@openhealth/oht-custom-parser-lib 0.5.61 → 0.5.63

package/dist/index.d.ts

@@ -1,4 +1,4 @@
-export { postDataImportFileUploadToCore, postReportPreviewToCore } from './service/reportCreator.service';
+export { postDataImportFileUploadToCore, postReportPreviewToCore, alignOhtExamAgnosticUpdatedWithMeasurements, } from './service/reportCreator.service';
 export { parseExternalPatientId, parseGender, isPatientAgeValid, getPatientAge, handleRejection, queryFileUploadsWithFilters, postFileUploadSetStatus, DigitalizationUpdateFields, getPartnerTransformationRules, } from './service/auxiliaryFunctions.service';
 export { ohtReportMeasurementsExtractor, } from './service/ohtReportMeasurementsExtractor.service';
 export { ohtMeasurementsExtractor, checkValueForPlausibleValues, extractReferenceRanges, extractReferenceAnnotation, parseExamValue, getRangeFromPositionAndRegex, extractUnit, extractValueFromGreaterLowerThan } from './service/ohtMeasurementsExtractor.service';
@@ -6,7 +6,7 @@ export { getSlackFileIssueNotificationMessage, sendMessageToSlack } from './serv
 export { aggregateMessages, aggregateBiMessages, publishToTopic, generateBIMessages } from './service/errorHandling.service';
 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 { 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, OhtExamAgnosticProcessing, OhtExamAgnosticUpdated, 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 { 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';

package/dist/index.js

@@ -3,12 +3,13 @@ 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.partnerSiloPath = exports.normalizePartnerMappingKey = 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.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.alignOhtExamAgnosticUpdatedWithMeasurements = 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.partnerSiloPath = exports.normalizePartnerMappingKey = 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 = exports.ValidationError = void 0;
 // ### SERVICES ###
 var reportCreator_service_1 = require("./service/reportCreator.service");
 Object.defineProperty(exports, "postDataImportFileUploadToCore", { enumerable: true, get: function () { return reportCreator_service_1.postDataImportFileUploadToCore; } });
 Object.defineProperty(exports, "postReportPreviewToCore", { enumerable: true, get: function () { return reportCreator_service_1.postReportPreviewToCore; } });
+Object.defineProperty(exports, "alignOhtExamAgnosticUpdatedWithMeasurements", { enumerable: true, get: function () { return reportCreator_service_1.alignOhtExamAgnosticUpdatedWithMeasurements; } });
 var auxiliaryFunctions_service_1 = require("./service/auxiliaryFunctions.service");
 Object.defineProperty(exports, "parseExternalPatientId", { enumerable: true, get: function () { return auxiliaryFunctions_service_1.parseExternalPatientId; } });
 Object.defineProperty(exports, "parseGender", { enumerable: true, get: function () { return auxiliaryFunctions_service_1.parseGender; } });

package/dist/index.js.map

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

@@ -151,5 +151,6 @@ declare function ohtReportMeasurementsExtractor(isReportPreview: boolean, exams:
     unknownUnits: UnknownUnits[];
     unmappedLabKeys: UnmappedLabKey[];
     isReportCorrectlyParsed: boolean;
+    labKeyBiomarkerIds: Record<string, number>;
 }>;
 export { ohtReportMeasurementsExtractor, };

