@openhealth/oht-custom-parser-lib 0.5.45 → 0.5.47

package/dist/index.d.ts

@@ -1,11 +1,11 @@
 export { postDataImportFileUploadToCore, postReportPreviewToCore } from './service/reportCreator.service';
-export { parseExternalPatientId, parseGender, isPatientAgeValid, handleRejection, queryFileUploadsWithFilters, postFileUploadSetStatus, DigitalizationUpdateFields } from './service/auxiliaryFunctions.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';
 export { getSlackFileIssueNotificationMessage, sendMessageToSlack } from './service/slackMessages.service';
 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, } from './types/custom-parser.types';
+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, OhtRange, OriginalExam, } from './types/oht.types';
 export { ErrorMessage, ErrorCode, ERROR_CATALOG, ERROR_MESSAGES, getErrorMessage, getRejectReason, } from './types/error.types';
 export { handleError, ValidationError, JSON_VALIDATION_ERROR_NAME, shouldSendSlackNotification, extractFormattedRejectReason, mapErrorToRejectReason, } from './service/fileUploadErrorHandler.service';

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.mapErrorToRejectReason = exports.extractFormattedRejectReason = 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.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = 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 = void 0;
+exports.shouldSendSlackNotification = exports.JSON_VALIDATION_ERROR_NAME = exports.ValidationError = exports.handleError = exports.getRejectReason = exports.getErrorMessage = exports.ERROR_MESSAGES = exports.ERROR_CATALOG = exports.ErrorCode = exports.RejectReason = exports.UploadType = exports.Sex = exports.DataImportFileUploadStatus = exports.BiomarkerValueType = exports.MeasurementValueComparator = exports.DigitizationStatus = exports.PipelineStep = exports.ReferenceRangeType = exports.BiomarkerCompatibility = exports.ManualCheck = exports.AcfBiomarkerGenericDisclaimerLogic = exports.AcfBiomarkerRangeAnnotationCheck = exports.unitSynonyms = exports.validateTransformationRuleExpression = exports.applyTransformationRules = exports.generateBIMessages = exports.publishToTopic = exports.aggregateBiMessages = exports.aggregateMessages = exports.sendMessageToSlack = exports.getSlackFileIssueNotificationMessage = exports.extractValueFromGreaterLowerThan = exports.extractUnit = exports.getRangeFromPositionAndRegex = exports.parseExamValue = exports.extractReferenceAnnotation = exports.extractReferenceRanges = exports.checkValueForPlausibleValues = exports.ohtMeasurementsExtractor = exports.ohtReportMeasurementsExtractor = exports.getPartnerTransformationRules = exports.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.getPatientAge = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.postReportPreviewToCore = exports.postDataImportFileUploadToCore = void 0;
+exports.mapToOhtReport = exports.fetchActiveMappingRules = exports.lisXmlToJson = exports.lisCsvToExamRows = exports.parseRange = exports.getMappedBiomarkersLatest = exports.getMappedBiomarkers = exports.getLowerThanPatterns = exports.getGreaterThanPatterns = exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = exports.applyFormat = exports.extractFromPath = exports.resolveUnitFromSynonyms = exports.fetchSynonymUnits = exports.processAppendedMappings = exports.isBiomarkerExternalNoVisualRange = exports.isBiomarkerValueNumerical = exports.extractValue = exports.parseErrorObj = exports.makeApiCallWithRetry = exports.runWithContextAsync = exports.runWithContext = exports.getRequestScopedFilename = exports.getRequestIdFromContext = exports.processingLogger = exports.mapErrorToRejectReason = exports.extractFormattedRejectReason = void 0;
 // ### SERVICES ###
 var reportCreator_service_1 = require("./service/reportCreator.service");
 Object.defineProperty(exports, "postDataImportFileUploadToCore", { enumerable: true, get: function () { return reportCreator_service_1.postDataImportFileUploadToCore; } });
@@ -13,9 +13,11 @@ 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; } });
 Object.defineProperty(exports, "isPatientAgeValid", { enumerable: true, get: function () { return auxiliaryFunctions_service_1.isPatientAgeValid; } });
+Object.defineProperty(exports, "getPatientAge", { enumerable: true, get: function () { return auxiliaryFunctions_service_1.getPatientAge; } });
 Object.defineProperty(exports, "handleRejection", { enumerable: true, get: function () { return auxiliaryFunctions_service_1.handleRejection; } });
 Object.defineProperty(exports, "queryFileUploadsWithFilters", { enumerable: true, get: function () { return auxiliaryFunctions_service_1.queryFileUploadsWithFilters; } });
 Object.defineProperty(exports, "postFileUploadSetStatus", { enumerable: true, get: function () { return auxiliaryFunctions_service_1.postFileUploadSetStatus; } });
+Object.defineProperty(exports, "getPartnerTransformationRules", { enumerable: true, get: function () { return auxiliaryFunctions_service_1.getPartnerTransformationRules; } });
 var ohtReportMeasurementsExtractor_service_1 = require("./service/ohtReportMeasurementsExtractor.service");
 Object.defineProperty(exports, "ohtReportMeasurementsExtractor", { enumerable: true, get: function () { return ohtReportMeasurementsExtractor_service_1.ohtReportMeasurementsExtractor; } });
 var ohtMeasurementsExtractor_service_1 = require("./service/ohtMeasurementsExtractor.service");

