@openhealth/oht-custom-parser-lib 0.4.2 → 0.5.2

package/dist/index.d.ts

@@ -7,8 +7,10 @@ export { aggregateMessages, aggregateBiMessages, publishToTopic, generateBIMessa
 export { applyRules as applyTransformationRules, validateJsonataExpression as validateTransformationRuleExpression, } from './service/transformationRules.service';
 export { LabToOhtContract, LabToOhtMapper, UnknownMeasurementExtraction, ReferenceAsAnnotation, UnitExtraction, RangeExtraction, RangeExtractionResponse, ValueExtraction, unitSynonyms, ValueExtractionResponse, SynonymUnit, UnknownUnits, } 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 } from './types/error.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 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.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;
+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;
 // ### SERVICES ###
 var reportCreator_service_1 = require("./service/reportCreator.service");
 Object.defineProperty(exports, "postDataImportFileUploadToCore", { enumerable: true, get: function () { return reportCreator_service_1.postDataImportFileUploadToCore; } });
@@ -55,6 +55,24 @@ 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

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

@@ -15,6 +15,8 @@ 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

@@ -13,14 +13,13 @@ exports.postFileUploadSetStatus = postFileUploadSetStatus;
 exports.getPartnerTransformationRules = getPartnerTransformationRules;
 const moment_1 = __importDefault(require("moment/moment"));
 const apiUtils_1 = require("../util-ts/apiUtils");
-const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
+const processingLogger_service_1 = require("./processingLogger.service");
 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)
@@ -61,6 +60,8 @@ 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) {
@@ -188,7 +189,7 @@ async function postFileUploadSetStatus(payload, fileUploadId, filename, ohtCoreA
         formattedPayload.digitalization = digitalization;
     }
     const processingResponse = await (0, apiUtils_1.makeApiCallWithRetry)('post', ohtCoreFileUploadSetStatusUrl, formattedPayload, ohtCoreApiKey);
-    logger.info({ resp: processingResponse?.data }, `Resp: POST status: ${payload.status} /file-uploads/${fileUploadId}, filename: ${filename}`);
+    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

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

@@ -1 +1 @@
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+{"version":3,"file":"auxiliaryFunctions.service.js","sourceRoot":"","sources":["../../service/auxiliaryFunctions.service.ts"],"names":[],"mappings":";;;;;AAiTE,wDAAsB;AACtB,kCAAW;AACX,8CAAiB;AACjB,sCAAa;AACb,0CAAe;AACf,kEAA2B;AAC3B,0DAAuB;AACvB,sEAA6B;AAxT/B,2DAAmC;AAEnC,kDAAyD;AACzD,yEAA8D;AAC9D,kDAA+M;AAC/M,kDAA0B;AAC1B,uFAA+D;AAC/D,2DAAmC;AAInC,eAAK,CAAC,MAAM,CAAC,2BAAiB,CAAC,CAAC;AAChC,eAAK,CAAC,MAAM,CAAC,aAAG,CAAC,CAAC;AAElB,MAAM,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC;AAE9C,SAAS,aAAa,CAAC,YAAmB,EAAE,gBAAuB;IAC/D,IAAI,CAAC,gBAAgB,IAAI,CAAC,YAAY;QAAE,OAAO,IAAI,CAAC;IAEpD,2DAA2D;IAC3D,MAAM,OAAO,GAAG,IAAA,gBAAM,EAAC,YAAY,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;IACpD,MAAM,SAAS,GAAG,IAAA,gBAAM,EAAC,gBAAgB,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;IAE1D,OAAO,OAAO,CAAC,IAAI,CAAC,SAAS,EAAE,OAAO,CAAC,CAAC;AAC5C,CAAC;AAED,SAAS,iBAAiB,CAAC,YAAmB,EAAE,gBAAuB;IACnE,MAAM,UAAU,GAAG,aAAa,CAAC,YAAY,EAAE,gBAAgB,CAAC,CAAC;IAEjE,IAAI,UAAU,KAAK,IAAI,EAAE,CAAC;QACtB,OAAO,KAAK,CAAC;IACjB,CAAC;IAED,OAAO,UAAU,IAAI,EAAE,IAAI,UAAU,IAAI,GAAG,CAAC;AACjD,CAAC;AAED,SAAS,sBAAsB,CAAC,iBAA0B;IACtD,OAAO,iBAAiB,KAAK,SAAS,IAAI,iBAAiB,CAAC,MAAM,GAAG,CAAC,CAAC;AAC3E,CAAC;AAED,SAAS,WAAW,CAAC,aAAsB;IACvC,MAAM,MAAM,GAAG,aAAa,EAAE,WAAW,EAAE,CAAC;IAE5C,QAAQ,MAAM,EAAE,CAAC;QACb,KAAK,GAAG,CAAC;QACT,KAAK,WAAW,CAAC;QACjB,KAAK,MAAM;YACP,OAAO,EAAE,GAAG,EAAE,eAAG,CAAC,IAAI,EAAE,uBAAuB,EAAE,IAAI,EAAE,CAAC;QAC5D,KAAK,GAAG,CAAC;QACT,KAAK,UAAU,CAAC;QAChB,KAAK,QAAQ;YACT,OAAO,EAAE,GAAG,EAAE,eAAG,CAAC,MAAM,EAAE,uBAAuB,EAAE,IAAI,EAAE,CAAC;QAC9D;YACI,OAAO,EAAE,GAAG,EAAE,eAAG,CAAC,KAAK,EAAE,uBAAuB,EAAE,KAAK,EAAE,CAAC;IAClE,CAAC;AACL,CAAC;AAED;;;;;;;;;GASG;AACH,SAAS,eAAe,CAAC,SAAiB,EAAE,aAA6B,EAAE,cAAuB,IAAI,EAAE,cAAuB,KAAK,EAAE,WAAoB,KAAK;IAC3J,MAAM,cAAc,GAAG,UAAU,CAAC;IAClC,MAAM,cAAc,GAAG,SAAS,CAAC,WAAW,EAAE,CAAC;IAE/C,0DAA0D;IAC1D,IAAI,YAA0B,CAAC;IAE/B,kEAAkE;IAClE,IAAI,cAAc,KAAK,YAAY,IAAI,cAAc,KAAK,aAAa,EAAE,CAAC;QACtE,YAAY,GAAG,wBAAY,CAAC,eAAe,CAAC;IAChD,CAAC;SACI,IAAI,cAAc,KAAK,mBAAmB,IAAI,cAAc,KAAK,qBAAqB,IAAI,cAAc,KAAK,oBAAoB,EAAE,CAAC;QACrI,YAAY,GAAG,wBAAY,CAAC,2BAA2B,CAAC;IAC5D,CAAC;SACI,IAAI,cAAc,KAAK,YAAY,IAAI,cAAc,KAAK,aAAa,EAAE,CAAC;QAC3E,YAAY,GAAG,wBAAY,CAAC,mBAAmB,CAAC;IACpD,CAAC;SACI,IAAI,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,IAAI,cAAc,CAAC,QAAQ,CAAC,YAAY,CAAC,IAAI,cAAc,CAAC,QAAQ,CAAC,mBAAmB,CAAC,EAAE,CAAC;QACrI,YAAY,GAAG,wBAAY,CAAC,yBAAyB,CAAC;IAC1D,CAAC;SACI,IAAI,cAAc,CAAC,QAAQ,CAAC,YAAY,CAAC,IAAI,cAAc,CAAC,QAAQ,CAAC,cAAc,CAAC,IAAI,cAAc,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;QAC/H,YAAY,GAAG,wBAAY,CAAC,oBAAoB,CAAC;IACrD,CAAC;IACD,sEAAsE;IACtE,yDAAyD;SACpD,IAAI,cAAc,CAAC,QAAQ,CAAC,UAAU,CAAC;QACxC,CAAC,cAAc,CAAC,QAAQ,CAAC,KAAK,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,SAAS,CAAC,IAAI,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,CAAC;QACnH,YAAY,GAAG,wBAAY,CAAC,eAAe,CAAC;IAChD,CAAC;IACD,oDAAoD;SAC/C,IAAI,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC;QACpC,CAAC,cAAc,CAAC,QAAQ,CAAC,MAAM,CAAC,IAAI,cAAc,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC;QAC5E,YAAY,GAAG,wBAAY,CAAC,iBAAiB,CAAC;IAClD,CAAC;IACD,uBAAuB;SAClB,IAAI,cAAc,CAAC,QAAQ,CAAC,eAAe,CAAC;QACxC,cAAc,CAAC,QAAQ,CAAC,aAAa,CAAC;QACtC,cAAc,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;QAC1C,YAAY,GAAG,wBAAY,CAAC,iBAAiB,CAAC;IAClD,CAAC;IACD,0BAA0B;SACrB,IAAI,cAAc,CAAC,QAAQ,CAAC,UAAU,CAAC;QACnC,cAAc,CAAC,QAAQ,CAAC,sBAAsB,CAAC,EAAE,CAAC;QACvD,YAAY,GAAG,wBAAY,CAAC,sBAAsB,CAAC;IACvD,CAAC;IACD,2EAA2E;SACtE,IAAI,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE,CAAC;QAC5C,YAAY,GAAG,wBAAY,CAAC,qBAAqB,CAAC;IACtD,CAAC;IACD,iCAAiC;SAC5B,IAAI,cAAc,CAAC,QAAQ,CAAC,MAAM,CAAC;QAC/B,cAAc,CAAC,QAAQ,CAAC,YAAY,CAAC;QACrC,cAAc,CAAC,QAAQ,CAAC,cAAc,CAAC,EAAE,CAAC;QAC/C,YAAY,GAAG,wBAAY,CAAC,eAAe,CAAC;IAChD,CAAC;IACD,sCAAsC;SACjC,IAAI,cAAc,CAAC,QAAQ,CAAC,aAAa,CAAC;QACtC,cAAc,CAAC,QAAQ,CAAC,QAAQ,CAAC;QACjC,cAAc,CAAC,QAAQ,CAAC,eAAe,CAAC,EAAE,CAAC;QAChD,YAAY,GAAG,wBAAY,CAAC,kBAAkB,CAAC;IACnD,CAAC;IACD,mBAAmB;SACd,IAAI,cAAc,CAAC,QAAQ,CAAC,aAAa,CAAC;QACtC,cAAc,CAAC,QAAQ,CAAC,eAAe,CAAC;QACxC,cAAc,CAAC,QAAQ,CAAC,cAAc,CAAC,EAAE,CAAC;QAC/C,YAAY,GAAG,wBAAY,CAAC,gBAAgB,CAAC;IACjD,CAAC;IACD,yBAAyB;SACpB,IAAI,cAAc,CAAC,QAAQ,CAAC,cAAc,CAAC;QACvC,cAAc,CAAC,QAAQ,CAAC,iBAAiB,CAAC,EAAE,CAAC;QAClD,YAAY,GAAG,wBAAY,CAAC,sBAAsB,CAAC;IACvD,CAAC;IACD,+CAA+C;SAC1C,CAAC;QACF,YAAY,GAAG,wBAAY,CAAC,8BAA8B,CAAC;IAC/D,CAAC;IAED,aAAa,CAAC,IAAI,CAAC;QACf,WAAW,EAAE,EAAC,KAAK,EAAE,WAAW,EAAE,KAAK,EAAE,WAAW,EAAE,EAAE,EAAE,QAAQ,EAAC;QACnE,OAAO,EAAE,kBAAkB,SAAS,4BAA4B,YAAY,EAAE;KACjF,CAAC,CAAC;IAEH,OAAO,EAAE,cAAc,EAAE,YAAY,EAAE,CAAC;AAC5C,CAAC;AAOD,KAAK,UAAU,2BAA2B,CAAC,OAA2B,EAAE,aAAqB;IACzF,MAAM,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC;IAC9C,MAAM,UAAU,GAAG,GAAG,YAAY,wBAAwB,CAAA;IAE1D,MAAM,SAAS,GAAG;QACd,SAAS,EAAE,CAAC,GAAG,OAAO,CAAC;KAC1B,CAAA;IAED,MAAM,aAAa,GAAG,MAAM,IAAA,+BAAoB,EAC9C,MAAM,EACN,UAAU,EACV,SAAS,EACT,aAAa,CACd,CAAC;IAEF,OAAO,aAAa,EAAE,IAAI,EAAE,KAAK,CAAA;AACrC,CAAC;AAeD,KAAK,UAAU,uBAAuB,CACpC,OAIC,EACD,YAAoB,EACpB,QAAgB,EAChB,aAAqB;IAEnB,MAAM,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC;IAC9C,MAAM,6BAA6B,GAAG,GAAG,YAAY,+BAA+B,YAAY,EAAE,CAAC;IAEnG,8DAA8D;IAC9D,MAAM,gBAAgB,GAIlB;QACF,MAAM,EAAE,OAAO,CAAC,MAAM;QACtB,GAAG,CAAC,OAAO,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package/dist/service/fileUploadErrorHandler.service.d.ts

@@ -0,0 +1,26 @@
+import { RejectReason } from '../types/oht.types';
+/**
+ * Validation error for parser/report validation (rejectReason + optional field).
+ * Used by mapErrorToRejectReason and handleError.
+ */
+export declare class ValidationError extends Error {
+    rejectReason: RejectReason;
+    fieldName?: string;
+    constructor(message: string, rejectReason: RejectReason, fieldName?: string);
+}
+/**
+ * Whether to send Slack notification for this reject reason (not in silent list).
+ */
+export declare function shouldSendSlackNotification(rejectReason: RejectReason | undefined, silentRejectReasons: RejectReason[]): boolean;
+/**
+ * Formats reject reason with field name and context for better client messages.
+ */
+export declare function extractFormattedRejectReason(rejectReason: RejectReason, fieldName?: string, errorMessage?: string): string;
+/**
+ * Maps error to an appropriate RejectReason.
