@openhealth/oht-custom-parser-lib 0.5.55 → 0.5.57

package/dist/index.d.ts

@@ -7,10 +7,11 @@ export { aggregateMessages, aggregateBiMessages, publishToTopic, generateBIMessa
 export { applyRules as applyTransformationRules, validateJsonataExpression as validateTransformationRuleExpression, } from './service/transformationRules.service';
 export { LabToOhtContract, LabToOhtMapper, UnknownMeasurementExtraction, ReferenceAsAnnotation, UnitExtraction, RangeExtraction, RangeExtractionResponse, ValueExtraction, unitSynonyms, ValueExtractionResponse, SynonymUnit, UnknownUnits, TransformationRulesChains, } from './types/custom-parser.types';
 export { AcfBiomarkerRangeAnnotationCheck, AcfBiomarkerGenericDisclaimerLogic, ManualCheck, BiomarkerCompatibility, ReferenceRangeType, AcfReferenceRange, VisualRange, NameAlias, AlternativeUnit, BiomarkerAcf, Biomarker, PipelineStep, DigitizationStatus, MeasurementValueComparator, BiomarkerValueType, DataImportFileUploadStatus, Sex, Digitization, PatientInfo, UnknownMeasurement, UnmappedLabKey, Measurement, DataImportFileUpload, MessagePayload, SignedUpload, ReportStyleConfig, LanguageCode, BiomarkerCustomisation, PartnerCustomPanel, ReportDisplaySettings, ReportCustomisation, OHTPartner, UploadType, PartnerCustomization, RejectReason, AnnotationLabKey, ExtractionPath, AnnotationConfig, OhtReport, OhtMetadata, OhtPatient, Exam, OhtExam, ExamKind, OhtRange, OriginalExam, } from './types/oht.types';
-export { ErrorMessage, ErrorCode, ERROR_CATALOG, ERROR_MESSAGES, getErrorMessage, getRejectReason, } from './types/error.types';
+export { ErrorMessage, ErrorCode, ERROR_CATALOG, ERROR_MESSAGES, getErrorMessage, getRejectReason, ParsingErrorType, ParsingErrorSeverity, PARSING_ERROR_CATALOG, LocalParsingError, ErrorProfilePayload, RecordParsingErrorDetails, } from './types/error.types';
 export { handleError, ValidationError, JSON_VALIDATION_ERROR_NAME, shouldSendSlackNotification, extractFormattedRejectReason, mapErrorToRejectReason, } from './service/fileUploadErrorHandler.service';
 export type { TransformationRule, TransformationContext, ApplyRulesResult as TransformationApplyRulesResult, ApplyRulesOptions as TransformationApplyRulesOptions, ValidationResult as TransformationValidationResult, } from './types/transformationRules.types';
-export { processingLogger, ProcessingContext, StageDuration, getRequestIdFromContext, getRequestScopedFilename, runWithContext, runWithContextAsync, } from './service/processingLogger.service';
+export { processingLogger, ProcessingContext, StageDuration, getRequestIdFromContext, getCurrentRequestId, getRequestScopedFilename, runWithContext, runWithContextAsync, } from './service/processingLogger.service';
+export { parsingErrorService, initParsingErrorRequestState, clearParsingErrorRequestState, } from './service/parsingErrorService.service';
 export { makeApiCallWithRetry, parseErrorObj } from './util-ts/apiUtils';
 export { extractValue, isBiomarkerValueNumerical, isBiomarkerExternalNoVisualRange, processAppendedMappings, fetchSynonymUnits, resolveUnitFromSynonyms, extractFromPath, applyFormat } from './util-ts/dataUtils';
 export { readFileFromBucket, uploadFileBufferToGCS } from './util-ts/googleStorageUtils';