package/dist/service/ohtReportMeasurementsExtractor.service.js

@@ -241,6 +241,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
     const unknownMeasurements = [];
     const unknownUnits = [];
     const unmappedLabKeys = [];
+    const labKeyBiomarkerIds = {};
     let isReportCorrectlyParsed = true;
     // Check if we have exams
     const labKeys = exams.map(e => e.ohtExam.labKey);
@@ -256,6 +257,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             unknownUnits,
             unmappedLabKeys,
             isReportCorrectlyParsed: false,
+            labKeyBiomarkerIds,
         };
     }
     processingLogger_service_1.processingLogger.logInfo(`Processing lab file with ${labKeys.length} keys, filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`);
@@ -310,7 +312,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
         const labKey = exam.ohtExam.labKey;
         const backendMapping = mappedBiomarkers?.[labKey];
         if (backendMapping && !backendMapping.isIgnored) {
-            const { ohtBmId } = (0, extractionUtils_1.handleBiomarkerId)(backendMapping, labKey);
+            const { ohtBmId } = (0, extractionUtils_1.handleBiomarkerId)(backendMapping, labKey, isReportPreview);
             if (ohtBmId && ohtBmId !== -1) {
                 allPossibleOHTBmIds.push(ohtBmId);
             }
@@ -377,7 +379,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
         let finalOhtBmId;
         let annotationConfig;
         if (backendMapping) {
-            const { ohtBmId, annotationConfig: config } = (0, extractionUtils_1.handleBiomarkerId)(backendMapping, labKey);
+            const { ohtBmId, annotationConfig: config } = (0, extractionUtils_1.handleBiomarkerId)(backendMapping, labKey, isReportPreview);
             finalOhtBmId = ohtBmId;
             annotationConfig = {
                 enabled: config.enabled,
@@ -602,6 +604,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                 originalName: originalName,
             };
             measurements.push(measurement);
+            labKeyBiomarkerIds[labKey] = ohtBiomarker.id;
             isReportCorrectlyParsed = isReportCorrectlyParsed && isMeasurementCorrectlyParsed;
         }
         else {
@@ -641,12 +644,14 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
     // Log summary of processing
     const backendMappedCount = measurements.length;
     const unmappedCount = unknownMeasurements.length;
+    parsingErrorService_service_1.parsingErrorService.recordMetric(backendMappedCount, 'custom:measurements');
+    parsingErrorService_service_1.parsingErrorService.recordMetric(unmappedCount, 'custom:unknownMeasurements');
     processingLogger_service_1.processingLogger.logInfo(`Processing completed for ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}:`, {
         total_lab_keys: labKeys.length,
         backend_mapped_biomarkers: backendMappedCount,
         unmapped_biomarkers: unmappedCount,
         total_processed: exams.length,
-        errors: parsingErrorService_service_1.parsingErrorService.getLocalErrors().length,
+        errors: parsingErrorService_service_1.parsingErrorService.getLocalErrors().filter((e) => e.errorType !== error_types_1.ParsingErrorType.PARSING_METRIC).length,
     });
     return {
         measurements,
@@ -654,6 +659,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
         unknownUnits,
         unmappedLabKeys,
         isReportCorrectlyParsed,
+        labKeyBiomarkerIds,
     };
 }
 //# sourceMappingURL=ohtReportMeasurementsExtractor.service.js.map

package/dist/service/ohtReportMeasurementsExtractor.service.js.map

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

@@ -17,6 +17,11 @@ declare class ParsingErrorService {
      * Resolves message/clientMessage from catalog + details, stores Layer 1, syncs logger once.
      */
     record(errorType: ParsingErrorType, details?: RecordParsingErrorDetails, options?: RecordParsingErrorOptions): LocalParsingError;
+    /**
+     * Records a non-issue info metric (e.g. per-file measurement counts).
+     * Skips when count <= 0. Does not sync to processingLogger.
+     */
+    recordMetric(count: number, contextKey: string, details?: Omit<RecordParsingErrorDetails, 'customContextKey' | 'occurrenceCount'>): void;
     getLocalErrors(): LocalParsingError[];
     getAggregatedNotes(): string;
     getAggregatedSlack(): string;

package/dist/service/parsingErrorService.service.js

@@ -22,6 +22,7 @@ function createEmptyParsingErrorState() {
     return { localErrors: [] };
 }
 const SEVERITY_RANK = {
+    info: 0,
     warning: 1,
     error: 2,
     critical: 3,
@@ -37,6 +38,9 @@ function getMutableState() {
 }
 /** Maps a LocalParsingError to a single processingLogger call (severity → warning/error). */
 function syncToProcessingLogger(localError) {
+    if (localError.severity === 'info') {
+        return;
+    }
     const catalog = error_types_1.PARSING_ERROR_CATALOG[localError.errorType];
     if (localError.severity === 'critical') {
         const rejectReason = localError.rejectReason ?? catalog.rejectReason;
@@ -105,6 +109,7 @@ class ParsingErrorService {
             ohtExam: details?.ohtExam,
             originalExam: details?.originalExam,
             timestamp: new Date(),
+            occurrenceCount: details?.occurrenceCount,
         };
         const state = getMutableState();
         if (state === null) {
@@ -115,6 +120,21 @@ class ParsingErrorService {
         syncToProcessingLogger(localError);
         return localError;
     }
+    /**
+     * Records a non-issue info metric (e.g. per-file measurement counts).
+     * Skips when count <= 0. Does not sync to processingLogger.
+     */
+    recordMetric(count, contextKey, details) {
+        if (count <= 0) {
+            return;
+        }
+        this.record(error_types_1.ParsingErrorType.PARSING_METRIC, {
+            ...details,
+            customContextKey: contextKey,
+            occurrenceCount: count,
+            messageSuffix: String(count),
+        });
+    }
     getLocalErrors() {
         return [...(getMutableState()?.localErrors ?? [])];
     }
@@ -187,7 +207,12 @@ class ParsingErrorService {
                 source: 'AgnosticParser',
                 uploadedByUserId: ctx.uploadedByUserId,
             };
-            if (group.length === 1) {
+            const metricCount = representative.occurrenceCount;
+            if (metricCount != null && metricCount > 1) {
+                payload.occurrence = snapshots[snapshots.length - 1];
+                payload.occurrencesCount = metricCount;
+            }
+            else if (group.length === 1) {
                 payload.occurrence = snapshots[0];
             }
             else {