+ */
+export declare function mapErrorToRejectReason(error: Error, errorMessage: string, statusCode?: number, responseData?: any): RejectReason;
+/**
+ * Handles file-upload processing errors: updates status, notifies Slack, logs with error_code.
+ */
+export declare function handleError(error: Error, fileName: string, signedUploadId: string | undefined, apiKey: string, ohapiUrl: string, cloudEventId?: string, partnerName?: string, silentRejectReasons?: RejectReason[]): Promise<void>;

package/dist/service/fileUploadErrorHandler.service.js

@@ -0,0 +1,257 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ValidationError = void 0;
+exports.shouldSendSlackNotification = shouldSendSlackNotification;
+exports.extractFormattedRejectReason = extractFormattedRejectReason;
+exports.mapErrorToRejectReason = mapErrorToRejectReason;
+exports.handleError = handleError;
+const oht_types_1 = require("../types/oht.types");
+const slackMessages_service_1 = require("./slackMessages.service");
+const auxiliaryFunctions_service_1 = require("./auxiliaryFunctions.service");
+const apiUtils_1 = require("../util-ts/apiUtils");
+const processingLogger_service_1 = require("./processingLogger.service");
+const error_types_1 = require("../types/error.types");
+const dayjs_1 = __importDefault(require("dayjs"));
+const utc_1 = __importDefault(require("dayjs/plugin/utc"));
+dayjs_1.default.extend(utc_1.default);
+/**
+ * Validation error for parser/report validation (rejectReason + optional field).
+ * Used by mapErrorToRejectReason and handleError.
+ */
+class ValidationError extends Error {
+    constructor(message, rejectReason, fieldName) {
+        super(message);
+        this.name = 'ValidationError';
+        this.rejectReason = rejectReason;
+        this.fieldName = fieldName;
+    }
+}
+exports.ValidationError = ValidationError;
+/**
+ * Whether to send Slack notification for this reject reason (not in silent list).
+ */
+function shouldSendSlackNotification(rejectReason, silentRejectReasons) {
+    if (!rejectReason || silentRejectReasons.length === 0) {
+        return true;
+    }
+    return !silentRejectReasons.includes(rejectReason);
+}
+/**
+ * Formats reject reason with field name and context for better client messages.
+ */
+function extractFormattedRejectReason(rejectReason, fieldName, errorMessage) {
+    const baseRejectReason = String(rejectReason);
+    if (rejectReason === oht_types_1.RejectReason.INVALID_DATA_FORMAT && errorMessage) {
+        const formattedMatch = errorMessage.match(/Invalid Data Format \[expected: ([^\]]+), received: ([^\]]+)\]/);
+        if (formattedMatch) {
+            const expectedFormat = formattedMatch[1];
+            const receivedFormat = formattedMatch[2];
+            const fieldPart = fieldName ? ` for '${fieldName}'` : '';
+            return `Invalid Data Format${fieldPart} [expected: ${expectedFormat}, received: ${receivedFormat}]`;
+        }
+    }
+    if (fieldName) {
+        switch (rejectReason) {
+            case oht_types_1.RejectReason.INCOMPLETE_DATA:
+                if (fieldName === 'patient.id') {
+                    return `Patient external ID conflict: '${fieldName}' does not match user's external reference`;
+                }
+                return `${baseRejectReason} - Missing or invalid '${fieldName}'`;
+            case oht_types_1.RejectReason.MISSING_EXAM_DATE:
+                return `${baseRejectReason} - Missing '${fieldName}'`;
+            case oht_types_1.RejectReason.MISSING_LAB_ORDER_ID:
+                return `${baseRejectReason} - Missing '${fieldName}'`;
+            case oht_types_1.RejectReason.MISSING_EXTERNAL_PATIENT_ID:
+                return `${baseRejectReason} - Missing '${fieldName}'`;
+            case oht_types_1.RejectReason.MISSING_PATIENT_SEX:
+                return `${baseRejectReason} - Missing '${fieldName}'`;
+            case oht_types_1.RejectReason.INVALID_DATA_NO_BIOMARKER_DATA:
+                return `${baseRejectReason} - Invalid '${fieldName}'`;
+            default:
+                return `${baseRejectReason} - Issue with '${fieldName}'`;
+        }
+    }
+    return baseRejectReason;
+}
+function isPatientExternalIdConflict(statusCode, errorMessage, responseData) {
+    const lowerMessage = errorMessage.toLowerCase();
+    const is409Error = statusCode === 409 ||
+        lowerMessage.includes('status code 409') ||
+        lowerMessage.includes('409');
+    if (!is409Error)
+        return false;
+    const isExplicitlyNotPatientConflict = lowerMessage.includes('duplicate') &&
+        !lowerMessage.includes('patient') &&
+        !lowerMessage.includes('external');
+    return !isExplicitlyNotPatientConflict;
+}
+/**
+ * Maps error to an appropriate RejectReason.
