@openhealth/oht-custom-parser-lib 0.2.75 → 0.2.76

package/dist/index.d.ts

@@ -1,12 +1,12 @@
 export { postDataImportFileUploadToCore, postReportPreviewToCore } from './service/reportCreator.service';
 export { parseExternalPatientId, parseGender, isPatientAgeValid, handleRejection, queryFileUploadsWithFilters, postFileUploadSetStatus, DigitalizationUpdateFields } from './service/auxiliaryFunctions.service';
-export { ohtAgnosticMeasurementsExtractor, agnosticCheckValueForPlausibleValues, agnosticExtractReferenceRanges, agnosticExtractReferenceAnnotation, agnosticParseExamValue, agnosticExtractUnit, agnosticExtractValueFromGreaterLowerThan } from './service/ohtAgnosticMeasurementsExtractor.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';

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.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.agnosticExtractValueFromGreaterLowerThan = exports.agnosticExtractUnit = exports.agnosticParseExamValue = exports.agnosticExtractReferenceAnnotation = exports.agnosticExtractReferenceRanges = exports.agnosticCheckValueForPlausibleValues = exports.ohtAgnosticMeasurementsExtractor = 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 = exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = exports.resolveUnitFromSynonyms = exports.fetchSynonymUnits = exports.processAppendedMappings = 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; } });
@@ -16,14 +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 ohtAgnosticMeasurementsExtractor_service_1 = require("./service/ohtAgnosticMeasurementsExtractor.service");
-Object.defineProperty(exports, "ohtAgnosticMeasurementsExtractor", { enumerable: true, get: function () { return ohtAgnosticMeasurementsExtractor_service_1.ohtAgnosticMeasurementsExtractor; } });
-Object.defineProperty(exports, "agnosticCheckValueForPlausibleValues", { enumerable: true, get: function () { return ohtAgnosticMeasurementsExtractor_service_1.agnosticCheckValueForPlausibleValues; } });
-Object.defineProperty(exports, "agnosticExtractReferenceRanges", { enumerable: true, get: function () { return ohtAgnosticMeasurementsExtractor_service_1.agnosticExtractReferenceRanges; } });
-Object.defineProperty(exports, "agnosticExtractReferenceAnnotation", { enumerable: true, get: function () { return ohtAgnosticMeasurementsExtractor_service_1.agnosticExtractReferenceAnnotation; } });
-Object.defineProperty(exports, "agnosticParseExamValue", { enumerable: true, get: function () { return ohtAgnosticMeasurementsExtractor_service_1.agnosticParseExamValue; } });
-Object.defineProperty(exports, "agnosticExtractUnit", { enumerable: true, get: function () { return ohtAgnosticMeasurementsExtractor_service_1.agnosticExtractUnit; } });
-Object.defineProperty(exports, "agnosticExtractValueFromGreaterLowerThan", { enumerable: true, get: function () { return ohtAgnosticMeasurementsExtractor_service_1.agnosticExtractValueFromGreaterLowerThan; } });
+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; } });