package/dist/service/parsingErrorService.service.js.map

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

@@ -1,9 +1,14 @@
-import { DataImportFileUpload, UnknownMeasurementsBulk, Measurement, UnknownMeasurement } from '../types/oht.types';
+import { DataImportFileUpload, UnknownMeasurementsBulk, Measurement, UnknownMeasurement, Exam, OhtExamAgnosticUpdated } from '../types/oht.types';
 import { UnknownUnits } from '../types/custom-parser.types';
+/**
+ * Builds OhtExamAgnosticUpdated payloads for the report-preview callback: aligns ohtExamAgnosticUpdated
+ * unit/value with extracted measurements and attaches agnostic-processing metadata for oht-core assertions.
+ */
+declare function alignOhtExamAgnosticUpdatedWithMeasurements(transformedExams: Exam[], measurements: Measurement[], labKeyBiomarkerIds: Record<string, number>, appliedRulesByLabKey: Record<string, string[]>): OhtExamAgnosticUpdated[];
 /**
  * Posts report preview data (measurements and unknownMeasurements) to OHT Core API.
  * Uses the shared makeApiCallWithRetry helper (Basic auth) from oht-custom-parser-lib.
  */
-declare function postReportPreviewToCore(reportPreviewId: string, measurements: Measurement[], unknownMeasurements: UnknownMeasurement[], filename: string, unknownUnits: UnknownUnits[], partnerId: string, isReportParsedCorrectly: boolean, notes: string, ohtCoreApiKey: string): Promise<void>;
+declare function postReportPreviewToCore(reportPreviewId: string, measurements: Measurement[], unknownMeasurements: UnknownMeasurement[], filename: string, unknownUnits: UnknownUnits[], partnerId: string, isReportParsedCorrectly: boolean, notes: string, ohtCoreApiKey: string, ohtExamAgnosticUpdated?: OhtExamAgnosticUpdated[]): Promise<void>;
 declare function postDataImportFileUploadToCore(dataImportFileUpload: DataImportFileUpload, unknownMeasurements: UnknownMeasurementsBulk, unknownUnits: UnknownUnits[], rejectedStatus: string | undefined, rejectReason: string | undefined, isReportParsedCorrectly: boolean, filename: string, ohtCoreApiKey: string, partnerMappingKey?: string): Promise<DataImportFileUpload | null>;
-export { postDataImportFileUploadToCore, postReportPreviewToCore };
+export { postDataImportFileUploadToCore, postReportPreviewToCore, alignOhtExamAgnosticUpdatedWithMeasurements };