package/dist/index.js

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.shouldSendSlackNotification = exports.JSON_VALIDATION_ERROR_NAME = exports.ValidationError = exports.handleError = exports.getRejectReason = exports.getErrorMessage = exports.ERROR_MESSAGES = exports.ERROR_CATALOG = exports.ErrorCode = exports.RejectReason = exports.UploadType = exports.Sex = exports.DataImportFileUploadStatus = exports.BiomarkerValueType = exports.MeasurementValueComparator = exports.DigitizationStatus = exports.PipelineStep = exports.ReferenceRangeType = exports.BiomarkerCompatibility = exports.ManualCheck = exports.AcfBiomarkerGenericDisclaimerLogic = exports.AcfBiomarkerRangeAnnotationCheck = exports.unitSynonyms = exports.validateTransformationRuleExpression = exports.applyTransformationRules = exports.generateBIMessages = exports.publishToTopic = exports.aggregateBiMessages = exports.aggregateMessages = exports.sendMessageToSlack = exports.getSlackFileIssueNotificationMessage = exports.extractValueFromGreaterLowerThan = exports.extractUnit = exports.getRangeFromPositionAndRegex = exports.parseExamValue = exports.extractReferenceAnnotation = exports.extractReferenceRanges = exports.checkValueForPlausibleValues = exports.ohtMeasurementsExtractor = exports.ohtReportMeasurementsExtractor = exports.getPartnerTransformationRules = exports.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.getPatientAge = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.postReportPreviewToCore = exports.postDataImportFileUploadToCore = void 0;
-exports.mapToOhtReport = exports.fetchActiveMappingRules = exports.lisXmlToJson = exports.lisCsvToExamRows = exports.parseRange = exports.getMappedBiomarkersLatest = exports.getMappedBiomarkers = exports.getLowerThanPatterns = exports.getGreaterThanPatterns = exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = exports.applyFormat = exports.extractFromPath = exports.resolveUnitFromSynonyms = exports.fetchSynonymUnits = exports.processAppendedMappings = exports.isBiomarkerExternalNoVisualRange = exports.isBiomarkerValueNumerical = exports.extractValue = exports.parseErrorObj = exports.makeApiCallWithRetry = exports.runWithContextAsync = exports.runWithContext = exports.getRequestScopedFilename = exports.getRequestIdFromContext = exports.processingLogger = exports.mapErrorToRejectReason = exports.extractFormattedRejectReason = void 0;
+exports.ValidationError = exports.handleError = exports.PARSING_ERROR_CATALOG = exports.ParsingErrorType = exports.getRejectReason = exports.getErrorMessage = exports.ERROR_MESSAGES = exports.ERROR_CATALOG = exports.ErrorCode = exports.RejectReason = exports.UploadType = exports.Sex = exports.DataImportFileUploadStatus = exports.BiomarkerValueType = exports.MeasurementValueComparator = exports.DigitizationStatus = exports.PipelineStep = exports.ReferenceRangeType = exports.BiomarkerCompatibility = exports.ManualCheck = exports.AcfBiomarkerGenericDisclaimerLogic = exports.AcfBiomarkerRangeAnnotationCheck = exports.unitSynonyms = exports.validateTransformationRuleExpression = exports.applyTransformationRules = exports.generateBIMessages = exports.publishToTopic = exports.aggregateBiMessages = exports.aggregateMessages = exports.sendMessageToSlack = exports.getSlackFileIssueNotificationMessage = exports.extractValueFromGreaterLowerThan = exports.extractUnit = exports.getRangeFromPositionAndRegex = exports.parseExamValue = exports.extractReferenceAnnotation = exports.extractReferenceRanges = exports.checkValueForPlausibleValues = exports.ohtMeasurementsExtractor = exports.ohtReportMeasurementsExtractor = exports.getPartnerTransformationRules = exports.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.getPatientAge = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.postReportPreviewToCore = exports.postDataImportFileUploadToCore = void 0;
+exports.mapToOhtReport = exports.fetchActiveMappingRules = exports.lisXmlToJson = exports.lisCsvToExamRows = exports.parseRange = exports.getMappedBiomarkersLatest = exports.getMappedBiomarkers = exports.getLowerThanPatterns = exports.getGreaterThanPatterns = exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = exports.applyFormat = exports.extractFromPath = exports.resolveUnitFromSynonyms = exports.fetchSynonymUnits = exports.processAppendedMappings = exports.isBiomarkerExternalNoVisualRange = exports.isBiomarkerValueNumerical = exports.extractValue = exports.parseErrorObj = exports.makeApiCallWithRetry = exports.clearParsingErrorRequestState = exports.initParsingErrorRequestState = exports.parsingErrorService = exports.runWithContextAsync = exports.runWithContext = exports.getRequestScopedFilename = exports.getCurrentRequestId = exports.getRequestIdFromContext = exports.processingLogger = exports.mapErrorToRejectReason = exports.extractFormattedRejectReason = exports.shouldSendSlackNotification = exports.JSON_VALIDATION_ERROR_NAME = void 0;
 // ### SERVICES ###
 var reportCreator_service_1 = require("./service/reportCreator.service");
 Object.defineProperty(exports, "postDataImportFileUploadToCore", { enumerable: true, get: function () { return reportCreator_service_1.postDataImportFileUploadToCore; } });
@@ -63,6 +63,8 @@ Object.defineProperty(exports, "ERROR_CATALOG", { enumerable: true, get: functio
 Object.defineProperty(exports, "ERROR_MESSAGES", { enumerable: true, get: function () { return error_types_1.ERROR_MESSAGES; } });
 Object.defineProperty(exports, "getErrorMessage", { enumerable: true, get: function () { return error_types_1.getErrorMessage; } });
 Object.defineProperty(exports, "getRejectReason", { enumerable: true, get: function () { return error_types_1.getRejectReason; } });
+Object.defineProperty(exports, "ParsingErrorType", { enumerable: true, get: function () { return error_types_1.ParsingErrorType; } });
+Object.defineProperty(exports, "PARSING_ERROR_CATALOG", { enumerable: true, get: function () { return error_types_1.PARSING_ERROR_CATALOG; } });
 var fileUploadErrorHandler_service_1 = require("./service/fileUploadErrorHandler.service");
 Object.defineProperty(exports, "handleError", { enumerable: true, get: function () { return fileUploadErrorHandler_service_1.handleError; } });
 Object.defineProperty(exports, "ValidationError", { enumerable: true, get: function () { return fileUploadErrorHandler_service_1.ValidationError; } });
@@ -74,9 +76,14 @@ Object.defineProperty(exports, "mapErrorToRejectReason", { enumerable: true, get
 var processingLogger_service_1 = require("./service/processingLogger.service");
 Object.defineProperty(exports, "processingLogger", { enumerable: true, get: function () { return processingLogger_service_1.processingLogger; } });
 Object.defineProperty(exports, "getRequestIdFromContext", { enumerable: true, get: function () { return processingLogger_service_1.getRequestIdFromContext; } });
+Object.defineProperty(exports, "getCurrentRequestId", { enumerable: true, get: function () { return processingLogger_service_1.getCurrentRequestId; } });
 Object.defineProperty(exports, "getRequestScopedFilename", { enumerable: true, get: function () { return processingLogger_service_1.getRequestScopedFilename; } });
 Object.defineProperty(exports, "runWithContext", { enumerable: true, get: function () { return processingLogger_service_1.runWithContext; } });
 Object.defineProperty(exports, "runWithContextAsync", { enumerable: true, get: function () { return processingLogger_service_1.runWithContextAsync; } });
+var parsingErrorService_service_1 = require("./service/parsingErrorService.service");
+Object.defineProperty(exports, "parsingErrorService", { enumerable: true, get: function () { return parsingErrorService_service_1.parsingErrorService; } });
+Object.defineProperty(exports, "initParsingErrorRequestState", { enumerable: true, get: function () { return parsingErrorService_service_1.initParsingErrorRequestState; } });
+Object.defineProperty(exports, "clearParsingErrorRequestState", { enumerable: true, get: function () { return parsingErrorService_service_1.clearParsingErrorRequestState; } });
 // ### UTIL-TS ###
 var apiUtils_1 = require("./util-ts/apiUtils");
 Object.defineProperty(exports, "makeApiCallWithRetry", { enumerable: true, get: function () { return apiUtils_1.makeApiCallWithRetry; } });