package/dist/index.js.map

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

@@ -0,0 +1,157 @@
+import { UnknownUnits, TransformationRulesChains } from "../types/custom-parser.types";
+import { Measurement, PatientInfo, UnknownMeasurement, Exam, UnmappedLabKey } from "../types/oht.types";
+import { ErrorMessage } from "../types/error.types";
+type ApplyTransformationRulesResult = {
+    transformedExams: Exam[];
+    applicationErrorMessages: string[];
+};
+/**
+ * Extracts measurements from OHT report exams by processing each exam through biomarker mapping,
+ * transformation rules, and value extraction.
+ *
+ * This function is the main entry point for converting raw exam data into standardized OHT measurements.
+ * It handles biomarker mapping, unit extraction, value parsing, range extraction, and error reporting.
+ *
+ * ## Processing Flow:
+ *
+ * ### Step 1: Initialization and Validation
+ * - Validates that exams array is not empty
+ * - Initializes result arrays (measurements, unknownMeasurements, unknownUnits, unmappedLabKeys)
+ * - Sets up error tracking and transformation rules error tracking
+ *
+ * ### Step 2: Fetch Biomarker Mappings
+ * - Calls `getMappedBiomarkers()` to retrieve biomarker mappings from OHT Core backend
+ * - Maps labKeys to OHT biomarker IDs (ohtBmId) for the given partner
+ * - 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
+ *
+ * ### Step 4: Collect Biomarker IDs and Fetch Biomarker Details
+ * - Iterates through all exams to collect unique OHT biomarker IDs from mappings
+ * - Filters out ignored biomarkers and unmapped biomarkers (ohtBmId === -1)
+ * - Makes API call to OHT Core to fetch full biomarker details (standard units, ranges, etc.)
+ * - Fetches synonym units from API if partnerId is provided (for unit resolution)
+ *
+ * ### Step 5: Process Each Exam
+ * For each exam in the input array:
+ *
+ * #### 5.1: Create UnmappedLabKey (Always)
+ * - **Always** creates an `unmappedLabKey` entry for every exam, regardless of mapping status
+ * - This ensures all labKeys are tracked for unmapped biomarker analysis
+ * - Includes exam metadata: labKey, biomarkerName, value, unit, annotation, originalName, dataOrigin
+ *
+ * #### 5.2: Check Biomarker Mapping Status
+ * - Retrieves backend mapping for the exam's labKey
+ * - Skips processing if biomarker is marked as `isIgnored === true`
+ * - Uses `handleBiomarkerId()` to determine final `ohtBmId` and `annotationConfig`
+ *   - Handles unmapped biomarkers (ohtBmId === -1)
+ *   - Handles `keepAsUnmapped` flag override
+ *
+ * #### 5.3: Process Mapped Biomarkers (ohtBmId !== -1 and !== undefined)
+ *
+ * ##### 5.3.1: Duplicate Check
+ * - Checks if biomarker ID already exists in measurements array
+ * - If duplicate, logs warning and adds error message, then continues to next exam
+ *
+ * ##### 5.3.2: Fetch Biomarker Details
+ * - Finds biomarker object from API response using `ohtBmId`
+ * - If not found, logs warning, adds error, and continues to next exam
+ *
+ * ##### 5.3.3: Extract Unit
+ * - Calls `ohtReportExtractUnit()` to extract and validate unit
+ * - Handles arbitrary units, standard units, alternative units, and synonym units
+ * - If unit cannot be resolved, adds to `unknownUnits` array
+ * - Logs warning and marks measurement as incorrectly parsed if unit extraction fails
+ *
+ * ##### 5.3.4: Parse Exam Value
+ * - Calls `ohtReportParseExamValue()` to extract value from exam
+ * - Determines value type (NUMERICAL or ALPHANUMERICAL) based on biomarker configuration
+ * - Handles greater than/less than comparators (e.g., ">10", "<5")
+ * - Logs warning and marks measurement as incorrectly parsed if value extraction fails
+ *
+ * ##### 5.3.5: Handle Numerical Without Valid Result
+ * - Checks if value is numerical but cannot be parsed as a valid number
+ * - If true, creates `unknownMeasurement` and continues to next exam
+ *
+ * ##### 5.3.6: Validate Plausible Values (for NUMERICAL biomarkers)
+ * - Calls `ohtReportCheckValueForPlausibleValues()` to validate value is within expected range
+ * - Converts value to standard unit if necessary using conversion factors
+ * - Logs warning and marks measurement as incorrectly parsed if value is not plausible
+ *
+ * ##### 5.3.7: Extract Reference Ranges (for NUMERICAL biomarkers)
+ * - Calls `ohtReportExtractReferenceRanges()` which uses `parseRange()` internally
+ * - Extracts min/max normal values based on patient age, sex, and range data
+ * - Filters ranges by patient demographics and selects most appropriate range
+ * - Logs warning and marks measurement as incorrectly parsed if range extraction fails
+ *
+ * ##### 5.3.8: Extract Reference Annotation
+ * - Calls `ohtReportExtractReferenceAnnotation()` to extract annotation text
+ * - Handles appended mappings (combines values from multiple related biomarkers)
+ * - Merges annotation from exam data with appended mapping results
+ *
+ * ##### 5.3.9: Build Measurement Object
+ * - Constructs complete `Measurement` object with all extracted data:
+ *   - Biomarker ID, value type, value, alphanumeric value
+ *   - Unit, original unit, arbitrary unit flag
+ *   - Reference range (min/max normal values)
+ *   - Range annotation
+ *   - Material, method
+ *   - Collection dates (collectionDate, effectiveDate, examCollectionDate, examEffectiveDate)
+ *   - Original name for document search
+ *   - Digitalization approval flags
+ * - Adds measurement to `measurements` array
+ *
+ * #### 5.4: Process Unmapped Biomarkers (no mapping or ohtBmId === -1)
+ * - Creates `unknownMeasurement` object with:
+ *   - LabKey, biomarker name (mnemonic:examName), value, unit, annotation
+ *   - Data origin information
+ *   - Original exam data for reference
+ * - Adds to `unknownMeasurements` array
+ *
+ * ### Step 6: Summary and Return
+ * - Logs processing summary (total labKeys, mapped biomarkers, unmapped biomarkers, errors)
+ * - Returns result object containing:
+ *   - `measurements`: Array of successfully parsed and mapped measurements
+ *   - `unknownMeasurements`: Array of measurements that could not be mapped or parsed
+ *   - `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
+ * - Errors are categorized by destination (slack, notes, bi)
+ * - Processing continues even if individual exams fail
+ * - Errors are logged with context (filename, labKey, ohtBmId, etc.)
+ *
+ * ## Key Behaviors:
+ * - **UnmappedLabKeys**: Always created for ALL exams, regardless of mapping status
+ * - **UnknownMeasurements**: Created when:
+ *   - No backend mapping exists for labKey
+ *   - ohtBmId === -1 (explicitly unmapped)
+ *   - Value is numerical but cannot be parsed as valid number
+ * - **Measurements**: Created only when biomarker is successfully mapped and all extraction steps succeed
+ *
+ * @param exams - Array of Exam objects containing ohtExam and originalExam data
+ * @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 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)
+ * @returns Promise resolving to extraction result with measurements, unknownMeasurements, unknownUnits, unmappedLabKeys, parsing status, and transformation errors
+ */
+declare function ohtReportMeasurementsExtractor(exams: Exam[], sourceFilename: string, patientInfo: PatientInfo, documentDate: Date | undefined, transformationRules: TransformationRulesChains, ohtCoreApiKey: string, partnerId: string, errorMessages: ErrorMessage[]): Promise<{
+    measurements: Measurement[];
+    unknownMeasurements: UnknownMeasurement[];
+    unknownUnits: UnknownUnits[];
+    unmappedLabKeys: UnmappedLabKey[];
+    isReportCorrectlyParsed: boolean;
+    transformationRulesErrors: string[];
+}>;
+export { ApplyTransformationRulesResult, ohtReportMeasurementsExtractor, };