package/dist/service/reportCreator.service.js

@@ -5,6 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.postDataImportFileUploadToCore = postDataImportFileUploadToCore;
 exports.postReportPreviewToCore = postReportPreviewToCore;
+exports.alignOhtExamAgnosticUpdatedWithMeasurements = alignOhtExamAgnosticUpdatedWithMeasurements;
 const oht_types_1 = require("../types/oht.types");
 const processingLogger_service_1 = require("./processingLogger.service");
 const dotenv_1 = __importDefault(require("dotenv"));
@@ -13,11 +14,48 @@ const apiUtils_1 = require("../util-ts/apiUtils");
 const errorHandling_service_1 = require("./errorHandling.service");
 dotenv_1.default.config({ path: `.env.local` });
 const OHT_CORE_URL = process.env.OHT_CORE_URL;
+function normalizeUnitForComparison(unit) {
+    return unit?.toLowerCase().replaceAll(/ /g, '') ?? '';
+}
+/**
+ * Builds OhtExamAgnosticUpdated payloads for the report-preview callback: aligns ohtExamAgnosticUpdated
+ * unit/value with extracted measurements and attaches agnostic-processing metadata for oht-core assertions.
+ */
+function alignOhtExamAgnosticUpdatedWithMeasurements(transformedExams, measurements, labKeyBiomarkerIds, appliedRulesByLabKey) {
+    const measurementsByBiomarkerId = new Map(measurements.map((m) => [m.biomarkerId, m]));
+    return transformedExams.map((exam) => {
+        const labKey = exam.ohtExam.labKey;
+        const biomarkerId = labKeyBiomarkerIds[labKey];
+        const measurement = biomarkerId != null ? measurementsByBiomarkerId.get(biomarkerId) : undefined;
+        const appliedRuleIds = appliedRulesByLabKey[labKey] ?? [];
+        const unitBeforeSynonym = exam.ohtExam.unit ?? '';
+        const ohtExamAgnosticUpdated = measurement
+            ? {
+                ...exam.ohtExam,
+                unit: measurement.unit,
+                value: measurement.value != null
+                    ? String(measurement.value)
+                    : measurement.alphanumericValue ?? exam.ohtExam.value,
+            }
+            : { ...exam.ohtExam };
+        const ohtExamAgnosticProcessing = {
+            transformationRulesApplied: appliedRuleIds.length > 0,
+            synonymUnitApplied: measurement
+                ? normalizeUnitForComparison(unitBeforeSynonym) !==
+                    normalizeUnitForComparison(measurement.unit)
+                : false,
+            ...(appliedRuleIds.length > 0
+                ? { appliedTransformationRuleIds: appliedRuleIds }
+                : {}),
+        };
+        return { ohtExamAgnosticUpdated, ohtExamAgnosticProcessing };
+    });
+}
 /**
  * Posts report preview data (measurements and unknownMeasurements) to OHT Core API.
  * Uses the shared makeApiCallWithRetry helper (Basic auth) from oht-custom-parser-lib.
  */
-async function postReportPreviewToCore(reportPreviewId, measurements, unknownMeasurements, filename, unknownUnits, partnerId, isReportParsedCorrectly, notes, ohtCoreApiKey) {
+async function postReportPreviewToCore(reportPreviewId, measurements, unknownMeasurements, filename, unknownUnits, partnerId, isReportParsedCorrectly, notes, ohtCoreApiKey, ohtExamAgnosticUpdated) {
     if (!OHT_CORE_URL) {
         throw new Error(`ERROR: OHT_CORE_URL is required for report preview, filename: ${filename}`);
     }
@@ -38,13 +76,15 @@ async function postReportPreviewToCore(reportPreviewId, measurements, unknownMea
             });
         }
     }
-    // Always send both arrays, with empty arrays if no data
     const requestBody = {
         status: status,
         measurements: measurements || [],
         unknownMeasurements: unknownMeasurements || [],
         notes: notes,
     };
+    if (ohtExamAgnosticUpdated && ohtExamAgnosticUpdated.length > 0) {
+        requestBody.ohtExamAgnosticUpdated = ohtExamAgnosticUpdated;
+    }
     processingLogger_service_1.processingLogger.logInfo(`postReportPreviewToCore: Sending report preview to OHT Core API (${(measurements || []).length} measurements, ${(unknownMeasurements || []).length} unknownMeasurements), filename: ${filename}`, {
         filename,
         report_preview_id: reportPreviewId,

package/dist/service/reportCreator.service.js.map

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package/dist/types/error.types.d.ts

@@ -5,7 +5,7 @@ export interface Destination {
     notes: boolean;
     bi: boolean;
 }
-export type ParsingErrorSeverity = 'warning' | 'error' | 'critical';
+export type ParsingErrorSeverity = 'info' | 'warning' | 'error' | 'critical';
 /** Canonical parsing error types — Layer 1 local + Layer 2 Core profiles. */
 export declare enum ParsingErrorType {
     VALUE_NOT_PLAUSIBLE = "VALUE_NOT_PLAUSIBLE",
@@ -28,7 +28,8 @@ export declare enum ParsingErrorType {
     FATAL_VALIDATION = "FATAL_VALIDATION",
     FATAL_NORMALIZATION = "FATAL_NORMALIZATION",
     FATAL_FILE_IO = "FATAL_FILE_IO",
-    FATAL_PARSER_ERROR = "FATAL_PARSER_ERROR"
+    FATAL_PARSER_ERROR = "FATAL_PARSER_ERROR",
+    PARSING_METRIC = "PARSING_METRIC"
 }
 export interface ParsingErrorCatalogEntry {
     severity: ParsingErrorSeverity;
@@ -58,6 +59,8 @@ export interface LocalParsingError {
     ohtExam?: OhtExam;
     originalExam?: OriginalExam;
     timestamp: Date;
+    /** When > 1, flush sends one snapshot with occurrencesCount instead of N snapshots. */
+    occurrenceCount?: number;
 }
 export interface ParsingErrorOccurrenceSnapshot {
     dataImportFileUploadId: string;
@@ -100,6 +103,7 @@ export interface RecordParsingErrorDetails {
     originalExam?: OriginalExam;
     destinations?: Partial<Destination>;
     severity?: ParsingErrorSeverity;
+    occurrenceCount?: number;
 }
 export interface RecordParsingErrorOptions {
     notifySlack?: boolean;