package/dist/index.js.map

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

@@ -46,5 +46,5 @@ declare function postFileUploadSetStatus(payload: {
     rejectReason?: string;
     isArchived?: boolean;
 }, fileUploadId: string, filename: string, ohtCoreApiKey: string): Promise<DataImportFileUpload>;
-declare function getPartnerTransformationRules(partnerId: string, labKeys: string[], ohtCoreApiKey: string): Promise<TransformationRulesChains>;
+declare function getPartnerTransformationRules(partnerId: string, labKeys: string[] | undefined, ohtCoreApiKey: string): Promise<TransformationRulesChains>;
 export { parseExternalPatientId, parseGender, isPatientAgeValid, getPatientAge, handleRejection, queryFileUploadsWithFilters, postFileUploadSetStatus, getPartnerTransformationRules, };

package/dist/service/auxiliaryFunctions.service.js

@@ -193,7 +193,9 @@ async function postFileUploadSetStatus(payload, fileUploadId, filename, ohtCoreA
     processingLogger_service_1.processingLogger.logInfo(`Resp: POST status: ${payload.status} /file-uploads/${fileUploadId}, filename: ${filename}`, { resp: processingResponse?.data });
     return processingResponse?.data;
 }
-// getPartnerTransformationRules fetches all the available partner transformation rules
+// getPartnerTransformationRules fetches all the available partner transformation rules.
+// When labKeys is undefined, all chains for the partner are returned (no labKey filter applied),
+// which includes ohtReport.* chains used to build the OhtReport from raw JSON.
 async function getPartnerTransformationRules(partnerId, labKeys, ohtCoreApiKey) {
     // Fetch every partner transformation rule
     const ohtCoreTransformationRulesUrl = `${OHT_CORE_URL}/v1/customparser/partners/${partnerId}/transformation-rules`;
@@ -212,16 +214,12 @@ async function getPartnerTransformationRules(partnerId, labKeys, ohtCoreApiKey)
             updatedAt: dayjs_1.default.utc(rule.updatedAt).toDate(),
         });
     }, new Map());
-    // Fetch the rule chains for the requested labKeys
+    // Fetch the rule chains — when labKeys is provided, filter by them; otherwise fetch all chains
     const ohtCoreTransformationRulesChainsUrl = `${OHT_CORE_URL}/v1/customparser/partners/${partnerId}/transformation-rules-chains/query`;
-    const rulesChainsResponse = await (0, apiUtils_1.makeApiCallWithRetry)('POST', ohtCoreTransformationRulesChainsUrl, {
-        filters: [
-            {
-                field: 'labKey',
-                multiSearch: labKeys,
-            }
-        ],
-    }, ohtCoreApiKey);
+    const chainsBody = labKeys !== undefined
+        ? { filters: [{ field: 'labKey', multiSearch: labKeys }] }
+        : {};
+    const rulesChainsResponse = await (0, apiUtils_1.makeApiCallWithRetry)('POST', ohtCoreTransformationRulesChainsUrl, chainsBody, ohtCoreApiKey);
     // Hydrate the rules chains with the actual rules
     return (rulesChainsResponse?.data?.items ?? [])
         .reduce((map, chainItem) => {

