sourceFilename: string, patientInfo: PatientInfo, documentDate: Date | undefined, transformationRules: TransformationRulesChains, ohtCoreApiKey: string, partnerId: string, errorMessages: ErrorMessage[]): Promise<{
+declare function ohtReportMeasurementsExtractor(isReportPreview: boolean, exams: Exam[], sourceFilename: string, patientInfo: PatientInfo, documentDate: Date | undefined, transformationRules: TransformationRulesChains, allowMultiMeasurementsPerBiomarker: boolean, ohtCoreApiKey: string, partnerId: string, errorMessages: ErrorMessage[]): Promise<{
     measurements: Measurement[];
     unknownMeasurements: UnknownMeasurement[];
     unknownUnits: UnknownUnits[];