package/dist/types/error.types.js

@@ -30,6 +30,7 @@ var ParsingErrorType;
     ParsingErrorType["FATAL_NORMALIZATION"] = "FATAL_NORMALIZATION";
     ParsingErrorType["FATAL_FILE_IO"] = "FATAL_FILE_IO";
     ParsingErrorType["FATAL_PARSER_ERROR"] = "FATAL_PARSER_ERROR";
+    ParsingErrorType["PARSING_METRIC"] = "PARSING_METRIC";
 })(ParsingErrorType || (exports.ParsingErrorType = ParsingErrorType = {}));
 const defaultDestinations = { slack: false, notes: false, bi: false };
 exports.PARSING_ERROR_CATALOG = {
@@ -234,6 +235,15 @@ exports.PARSING_ERROR_CATALOG = {
         destinations: { slack: false, notes: false, bi: false },
         pipelineStep: 'error_handling',
     },
+    [ParsingErrorType.PARSING_METRIC]: {
+        severity: 'info',
+        message: 'Parsing metric recorded',
+        clientMessage: 'Parsing metric recorded',
+        contextKey: '{customContextKey}',
+        destinations: { slack: false, notes: false, bi: true },
+        pipelineStep: 'extract_measurements',
+        warningCategory: 'measurements',
+    },
 };
 function resolveParsingErrorContextKey(catalogContextKey, details) {
     if (details?.customContextKey) {
@@ -242,6 +252,9 @@ function resolveParsingErrorContextKey(catalogContextKey, details) {
     if (catalogContextKey === '{labKey}') {
         return details?.labKey ?? 'custom:unexpected';
     }
+    if (catalogContextKey === '{customContextKey}') {
+        return details?.customContextKey ?? 'custom:unexpected';
+    }
     return catalogContextKey;
 }
 function buildParsingErrorMessage(catalogMessage, details) {

package/dist/types/error.types.js.map

@@ -1 +1 @@
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package/dist/types/oht.types.d.ts

@@ -209,8 +209,20 @@ export interface UnknownMeasurement {
     ohtExam?: OhtExam;
     originalExam?: OriginalExam;
 }
+export interface OhtExamAgnosticProcessing {
+    transformationRulesApplied: boolean;
+    synonymUnitApplied: boolean;
+    appliedTransformationRuleIds?: string[];
+}
+/** Per-exam payload sent on report-preview update (merge by labKey on oht-core). Mirrors oht-core OHTExamAgnosticUpdated. */
+export interface OhtExamAgnosticUpdated {
+    ohtExamAgnosticUpdated: OhtExam;
+    ohtExamAgnosticProcessing?: OhtExamAgnosticProcessing;
+}
 export interface Exam {
     ohtExam: OhtExam;
+    ohtExamAgnosticUpdated?: OhtExam;
+    ohtExamAgnosticProcessing?: OhtExamAgnosticProcessing;
     originalExam: OriginalExam;
 }
 export type ExamKind = 'panel' | 'organism' | 'antibiogram' | 'quantitative' | 'qualitative';

package/dist/types/oht.types.js.map

@@ -1 +1 @@
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package/dist/util-ts/extractionUtils.d.ts

@@ -11,9 +11,11 @@ declare function parseRange(exam: OhtExam, patientInfo: PatientInfo): RangeExtra
 * Converts backend biomarker id to know if it should be mapped or unmapped
 * @param backendMapping - The backend mapping configuration
 * @param labKey - The lab key identifier
+* @param isReportPreview - When true, trust ohtBmId from GET /mappings/latest (oht-core already
+*   sets -1 for keep_as_unmapped; keepAsUnmapped on needs_review is a UI flag only)
 * @returns The final ohtBmId and annotationConfig
 */
-declare function handleBiomarkerId(backendMapping: BackendBiomarkerMapping, labKey: string): {
+declare function handleBiomarkerId(backendMapping: BackendBiomarkerMapping, labKey: string, isReportPreview?: boolean): {
     ohtBmId: number;
     annotationConfig: {
         enabled: boolean;