+ */
+function mapErrorToRejectReason(error, errorMessage, statusCode, responseData) {
+    if (isPatientExternalIdConflict(statusCode, errorMessage, responseData)) {
+        return oht_types_1.RejectReason.INCOMPLETE_DATA;
+    }
+    const hasRejectReason = error instanceof ValidationError || 'rejectReason' in error;
+    if (hasRejectReason) {
+        const rejectReason = error.rejectReason;
+        if (rejectReason !== undefined && rejectReason !== null && rejectReason !== '') {
+            return rejectReason;
+        }
+    }
+    const lowerMessage = errorMessage.toLowerCase();
+    if (lowerMessage.includes('invalid data format') || lowerMessage.includes('invalid format') || lowerMessage.includes('iso 8601 format')) {
+        return oht_types_1.RejectReason.INVALID_DATA_FORMAT;
+    }
+    if (lowerMessage.includes('no biomarker') || lowerMessage.includes('invalid input') || lowerMessage.includes('no measurements')) {
+        return oht_types_1.RejectReason.INVALID_DATA_NO_BIOMARKER_DATA;
+    }
+    if (lowerMessage.includes('image quality') || lowerMessage.includes('low quality')) {
+        return oht_types_1.RejectReason.LOW_IMAGE_QUALITY;
+    }
+    if (lowerMessage.includes('underage') || (lowerMessage.includes('age') && lowerMessage.includes('invalid'))) {
+        return oht_types_1.RejectReason.UNDERAGE_PERSON;
+    }
+    if (lowerMessage.includes('language') || lowerMessage.includes('unsupported language')) {
+        return oht_types_1.RejectReason.LANGUAGE_NOT_SUPPORTED;
+    }
+    if (lowerMessage.includes('implausible') || lowerMessage.includes('invalid value')) {
+        return oht_types_1.RejectReason.IMPLAUSIBLE_DATA;
+    }
+    if (lowerMessage.includes('missing exam date') || lowerMessage.includes('no date') || lowerMessage.includes('date')) {
+        return oht_types_1.RejectReason.MISSING_EXAM_DATE;
+    }
+    if (lowerMessage.includes('missing unit') || lowerMessage.includes('incomplete') || lowerMessage.includes('missing data')) {
+        return oht_types_1.RejectReason.INCOMPLETE_DATA;
+    }
+    if (lowerMessage.includes('not an official') || lowerMessage.includes('not official')) {
+        return oht_types_1.RejectReason.NOT_AN_OFFICIAL_REPORT;
+    }
+    if (lowerMessage.includes('missing external patient') || lowerMessage.includes('missing patient id')) {
+        return oht_types_1.RejectReason.MISSING_EXTERNAL_PATIENT_ID;
+    }
+    if (lowerMessage.includes('unsupported') || lowerMessage.includes('not supported')) {
+        return oht_types_1.RejectReason.UNSUPPORTED_UPLOAD;
+    }
+    return oht_types_1.RejectReason.UNSUPPORTED_UPLOAD;
+}
+/**
+ * Handles file-upload processing errors: updates status, notifies Slack, logs with error_code.