package/dist/index.js.map

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

@@ -1,4 +1,3 @@
-import { ErrorMessage } from '../types/error.types';
 import { DataImportFileUpload, DataImportFileUploadStatus, DigitizationStatus, PipelineStep, RejectReason, Sex } from "../types/oht.types";
 import dayjs from 'dayjs';
 import { TransformationRulesChains } from "../types/custom-parser.types";
@@ -12,14 +11,8 @@ declare function parseGender(patientGender?: string): {
 /**
  * Maps parse type and error context to appropriate rejection reason
  * Uses a priority-based approach to ensure the most specific reason is selected
- *
- * @param parseType - The type of parsing that failed (e.g., "age", "exam date", "units")
- * @param errorMessages - Array to append error messages to
- * @param notifySlack - notifySlack
- * @param notifyNotes - notifyNotes
- * @returns Object containing rejectedStatus and rejectReason
  */
-declare function handleRejection(parseType: string, errorMessages: ErrorMessage[], notifySlack?: boolean, notifyNotes?: boolean, notifyBi?: boolean): {
+declare function handleRejection(parseType: string, notifySlack?: boolean, notifyNotes?: boolean, notifyBi?: boolean): {
     rejectedStatus: string;
     rejectReason: RejectReason.INVALID_DATA_NO_BIOMARKER_DATA | RejectReason.LOW_IMAGE_QUALITY | RejectReason.NO_IN_PANEL_BIOMARKER | RejectReason.UNDERAGE_PERSON | RejectReason.LANGUAGE_NOT_SUPPORTED | RejectReason.IMPLAUSIBLE_DATA | RejectReason.MISSING_EXAM_DATE | RejectReason.MISSING_LAB_ORDER_ID | RejectReason.MISSING_EXTERNAL_PATIENT_ID | RejectReason.MISSING_PATIENT_SEX | RejectReason.MISSING_PATIENT_BIRTHDATE | RejectReason.UNSUPPORTED_UPLOAD | RejectReason.INCOMPLETE_DATA | RejectReason.NOT_AN_OFFICIAL_REPORT;
 };