package/dist/util-ts/extractionUtils.js

@@ -428,14 +428,17 @@ function getGreaterThanPatternsLocal() {
 * Converts backend biomarker id to know if it should be mapped or unmapped
 * @param backendMapping - The backend mapping configuration
 * @param labKey - The lab key identifier
+* @param isReportPreview - When true, trust ohtBmId from GET /mappings/latest (oht-core already
+*   sets -1 for keep_as_unmapped; keepAsUnmapped on needs_review is a UI flag only)
 * @returns The final ohtBmId and annotationConfig
 */
-function handleBiomarkerId(backendMapping, labKey) {
+function handleBiomarkerId(backendMapping, labKey, isReportPreview = false) {
     // Handle unmapped biomarkers:
     // 1. ohtBmId: -1 means already unmapped in backend
-    // 2. keepAsUnmapped: true means override to unmapped (ohtBmId becomes -1)
+    // 2. keepAsUnmapped: true means override to unmapped (ohtBmId becomes -1), except in report
+    //    preview where GET /mappings/latest keeps real OHTBmID for needs_review/pending
     const isAlreadyUnmapped = backendMapping.ohtBmId === -1;
-    const shouldBeUnmapped = backendMapping.keepAsUnmapped === true;
+    const shouldBeUnmapped = !isReportPreview && backendMapping.keepAsUnmapped === true;
     const finalOhtBmId = shouldBeUnmapped ? -1 : backendMapping.ohtBmId;
     if (isAlreadyUnmapped) {
         processingLogger_service_1.processingLogger.logInfo(`Processing backend unmapped biomarker: ${labKey} (ohtBmId: -1)`);

package/dist/util-ts/extractionUtils.js.map

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package/dist/util-ts/loincMapping.d.ts

@@ -0,0 +1,5 @@
+import type { BackendBiomarkerMapping, LoincMapping } from '../types/oht.types';
+/** Prefer structured loincMapping; fall back to legacy taggedLoincCode. */
+export declare function getEffectiveLoincMapping(mapping: Pick<BackendBiomarkerMapping, 'loincMapping' | 'taggedLoincCode'> | null | undefined): LoincMapping | undefined;
+/** Build ohtBmId → effective loincMapping from fetched partner biomarker mappings. */
+export declare function buildLoincMappingByOhtBmId(mappedBiomarkers: Record<string, BackendBiomarkerMapping> | null | undefined): Map<number, LoincMapping>;

package/dist/util-ts/loincMapping.js

@@ -0,0 +1,81 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getEffectiveLoincMapping = getEffectiveLoincMapping;
+exports.buildLoincMappingByOhtBmId = buildLoincMappingByOhtBmId;
+const UUID_RE = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i;
+function trimField(value) {
+    return (value ?? '').trim();
+}
+function normalizeLoincCodeKey(code) {
+    return trimField(code).replace(/\s+/g, '');
+}
+function extractUuid(value) {
+    const trimmed = trimField(value);
+    if (!trimmed) {
+        return undefined;
+    }
+    const lower = trimmed.toLowerCase();
+    return UUID_RE.test(lower) ? lower : undefined;
+}
+function normalizeLoincMapping(lm) {
+    if (!lm) {
+        return undefined;
+    }
+    const loincCode = normalizeLoincCodeKey(lm.loincCode ?? '');
+    const bmObjectUuid = extractUuid(lm.bmObjectUuid);
+    if (!loincCode && !bmObjectUuid) {
+        return undefined;
+    }
+    const result = {};
+    if (loincCode) {
+        result.loincCode = loincCode;
+    }
+    if (bmObjectUuid) {
+        result.bmObjectUuid = bmObjectUuid;
+    }
+    return result;
+}
+/** Prefer structured loincMapping; fall back to legacy taggedLoincCode. */
+function getEffectiveLoincMapping(mapping) {
+    if (!mapping) {
+        return undefined;
+    }
+    const fromStructured = normalizeLoincMapping(mapping.loincMapping);
+    if (fromStructured) {
+        return fromStructured;
+    }
+    const tagged = trimField(mapping.taggedLoincCode);
+    if (!tagged) {
+        return undefined;
+    }
+    const uuid = extractUuid(tagged);
+    if (uuid && uuid === tagged.toLowerCase()) {
+        return { bmObjectUuid: uuid };
+    }
+    const codeKey = normalizeLoincCodeKey(tagged);
+    if (codeKey) {
+        return { loincCode: codeKey };
+    }
+    return undefined;
+}
+/** Build ohtBmId → effective loincMapping from fetched partner biomarker mappings. */
+function buildLoincMappingByOhtBmId(mappedBiomarkers) {
+    const index = new Map();
+    if (!mappedBiomarkers) {
+        return index;
+    }
+    for (const mapping of Object.values(mappedBiomarkers)) {
+        if (!mapping || mapping.isIgnored || mapping.ohtBmId <= 0) {
+            continue;
+        }
+        const effective = getEffectiveLoincMapping(mapping);
+        if (!effective) {
+            continue;
+        }
+        if (!index.has(mapping.ohtBmId)) {
+            index.set(mapping.ohtBmId, effective);
+        }
+    }
+    return index;
+}
+//# sourceMappingURL=loincMapping.js.map