+ */
+async function handleError(error, fileName, signedUploadId, apiKey, ohapiUrl, cloudEventId, partnerName, silentRejectReasons = []) {
+    const errorDetails = (0, apiUtils_1.parseErrorObj)(error);
+    const responseData = errorDetails.responseData;
+    const statusCode = errorDetails.status;
+    const axiosStatusCode = error.response?.status;
+    const finalStatusCode = statusCode || axiosStatusCode;
+    const errorMessage = responseData
+        ? `${error.message} - Response: ${JSON.stringify(responseData)}`
+        : error.message || 'Unknown error occurred';
+    const isIngestionError = finalStatusCode === 409 ||
+        errorMessage.toLowerCase().includes('ingestion') ||
+        errorDetails.config?.url?.includes('/ingestion');
+    const pipelineStep = isIngestionError
+        ? oht_types_1.PipelineStep.SENDING_RESULTS
+        : oht_types_1.PipelineStep.EXTRACTING_METADATA;
+    const errorType = error.constructor.name;
+    const rejectReason = mapErrorToRejectReason(error, errorMessage, finalStatusCode, responseData);
+    let fieldName;
+    if (error instanceof ValidationError) {
+        fieldName = error.fieldName;
+    }
+    else if (finalStatusCode === 409 && rejectReason === oht_types_1.RejectReason.INCOMPLETE_DATA) {
+        fieldName = 'patient.id';
+    }
+    const formattedRejectReason = extractFormattedRejectReason(rejectReason, fieldName, errorMessage);
+    if (!signedUploadId) {
+        const noUploadError = new Error((0, error_types_1.getErrorMessage)(error_types_1.ErrorCode.UPLOAD_MISSING_SIGNED_UPLOAD_ID));
+        processingLogger_service_1.processingLogger.addError(noUploadError, 'error_handling');
+        processingLogger_service_1.processingLogger.logError('Processing failed: Missing signed upload ID', noUploadError, {
+            error_code: error_types_1.ErrorCode.UPLOAD_MISSING_SIGNED_UPLOAD_ID,
+            cloud_event_id: cloudEventId,
+            partner_name: partnerName,
+        });
+        processingLogger_service_1.processingLogger.logEnd(false);
+        throw noUploadError;
+    }
+    try {
+        processingLogger_service_1.processingLogger.addError(error, 'error_handling');
+        const fileUploads = await (0, auxiliaryFunctions_service_1.queryFileUploadsWithFilters)([{ field: 'signedUploadId', search: signedUploadId }], apiKey);
+        const fileUploadId = fileUploads[0]?.id;
+        if (!fileUploadId) {
+            const notFoundError = new Error((0, error_types_1.getErrorMessage)(error_types_1.ErrorCode.UPLOAD_FILE_NOT_FOUND));
+            processingLogger_service_1.processingLogger.addError(notFoundError, 'error_handling');
+            processingLogger_service_1.processingLogger.logError('Processing failed: File upload not found', notFoundError, {
+                error_code: error_types_1.ErrorCode.UPLOAD_FILE_NOT_FOUND,
+                signed_upload_id: signedUploadId,
+                partner_name: partnerName,
+            });
+            processingLogger_service_1.processingLogger.logEnd(false);
+            return;
+        }
+        const fileUrl = `${ohapiUrl}/data-import/file-uploads/${fileUploadId}`;
+        const sendSlack = shouldSendSlackNotification(rejectReason, silentRejectReasons);
+        const fieldInfo = fieldName ? `\n*Field:* \`${fieldName}\`` : '';
+        const slackMessage = (0, slackMessages_service_1.getSlackFileIssueNotificationMessage)(`🚨 *AgnosticParser Processing Error*\n\n` +
+            `*Error:* ${errorType}: ${errorMessage}\n` +
+            `*Reject Reason:* ${formattedRejectReason}${fieldInfo}\n` +
+            `*File:* \`${fileName}\`\n` +
+            `*Partner:* ${partnerName || 'Unknown'}\n` +
+            `*File Upload ID:* \`${fileUploadId}\`\n` +
+            (cloudEventId ? `*Event ID:* \`${cloudEventId}\`\n` : ''), `AgnosticParser - ${partnerName || 'Unknown Partner'}`, fileUrl);
+        const [slackResult, statusResult] = await Promise.allSettled([
+            sendSlack ? (0, slackMessages_service_1.sendMessageToSlack)(slackMessage) : Promise.resolve(),
+            (0, auxiliaryFunctions_service_1.postFileUploadSetStatus)({
+                status: oht_types_1.DataImportFileUploadStatus.REJECTED,
+                digitalization: {
+                    status: oht_types_1.DigitizationStatus.ERROR,
+                    pipelineStep: pipelineStep,
+                    pipelineStepData: formattedRejectReason,
+                    timestamp: dayjs_1.default.utc().toISOString(),
+                },
+                ...(formattedRejectReason && { rejectReason: formattedRejectReason }),
+            }, fileUploadId, fileName, apiKey),
+        ]);
+        if (slackResult.status === 'rejected') {
+            processingLogger_service_1.processingLogger.logWarn('Slack notification failed', {
+                error_code: error_types_1.ErrorCode.UPLOAD_SLACK_FAILED,
+                file_upload_id: fileUploadId,
+                slack_error: (0, apiUtils_1.parseErrorObj)(slackResult.reason),
+            });
+        }
+        if (statusResult.status === 'rejected') {
+            const statusErrorDetails = (0, apiUtils_1.parseErrorObj)(statusResult.reason);
+            const statusResponseData = statusErrorDetails.responseData;
+            processingLogger_service_1.processingLogger.logError(`Failed to update file upload status: ${statusErrorDetails.message}${statusResponseData ? ` - ${JSON.stringify(statusResponseData)}` : ''}`, undefined, {
+                error_code: error_types_1.ErrorCode.UPLOAD_STATUS_UPDATE_FAILED,
+                file_upload_id: fileUploadId,
+                status_error: statusErrorDetails,