package/dist/service/auxiliaryFunctions.service.js

@@ -14,6 +14,8 @@ exports.getPartnerTransformationRules = getPartnerTransformationRules;
 const moment_1 = __importDefault(require("moment/moment"));
 const apiUtils_1 = require("../util-ts/apiUtils");
 const processingLogger_service_1 = require("./processingLogger.service");
+const parsingErrorService_service_1 = require("./parsingErrorService.service");
+const error_types_1 = require("../types/error.types");
 const oht_types_1 = require("../types/oht.types");
 const dayjs_1 = __importDefault(require("dayjs"));
 const customParseFormat_1 = __importDefault(require("dayjs/plugin/customParseFormat"));
@@ -57,14 +59,8 @@ function parseGender(patientGender) {
 /**
  * Maps parse type and error context to appropriate rejection reason
  * Uses a priority-based approach to ensure the most specific reason is selected
- *
- * @param parseType - The type of parsing that failed (e.g., "age", "exam date", "units")
- * @param errorMessages - Array to append error messages to
- * @param notifySlack - notifySlack
- * @param notifyNotes - notifyNotes
- * @returns Object containing rejectedStatus and rejectReason
  */
-function handleRejection(parseType, errorMessages, notifySlack = true, notifyNotes = false, notifyBi = false) {
+function handleRejection(parseType, notifySlack = true, notifyNotes = false, notifyBi = false) {
     const rejectedStatus = 'REJECTED';
     const lowerParseType = parseType.toLowerCase();
     // Priority-based mapping: check most specific cases first
@@ -138,12 +134,45 @@ function handleRejection(parseType, errorMessages, notifySlack = true, notifyNot
     else {
         rejectReason = oht_types_1.RejectReason.INVALID_DATA_NO_BIOMARKER_DATA;
     }
-    errorMessages.push({
-        destination: { slack: notifySlack, notes: notifyNotes, bi: notifyBi },
-        message: `File rejected: ${parseType} parsing failed. Reason: ${rejectReason}`,
-    });
+    const errorType = resolveRejectionParsingErrorType(lowerParseType, rejectReason);
+    const messageSuffix = errorType === error_types_1.ParsingErrorType.FATAL_VALIDATION
+        ? `File rejected: ${parseType} parsing failed. Reason: ${rejectReason}`
+        : String(rejectReason);
+    parsingErrorService_service_1.parsingErrorService.record(errorType, {
+        messageSuffix,
+        rejectReason,
+    }, { notifySlack, notifyNotes, notifyBi });
     return { rejectedStatus, rejectReason };
 }
+function resolveRejectionParsingErrorType(lowerParseType, rejectReason) {
+    if (lowerParseType === 'patientage' || lowerParseType === 'patient age') {
+        return error_types_1.ParsingErrorType.REJECTED_UNDERAGE_PATIENT;
+    }
+    if (lowerParseType === 'patientexternalid' ||
+        lowerParseType === 'patient external id' ||
+        lowerParseType === 'patient externalid') {
+        return error_types_1.ParsingErrorType.REJECTED_MISSING_PATIENT_ID;
+    }
+    if (lowerParseType === 'patientsex' || lowerParseType === 'patient sex') {
+        return error_types_1.ParsingErrorType.REJECTED_MISSING_PATIENT_SEX;
+    }
+    if (lowerParseType.includes('biomarker')) {
+        return error_types_1.ParsingErrorType.REJECTED_NO_BIOMARKERS;
+    }
+    if (rejectReason === oht_types_1.RejectReason.UNDERAGE_PERSON) {
+        return error_types_1.ParsingErrorType.REJECTED_UNDERAGE_PATIENT;
+    }
+    if (rejectReason === oht_types_1.RejectReason.MISSING_EXTERNAL_PATIENT_ID) {
+        return error_types_1.ParsingErrorType.REJECTED_MISSING_PATIENT_ID;
+    }
+    if (rejectReason === oht_types_1.RejectReason.MISSING_PATIENT_SEX) {
+        return error_types_1.ParsingErrorType.REJECTED_MISSING_PATIENT_SEX;
+    }
+    if (rejectReason === oht_types_1.RejectReason.NO_IN_PANEL_BIOMARKER) {
+        return error_types_1.ParsingErrorType.REJECTED_NO_BIOMARKERS;
+    }
+    return error_types_1.ParsingErrorType.FATAL_VALIDATION;
+}
 async function queryFileUploadsWithFilters(filters, ohtCoreApiKey) {
     const OHT_CORE_URL = process.env.OHT_CORE_URL;
     const ohtCoreUrl = `${OHT_CORE_URL}/v1/file-uploads/query`;