package/dist/util-ts/loincMapping.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,40 +1,40 @@
-{
-  "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.5.61",
-  "description": "Shared nodejs lib with with reusable functions",
-  "main": "dist/index.js",
-  "types": "dist/index.d.ts",
-  "files": [
-    "/dist"
-  ],
-  "scripts": {
-    "test": "jest"
-  },
-  "keywords": [],
-  "author": "",
-  "license": "ISC",
-  "dependencies": {
-    "@google-cloud/pubsub": "^4.10.0",
-    "@google-cloud/storage": "^7.7.0",
-    "axios": "^1.13.2",
-    "bottleneck": "^2.19.5",
-    "csv-parse": "^6.2.1",
-    "dayjs": "^1.11.13",
-    "dotenv": "^16.4.5",
-    "jsonata": "^2.1.0",
-    "moment": "^2.30.1",
-    "mongodb": "^6.3.0",
-    "pino": "^8.19.0",
-    "pino-pretty": "^11.3.0",
-    "xml2js": "^0.6.2"
-  },
-  "devDependencies": {
-    "@types/jest": "^29.5.14",
-    "@types/xml2js": "^0.4.14",
-    "axios-mock-adapter": "^2.1.0",
-    "jest": "^29.7.0",
-    "ts-jest": "^29.2.5",
-    "tsx": "^4.19.2",
-    "typescript": "^5.0.0"
-  }
-}
+{
+  "name": "@openhealth/oht-custom-parser-lib",
+  "version": "0.5.63",
+  "description": "Shared nodejs lib with with reusable functions",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "files": [
+    "/dist"
+  ],
+  "scripts": {
+    "test": "jest"
+  },
+  "keywords": [],
+  "author": "",
+  "license": "ISC",
+  "dependencies": {
+    "@google-cloud/pubsub": "^4.10.0",
+    "@google-cloud/storage": "^7.7.0",
+    "axios": "^1.13.2",
+    "bottleneck": "^2.19.5",
+    "csv-parse": "^6.2.1",
+    "dayjs": "^1.11.13",
+    "dotenv": "^16.4.5",
+    "jsonata": "^2.1.0",
+    "moment": "^2.30.1",
+    "mongodb": "^6.3.0",
+    "pino": "^8.19.0",
+    "pino-pretty": "^11.3.0",
+    "xml2js": "^0.6.2"
+  },
+  "devDependencies": {
+    "@types/jest": "^29.5.14",
+    "@types/xml2js": "^0.4.14",
+    "axios-mock-adapter": "^2.1.0",
+    "jest": "^29.7.0",
+    "ts-jest": "^29.2.5",
+    "tsx": "^4.19.2",
+    "typescript": "^5.0.0"
+  }
+}