+            });
+        }
+        // Single "Processing failed" log from logEnd(false), with full error detail in processing_summary.errors (message, step, stack, error_type)
+        processingLogger_service_1.processingLogger.logEnd(false);
+    }
+    catch (handleErrorException) {
+        const exceptionMessage = handleErrorException instanceof Error
+            ? handleErrorException.message
+            : String(handleErrorException);
+        const handlingError = handleErrorException instanceof Error
+            ? handleErrorException
+            : new Error(String(handleErrorException));
+        processingLogger_service_1.processingLogger.addError(handlingError, 'error_handling_failure');
+        processingLogger_service_1.processingLogger.logError(`Error handling failed: ${exceptionMessage}`, handlingError, {
+            error_code: error_types_1.ErrorCode.UPLOAD_HANDLING_FAILED,
+            signed_upload_id: signedUploadId,
+            partner_name: partnerName,
+            original_error: errorMessage,
+            original_error_type: errorType,
+            handling_error: exceptionMessage,
+        });
+        processingLogger_service_1.processingLogger.logEnd(false);
+        throw error;
+    }
+}
+//# sourceMappingURL=fileUploadErrorHandler.service.js.map

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package/dist/service/ohtMeasurementsExtractor.service.js

@@ -14,12 +14,11 @@ exports.extractValueFromGreaterLowerThan = extractValueFromGreaterLowerThan;
 const crypto_1 = __importDefault(require("crypto"));
 const dataUtils_1 = require("../util-ts/dataUtils");
 const regexUtils_1 = require("../util-ts/regexUtils");
-const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
+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 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) {
@@ -297,7 +296,7 @@ function checkValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, value,
     const isPlausibleValue = value >= plausibleLowerValue && value <= plausibleUpperValue;
     // Log if the value is not plausible
     if (!isPlausibleValue) {
-        logger.warn({ labToOhtMapper, value, standardUnit, plausibleLowerValue, plausibleUpperValue, filename }, `Value "${value} ${standardUnit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${labToOhtMapper.ohtBmId}" | "${labToOhtMapper.labKey}", filename: ${filename}`);
+        processingLogger_service_1.processingLogger.logWarn(`Value "${value} ${standardUnit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${labToOhtMapper.ohtBmId}" | "${labToOhtMapper.labKey}", filename: ${filename}`, { labToOhtMapper, value, standardUnit, plausibleLowerValue, plausibleUpperValue, filename });
     }
     return isPlausibleValue;
 }
@@ -307,9 +306,9 @@ function checkValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, value,
  *
  * @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
+ * @param patientInfo - PatientInfo
+ * @param documentDate - Source DocumentDate
+ * @returns Promise<ApplyTransformationRulesResult[]> - Array of transformed exams
  */
 async function applyTransformationRulesToExams(exams, transformationRules, patientInfo, documentDate) {
     if (transformationRules.size === 0) {
@@ -331,7 +330,7 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
     const ohtReport = {
         exams: exams.map(e => e.ohtExam),
     };
-    logger.info({ examsCount: exams.length, chainsCount: transformationRules.size, filename }, 'Applying transformation rules to exams...');
+    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 = [];
@@ -349,7 +348,7 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
                 contextJson: reportContext,
             });
             if (result.errors.length > 0) {
-                logger.warn({ labKey, errors: result.errors, filename }, 'Errors applying transformation rule(s) for labKey.');
+                processingLogger_service_1.processingLogger.logWarn('Errors applying transformation rule(s) for labKey.', { labKey, errors: result.errors, filename });
                 applicationErrorMessages.push(`${labKey}: ${result.errors.map(e => `(rule ID ${e.ruleId}) ${e.error}`).join('; ')}`);
                 // Keep original exam when transformation fails
                 transformedExams.push(exam);
@@ -358,7 +357,7 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
                 if (result.appliedRules.length > 0) {
                     transformedLabKeysCount++;
                 }
-                logger.info({ labKey, appliedRules: result.appliedRules.length, filename }, 'Done applying transformation rule(s) for labKey.');
+                processingLogger_service_1.processingLogger.logInfo('Done applying transformation rule(s) for labKey.', { labKey, applied_rules: result.appliedRules.length, filename });
                 // Preserve the synthetic ID through transformation
                 transformedExams.push({
                     _syntheticId: exam._syntheticId,
@@ -368,19 +367,19 @@ async function applyTransformationRulesToExams(exams, transformationRules, patie
             }
         }
         catch (error) {
-            logger.error({ labKey, error, filename }, 'Failed to apply transformation rules for labKey.');
+            processingLogger_service_1.processingLogger.logError('Failed to apply transformation rules for labKey.', error instanceof Error ? error : undefined, { labKey, filename });
             applicationErrorMessages.push(`${labKey}: Unhandled error occurred.`);
             // Keep original exam when transformation throws
             transformedExams.push(exam);