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

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

@@ -1,13 +1,6 @@
-import { UnknownUnits, TransformationRulesChains } from "../types/custom-parser.types";
+import { UnknownUnits } from "../types/custom-parser.types";
 import { Measurement, PatientInfo, UnknownMeasurement, Exam, UnmappedLabKey, PartnerCustomization } from "../types/oht.types";
 import { ErrorMessage } from "../types/error.types";
-type ExamWithSyntheticId = Exam & {
-    _syntheticId: string;
-};
-type ApplyTransformationRulesResult = {
-    transformedExams: ExamWithSyntheticId[];
-    applicationErrorMessages: string[];
-};
 /**
  * Extracts measurements from OHT report exams by processing each exam through biomarker mapping,
  * transformation rules, and value extraction.
@@ -28,7 +21,6 @@ type ApplyTransformationRulesResult = {
  * - Logs the number of mappings retrieved
  *
  * ### Step 3: Apply Transformation Rules
- * - Applies transformation rules to all exams using `applyTransformationRulesToExams()`
  * - Transformation rules can modify exam data before processing (e.g., normalize units, fix values)
  * - Creates a map of transformed exams for quick lookup during processing
  * - Collects and reports any transformation rule errors
@@ -127,7 +119,6 @@ type ApplyTransformationRulesResult = {
  *   - `unknownUnits`: Array of units that could not be resolved
  *   - `unmappedLabKeys`: Array of all labKeys (always created for every exam)
  *   - `isReportCorrectlyParsed`: Boolean indicating if all measurements were parsed correctly
- *   - `transformationRulesErrors`: Array of errors from transformation rules application
  *
  * ## Error Handling:
  * - All errors are added to the `errorMessages` array passed as parameter
@@ -147,21 +138,19 @@ type ApplyTransformationRulesResult = {
  * @param sourceFilename - Name of the source file being processed (for error reporting)
  * @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
  * @param partnerCustomization - `panelCustomisation` and `reportCustomisation` coming from `partnerConfig`.
- * @returns Promise resolving to extraction result with measurements, unknownMeasurements, unknownUnits, unmappedLabKeys, parsing status, and transformation errors
+ * @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, transformationRules: TransformationRulesChains, 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, errorMessages: ErrorMessage[], partnerCustomization?: PartnerCustomization): Promise<{
     measurements: Measurement[];
     unknownMeasurements: UnknownMeasurement[];
     unknownUnits: UnknownUnits[];
     unmappedLabKeys: UnmappedLabKey[];
     isReportCorrectlyParsed: boolean;
-    transformationRulesErrors: string[];
 }>;
-export { ApplyTransformationRulesResult, ohtReportMeasurementsExtractor, };
+export { ohtReportMeasurementsExtractor, };