package/readme.md

@@ -1,115 +1,115 @@
-# oht-custom-parser-lib
-
-`oht-custom-parser-lib` is a shared library designed for use across multiple Node.js cloud functions. It contains common MongoDB connectors and data utilities that can be reused to avoid code duplication and ensure consistency.
-
-## Table of Contents
-
-- [Installation](#installation)
-- [Usage](#usage)
-- [Development](#development)
-    - [Patch Versions](#patch-versions)
-    - [Publish to npm Registry](#publish-to-npm-registry)
-- [Using the Library in Cloud Functions](#using-the-library-in-cloud-functions)
-
-## Installation
-
-To install `oht-custom-parser-lib`, you can add it as a dependency in your project using npm:
-
-```bash
-npm install oht-custom-parser-lib
-```
-
-Or, if you want to install a specific version:
-
-```bash
-npm install oht-custom-parser-lib@<version>
-```
-
-## Usage
-
-After installing, you can import and use the library in your cloud functions:
-
-```javascript
-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
-
-When making changes to the `oht-custom-parser-lib`, you need to update the version number before publishing. Follow these steps:
-
-1. **Update the version number**: Use npm's version command to bump the version:
-    - **Patch** for bug fixes:
-      ```bash
-      npm version patch
-      ```
-    - **Minor** for new features:
-      ```bash
-      npm version minor
-      ```
-    - **Major** for breaking changes:
-      ```bash
-      npm version major
-      ```
-
-   This command will automatically update the version in the `package.json` and create a git tag.
-
-2. **Commit Changes**: Ensure your changes and the version bump are committed to the repository.
-
-### Publish to npm Registry
-
-After updating the version, you can publish the library to the npm registry:
-
-1. **Login to npm** (if you haven't already):
-   ```bash
-   npm login
-   ```
-
-2. **Publish the package**:
-   ```bash
-   npm publish
-   ```
-
-   If this is a private package, use:
-   ```bash
-   npm publish --access restricted
-   ```
-
-3. **Verify the publish**: You can check the package on [npmjs.com](https://www.npmjs.com/) to verify that the new version is available.
-
-## Using the Library in Cloud Functions
-
-To use `oht-custom-parser-lib` in your cloud functions:
-
-1. **Install the Library**: Add `oht-custom-parser-lib` as a dependency in the cloud function's `package.json`:
-
-   ```json
-   {
-     "dependencies": {
-       "oht-custom-parser-lib": "^1.0.0"
-     }
-   }
-   ```
-
-   Replace `^1.0.0` with the appropriate version as needed.
-
-2. **Install Dependencies**: Run `npm install` to install the library along with other dependencies.
-
-3. **Deploy Your Function**: Deploy your cloud function as usual, ensuring that the updated dependencies are included.
+# oht-custom-parser-lib
+
+`oht-custom-parser-lib` is a shared library designed for use across multiple Node.js cloud functions. It contains common MongoDB connectors and data utilities that can be reused to avoid code duplication and ensure consistency.
+
+## Table of Contents
+
+- [Installation](#installation)
+- [Usage](#usage)
+- [Development](#development)
+    - [Patch Versions](#patch-versions)
+    - [Publish to npm Registry](#publish-to-npm-registry)
+- [Using the Library in Cloud Functions](#using-the-library-in-cloud-functions)
+
+## Installation
+
+To install `oht-custom-parser-lib`, you can add it as a dependency in your project using npm:
+
+```bash
+npm install oht-custom-parser-lib
+```
+
+Or, if you want to install a specific version:
+
+```bash
+npm install oht-custom-parser-lib@<version>
+```
+
+## Usage
+
+After installing, you can import and use the library in your cloud functions:
+
+```javascript
+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
+
+When making changes to the `oht-custom-parser-lib`, you need to update the version number before publishing. Follow these steps:
+
+1. **Update the version number**: Use npm's version command to bump the version:
+    - **Patch** for bug fixes:
+      ```bash
+      npm version patch
+      ```
+    - **Minor** for new features:
+      ```bash
+      npm version minor
+      ```
+    - **Major** for breaking changes:
+      ```bash
+      npm version major
+      ```
+
+   This command will automatically update the version in the `package.json` and create a git tag.
+
+2. **Commit Changes**: Ensure your changes and the version bump are committed to the repository.
+
+### Publish to npm Registry
+
+After updating the version, you can publish the library to the npm registry:
+
+1. **Login to npm** (if you haven't already):
+   ```bash
+   npm login
+   ```
+
+2. **Publish the package**:
+   ```bash
+   npm publish
+   ```
+
+   If this is a private package, use:
+   ```bash
+   npm publish --access restricted
+   ```
+
+3. **Verify the publish**: You can check the package on [npmjs.com](https://www.npmjs.com/) to verify that the new version is available.
+
+## Using the Library in Cloud Functions
+
+To use `oht-custom-parser-lib` in your cloud functions:
+
+1. **Install the Library**: Add `oht-custom-parser-lib` as a dependency in the cloud function's `package.json`:
+
+   ```json
+   {
+     "dependencies": {
+       "oht-custom-parser-lib": "^1.0.0"
+     }
+   }
+   ```
+
+   Replace `^1.0.0` with the appropriate version as needed.
+
+2. **Install Dependencies**: Run `npm install` to install the library along with other dependencies.
+
+3. **Deploy Your Function**: Deploy your cloud function as usual, ensuring that the updated dependencies are included.