         }
     }
-    logger.info({
+    processingLogger_service_1.processingLogger.logInfo('Done applying the transformation rules to exams.', {
         filename,
-        examsCount: exams.length,
-        chainsCount: transformationRules.size,
-        transformedLabKeysCount,
-        labKeysWithRulesCount,
-    }, 'Done applying the transformation rules to exams.');
+        exams_count: exams.length,
+        chains_count: transformationRules.size,
+        transformed_lab_keys_count: transformedLabKeysCount,
+        lab_keys_with_rules_count: labKeysWithRulesCount,
+    });
     return {
         transformedExams,
         applicationErrorMessages
@@ -414,7 +413,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
         transformedExamsResult = await applyTransformationRulesToExams(examsWithIds, transformationRules, labToOhtContract.patientInfo, labToOhtContract.documentDate);
     }
     catch (error) {
-        logger.error({ error, filename }, 'Unhandled error while applying transformation rules to exams.');
+        processingLogger_service_1.processingLogger.logError('Unhandled error while applying transformation rules to exams.', error instanceof Error ? error : undefined, { filename });
         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}`,
@@ -476,7 +475,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
         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)) {
-                logger.warn({ labToOhtMapper }, `Biomarker already in measurements array, should investigate, filename: ${filename}`);
+                processingLogger_service_1.processingLogger.logWarn(`Biomarker already in measurements array, should investigate, filename: ${filename}`, { labToOhtMapper });
                 labToOhtContract.errorMessages.push({
                     destination: { slack: false, notes: false, bi: true },
                     message: `Biomarkers Duplicated keys:[PLACEHOLDER]`,
@@ -503,7 +502,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
                 });
             }
             if (!isUnitParsedCorrectly) {
-                logger.warn({ labToOhtMapper }, `Unit not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
+                processingLogger_service_1.processingLogger.logWarn(`Unit not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`, { labToOhtMapper });
                 labToOhtContract.errorMessages.push({
                     destination: { slack: true, notes: true, bi: true },
                     message: `Unit not extracted correctly for:[PLACEHOLDER]`,
@@ -513,7 +512,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
             }
             let { valueType, alphanumericalValue, numberValue, valueComparator, isValueParsedCorrectly } = parseExamValue(examObj, labToOhtMapper.valueExtraction, ohtBiomarker);
             if (!isValueParsedCorrectly) {
-                logger.warn({ labToOhtMapper }, `Value not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
+                processingLogger_service_1.processingLogger.logWarn(`Value not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`, { labToOhtMapper });
                 labToOhtContract.errorMessages.push({
                     destination: { slack: true, notes: true, bi: true },
                     message: `Value not extracted correctly for:[PLACEHOLDER]`,
@@ -549,7 +548,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
             if (isValueParsedCorrectly && valueType === 'NUMERICAL') {
                 const isPlausibleValue = numberValue !== null && checkValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, numberValue, isUnitParsedCorrectly);
                 if (!isPlausibleValue) {
-                    logger.warn({ labToOhtMapper }, `Value [${numberValue} ${unit}] is not plausible for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
+                    processingLogger_service_1.processingLogger.logWarn(`Value [${numberValue} ${unit}] is not plausible for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`, { labToOhtMapper });
                     labToOhtContract.errorMessages.push({
                         destination: { slack: true, notes: true, bi: true },
                         message: `Value is not plausible for:[PLACEHOLDER]`,
@@ -567,7 +566,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
                 to = extractedRange.to ?? null;
                 isRangeParsedCorrectly = extractedRange.isRangeParsedCorrectly;
                 if (!isRangeParsedCorrectly) {
-                    logger.warn({ labToOhtMapper }, `Range not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
+                    processingLogger_service_1.processingLogger.logWarn(`Range not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`, { labToOhtMapper });
                     labToOhtContract.errorMessages.push({
                         destination: { slack: true, notes: true, bi: true },
                         message: `Range not extracted correctly for:[PLACEHOLDER]`,
@@ -624,7 +623,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
             measurements.push(measurement);
         }
         else {
-            logger.warn(`Created an ungroupedBiomarker for id: ${labToOhtMapper.labKey}, filename: ${filename}`);
+            processingLogger_service_1.processingLogger.logWarn(`Created an ungroupedBiomarker for id: ${labToOhtMapper.labKey}, filename: ${filename}`);
             labToOhtContract.errorMessages.push({
                 destination: { slack: false, notes: false, bi: true },
                 message: `Created ungroupedBiomarkers for:[PLACEHOLDER]`,