package/dist/service/ohtReportMeasurementsExtractor.service.js

@@ -43,8 +43,6 @@ const extractionUtils_1 = require("../util-ts/extractionUtils");
 const processingLogger_service_1 = require("./processingLogger.service");
 const apiUtils_1 = require("../util-ts/apiUtils");
 const oht_types_1 = require("../types/oht.types");
-const transformationRules_service_1 = require("./transformationRules.service");
-const auxiliaryFunctions_service_1 = require("./auxiliaryFunctions.service");
 const path = __importStar(require("path"));
 const fs = __importStar(require("fs"));
 // Import version from package.json file
@@ -86,96 +84,6 @@ const OHT_CORE_URL = process.env.OHT_CORE_URL;
  * Current filename being processed (global state for error reporting)
  */
 let filename = '';
-/**
- * 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 with synthetic IDs
- * @param transformationRules - Mapping of labKey to transformation rule chains
- * @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) {
-        return {
-            transformedExams: exams,
-            applicationErrorMessages: []
-        };
-    }
-    const transformedExams = [];
-    // Prepare context for transformation rules
-    const reportContext = {
-        patient: {
-            sex: patientInfo.sex,
-            birthdate: patientInfo.birthdate,
-            age: (0, auxiliaryFunctions_service_1.getPatientAge)(documentDate, patientInfo.birthdate),
-        }
-    };
-    // Prepare the OHT exam data
-    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 });
-    let labKeysWithRulesCount = 0;
-    let transformedLabKeysCount = 0;
-    const applicationErrorMessages = [];
-    for (const exam of exams) {
-        const labKey = exam.ohtExam.labKey;
-        const rulesChain = transformationRules.get(labKey);
-        if (!rulesChain || rulesChain.length === 0) {
-            transformedExams.push(exam);
-            continue;
-        }
-        labKeysWithRulesCount++;
-        try {
-            const result = await (0, transformationRules_service_1.applyRules)(rulesChain, exam.ohtExam, {
-                ohtReportJson: ohtReport,
-                contextJson: reportContext,
-            });
-            if (result.errors.length > 0) {
-                processingLogger_service_1.processingLogger.addWarning('Errors applying transformation rule(s) for labKey.', 'apply_transformation_rules', {
-                    warningType: 'transformation_rule_errors',
-                    warningCategory: 'mapping',
-                    warningSeverity: 'critical',
-                    data: { labKey, errors: result.errors, filename },
-                });
-                applicationErrorMessages.push(`${labKey}: ${result.errors.map(e => `(rule ID ${e.ruleId}) ${e.error}`).join('; ')}`);
-                // Keep original exam when transformation fails
-                transformedExams.push(exam);
-            }
-            else {
-                if (result.appliedRules.length > 0) {
-                    transformedLabKeysCount++;
-                }
-                processingLogger_service_1.processingLogger.logInfo('Done applying transformation rule(s) for labKey.', { labKey, applied_rules: result.appliedRules.length, filename });
-                // Preserve the synthetic ID through transformation
-                transformedExams.push({
-                    _syntheticId: exam._syntheticId,
-                    ohtExam: result.data,
-                    originalExam: exam.originalExam
-                });
-            }
-        }
-        catch (error) {
-            processingLogger_service_1.processingLogger.logError('Failed to apply transformation rules for labKey.', error instanceof Error ? error : undefined, { labKey, filename });
-            applicationErrorMessages.push(`${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.', {
-        filename,
-        exams_count: exams.length,
-        chains_count: transformationRules.size,
-        transformed_lab_keys_count: transformedLabKeysCount,
-        lab_keys_with_rules_count: labKeysWithRulesCount,
-    });
-    return {
-        transformedExams,
-        applicationErrorMessages
-    };
-}
 /**
  * Extracts measurements from OHT report exams by processing each exam through biomarker mapping,
  * transformation rules, and value extraction.
@@ -196,7 +104,6 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
  * - Logs the number of mappings retrieved
  *
  * ### Step 3: Apply Transformation Rules
- * - Applies transformation rules to all exams using `applyTransformationRulesToExams()`
  * - Transformation rules can modify exam data before processing (e.g., normalize units, fix values)
  * - Creates a map of transformed exams for quick lookup during processing
  * - Collects and reports any transformation rule errors
@@ -295,7 +202,6 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
  *   - `unknownUnits`: Array of units that could not be resolved
  *   - `unmappedLabKeys`: Array of all labKeys (always created for every exam)
  *   - `isReportCorrectlyParsed`: Boolean indicating if all measurements were parsed correctly
- *   - `transformationRulesErrors`: Array of errors from transformation rules application
  *
  * ## Error Handling:
  * - All errors are added to the `errorMessages` array passed as parameter
