@openhealth/oht-custom-parser-lib 0.2.74 → 0.2.76

package/dist/index.d.ts

@@ -1,11 +1,12 @@
 export { postDataImportFileUploadToCore, postReportPreviewToCore } from './service/reportCreator.service';
 export { parseExternalPatientId, parseGender, isPatientAgeValid, handleRejection, queryFileUploadsWithFilters, postFileUploadSetStatus, DigitalizationUpdateFields } 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 { AcfBiomarkerRangeAnnotationCheck, AcfBiomarkerGenericDisclaimerLogic, ManualCheck, BiomarkerCompatibility, ReferenceRangeType, AcfReferenceRange, VisualRange, NameAlias, AlternativeUnit, BiomarkerAcf, Biomarker, PipelineStep, DigitizationStatus, MeasurementValueComparator, BiomarkerValueType, DataImportFileUploadStatus, Sex, Digitization, PatientInfo, UnknownMeasurement, Measurement, DataImportFileUpload, MessagePayload, SignedUpload, ReportStyleConfig, LanguageCode, BiomarkerCustomisation, PartnerCustomPanel, ReportDisplaySettings, ReportCustomisation, OHTPartner, UploadType, RejectReason, } from './types/oht.types';
+export { AcfBiomarkerRangeAnnotationCheck, AcfBiomarkerGenericDisclaimerLogic, ManualCheck, BiomarkerCompatibility, ReferenceRangeType, AcfReferenceRange, VisualRange, NameAlias, AlternativeUnit, BiomarkerAcf, Biomarker, PipelineStep, DigitizationStatus, MeasurementValueComparator, BiomarkerValueType, DataImportFileUploadStatus, Sex, Digitization, PatientInfo, UnknownMeasurement, UnmappedLabKey, Measurement, DataImportFileUpload, MessagePayload, SignedUpload, ReportStyleConfig, LanguageCode, BiomarkerCustomisation, PartnerCustomPanel, ReportDisplaySettings, ReportCustomisation, OHTPartner, UploadType, RejectReason, } from './types/oht.types';
 export { ErrorMessage } from './types/error.types';
 export type { TransformationRule, TransformationContext, ApplyRulesResult as TransformationApplyRulesResult, ApplyRulesOptions as TransformationApplyRulesOptions, ValidationResult as TransformationValidationResult, } from './types/transformationRules.types';
 export { makeApiCallWithRetry, parseErrorObj } from './util-ts/apiUtils';
@@ -14,3 +15,4 @@ export { readFileFromBucket, uploadFileBufferToGCS } from './util-ts/googleStora
 export { default as pinoLogger } from './util-ts/pinoLogger';
 export { getGreaterThanPatterns, getLowerThanPatterns } from './util-ts/regexUtils';
 export { getMappedBiomarkers, } from './util-ts/dataUtils';
+export { parseRange } from './util-ts/extractionUtils';

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.getGreaterThanPatterns = exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = 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.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.postReportPreviewToCore = exports.postDataImportFileUploadToCore = void 0;
-exports.getMappedBiomarkers = exports.getLowerThanPatterns = void 0;
+exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = 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.getMappedBiomarkers = exports.getLowerThanPatterns = exports.getGreaterThanPatterns = void 0;
 // ### SERVICES ###
 var reportCreator_service_1 = require("./service/reportCreator.service");
 Object.defineProperty(exports, "postDataImportFileUploadToCore", { enumerable: true, get: function () { return reportCreator_service_1.postDataImportFileUploadToCore; } });
@@ -16,6 +16,8 @@ Object.defineProperty(exports, "isPatientAgeValid", { enumerable: true, get: fun
 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; } });
+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");
 Object.defineProperty(exports, "ohtMeasurementsExtractor", { enumerable: true, get: function () { return ohtMeasurementsExtractor_service_1.ohtMeasurementsExtractor; } });
 Object.defineProperty(exports, "checkValueForPlausibleValues", { enumerable: true, get: function () { return ohtMeasurementsExtractor_service_1.checkValueForPlausibleValues; } });
@@ -74,4 +76,6 @@ Object.defineProperty(exports, "getGreaterThanPatterns", { enumerable: true, get
 Object.defineProperty(exports, "getLowerThanPatterns", { enumerable: true, get: function () { return regexUtils_1.getLowerThanPatterns; } });
 var dataUtils_2 = require("./util-ts/dataUtils");
 Object.defineProperty(exports, "getMappedBiomarkers", { enumerable: true, get: function () { return dataUtils_2.getMappedBiomarkers; } });
+var extractionUtils_1 = require("./util-ts/extractionUtils");
+Object.defineProperty(exports, "parseRange", { enumerable: true, get: function () { return extractionUtils_1.parseRange; } });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

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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 };