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

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

@@ -0,0 +1,59 @@
+import { LabToOhtContract, LabToOhtMapper, RangeExtractionResponse, SynonymUnit, UnknownUnits, TransformationRulesChains } from "../types/custom-parser.types";
+import { Biomarker, BiomarkerValueType, Measurement, MeasurementValueComparator, PatientInfo, UnknownMeasurement, Exam } from "../types/oht.types";
+/**
+ * Extracts unit from rawData (OhtExam object)
+ * @param rawData - OhtExam object (not a JSON string)
+ * @param ohtBiomarker - Biomarker information
+ * @param synonymUnits - Synonym units for unit resolution
+ * @param partnerId - Partner ID for synonym resolution
+ */
+declare function agnosticExtractUnit(rawData: any, ohtBiomarker: Biomarker, synonymUnits?: SynonymUnit[] | null, partnerId?: string | null | undefined): {
+    unit: string;
+    isUnitParsedCorrectly: boolean;
+    originalUnit: string;
+    isArbitraryUnit: boolean;
+    unknownUnit: string;
+};
+/**
+ * Extracts reference annotation from rawExam (OhtExam object)
+ * @param labToOhtMapper - Lab to OHT mapper configuration
+ * @param rawExam - OhtExam object (not a JSON string)
+ * @param patientInfo - Patient information
+ * @param documentDate - Document date
+ * @param exams - Array of exams for appended mappings
+ */
+declare function agnosticExtractReferenceAnnotation(labToOhtMapper: LabToOhtMapper, rawExam: any, patientInfo: PatientInfo, documentDate?: Date, exams?: Exam[]): string;
+/**
+ * Extracts reference ranges from rawData (OhtExam object)
+ * Always uses parseRange function from extractionUtils for range extraction
+ */
+declare function agnosticExtractReferenceRanges(labToOhtMapper: LabToOhtMapper, rawData: any, patientInfo: PatientInfo, documentDate?: Date): RangeExtractionResponse;
+declare function agnosticExtractValueFromGreaterLowerThan(value: string): {
+    extractedValue: number | null;
+    extractedValueComparator: MeasurementValueComparator | null;
+    valueParsedCorrectly: boolean;
+};
+/**
+ * Parses exam value from rawExamObj (OhtExam object)
+ * Now uses value directly from ohtExam
+ */
+declare function agnosticParseExamValue(rawExamObj: any, ohtBiomarker: Biomarker): {
+    valueType: BiomarkerValueType;
+    alphanumericalValue: string | null;
+    numberValue: number | null;
+    valueComparator: MeasurementValueComparator;
+    isValueParsedCorrectly: boolean;
+};
+declare function agnosticCheckValueForPlausibleValues(labToOhtMapper: LabToOhtMapper, ohtBiomarker: Biomarker, unit: string, value: number, isUnitParsedCorrectly: boolean): boolean;
+type ApplyTransformationRulesResult = {
+    transformedExams: Exam[];
+    applicationErrorMessages: string[];
+};
+declare function ohtAgnosticMeasurementsExtractor(labToOhtContract: LabToOhtContract, exams: Exam[], transformationRules: TransformationRulesChains, ohtCoreApiKey: string, partnerId?: string | null | undefined): Promise<{
+    measurements: Measurement[];
+    unknownMeasurements: UnknownMeasurement[];
+    unknownUnits: UnknownUnits[];
+    isReportCorrectlyParsed: boolean;
+    transformationRulesErrors: string[];
+}>;
+export { ApplyTransformationRulesResult, ohtAgnosticMeasurementsExtractor, agnosticCheckValueForPlausibleValues, agnosticExtractReferenceRanges, agnosticExtractReferenceAnnotation, agnosticParseExamValue, agnosticExtractUnit, agnosticExtractValueFromGreaterLowerThan };