@@ -315,23 +221,21 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
  * @param sourceFilename - Name of the source file being processed (for error reporting)
  * @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
  * @param partnerCustomization - `panelCustomisation` and `reportCustomisation` coming from `partnerConfig`.
- * @returns Promise resolving to extraction result with measurements, unknownMeasurements, unknownUnits, unmappedLabKeys, parsing status, and transformation errors
+ * @returns Promise resolving to extraction result with measurements, unknownMeasurements, unknownUnits, unmappedLabKeys, and parsing status
  */
-async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFilename, patientInfo, documentDate, transformationRules, allowMultiMeasurementsPerBiomarker, ohtCoreApiKey, partnerId, errorMessages, partnerCustomization) {
+async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFilename, patientInfo, documentDate, allowMultiMeasurementsPerBiomarker, ohtCoreApiKey, partnerId, errorMessages, partnerCustomization) {
     filename = sourceFilename;
     const measurements = [];
     const unknownMeasurements = [];
     const unknownUnits = [];
     const unmappedLabKeys = [];
     let isReportCorrectlyParsed = true;
-    let transformationRulesErrors = [];
     // Check if we have exams
     const labKeys = exams.map(e => e.ohtExam.labKey);
     if (labKeys.length === 0) {
@@ -347,7 +251,6 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             unknownUnits,
             unmappedLabKeys,
             isReportCorrectlyParsed: false,
-            transformationRulesErrors,
         };
     }
     processingLogger_service_1.processingLogger.logInfo(`Processing lab file with ${labKeys.length} keys, filename: ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}`);
@@ -389,34 +292,13 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
     else {
         processingLogger_service_1.processingLogger.logInfo(`No biomarker mappings found in backend for partner: ${partnerId}`);
     }
-    // Assign UUIDs to exams for tracking through transformation.
-    // This enables support for duplicate labKeys (double-hits).
+    // Assign UUIDs to exams for tracking through duplicate-labKey (double-hit) support.
     const examsWithIds = exams.map((exam) => ({
         ...exam,
         _syntheticId: crypto_1.default.randomUUID(),
     }));
-    // Apply transformation rules to all exams
-    let transformedExamsResult = { transformedExams: [], applicationErrorMessages: [] };
-    try {
-        transformedExamsResult = await applyTransformationRulesToExams(examsWithIds, transformationRules, patientInfo, documentDate);
-    }
-    catch (error) {
-        processingLogger_service_1.processingLogger.logError('Unhandled error while applying transformation rules to exams.', error instanceof Error ? error : undefined, { filename });
-        errorMessages.push({
-            destination: { slack: true, notes: true, bi: false },
-            message: `Failed applying the transformation rules for filename ${(0, processingLogger_service_1.getRequestScopedFilename)(filename)}. ${error instanceof Error ? error.message : error}`,
-        });
-    }
-    if (transformedExamsResult.applicationErrorMessages.length > 0) {
-        transformationRulesErrors = transformedExamsResult.applicationErrorMessages;
-        errorMessages.push({
-            destination: { slack: false, notes: true, bi: false },
-            message: `Failed applying some transformation rules:\n${transformedExamsResult.applicationErrorMessages.map((e) => `  - ${e}`).join("\n\n")}`,
-        });
-    }
-    const transformedExams = transformedExamsResult.transformedExams;
     // Use synthetic UUID as key to support duplicate labKeys (double-hits)
-    const transformedExamsMap = new Map(transformedExams.map(exam => [exam._syntheticId, exam]));
+    const transformedExamsMap = new Map(examsWithIds.map(exam => [exam._syntheticId, exam]));
     // Collect all possible OHT biomarker IDs from mapped biomarkers
     const allPossibleOHTBmIds = [];
     for (const exam of exams) {
@@ -681,7 +563,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             }
             let extractedAnnotation;
             // TODO: always extract annotation? or only if annotationConfig.enabled is true?
-            extractedAnnotation = (0, extractionUtils_1.ohtReportExtractReferenceAnnotation)(annotationConfig, transformedExamObj, patientInfo, documentDate, transformedExams, filename);
+            extractedAnnotation = (0, extractionUtils_1.ohtReportExtractReferenceAnnotation)(annotationConfig, transformedExamObj, patientInfo, documentDate, examsWithIds, filename);
             // Use material and method directly from ohtExam
             const material = transformedExamObj?.material ?? '';
             const method = transformedExamObj?.method ?? '';
@@ -782,7 +664,6 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
         unknownUnits,
         unmappedLabKeys,
         isReportCorrectlyParsed,
-        transformationRulesErrors,
     };
 }
 //# sourceMappingURL=ohtReportMeasurementsExtractor.service.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.5.45",
+  "version": "0.5.47",
   "description": "Shared nodejs lib with with reusable functions",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",