@openhealth/oht-custom-parser-lib 0.2.74 → 0.2.75

package/dist/service/ohtMeasurementsExtractor.service.d.ts

@@ -1,13 +1,5 @@
 import { LabToOhtContract, LabToOhtMapper, RangeExtraction, RangeExtractionResponse, UnitExtraction, ValueExtraction, 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 unitExtraction - Unit extraction configuration
- * @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 extractUnit(unitExtraction: UnitExtraction | undefined, rawData: any, ohtBiomarker: Biomarker, synonymUnits?: SynonymUnit[] | null, partnerId?: string | null | undefined): {
     unit: string;
     isUnitParsedCorrectly: boolean;
@@ -15,36 +7,17 @@ declare function extractUnit(unitExtraction: UnitExtraction | undefined, rawData
     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 extractReferenceAnnotation(labToOhtMapper: LabToOhtMapper, rawExam: any, patientInfo: PatientInfo, documentDate?: Date, exams?: Exam[]): string;
-/**
- * Extracts range from rawData (OhtExam object) using position and regex
- */
 declare const getRangeFromPositionAndRegex: (rangeExtraction: RangeExtraction, rawData: any) => {
     from: number | undefined;
     to: number | undefined;
 };
-/**
- * Extracts reference ranges from rawData (OhtExam object)
- * Custom extraction functions (extractionFunc, defaultRangeExtractionFunc) now receive OhtExam object
- */
 declare function extractReferenceRanges(labToOhtMapper: LabToOhtMapper, rawData: any, patientInfo: PatientInfo, documentDate?: Date): RangeExtractionResponse;
 declare function extractValueFromGreaterLowerThan(value: string): {
     extractedValue: number | null;
     extractedValueComparator: MeasurementValueComparator | null;
     valueParsedCorrectly: boolean;
 };
-/**
- * Parses exam value from rawExamObj (OhtExam object)
- * Custom extraction functions (extractionFunc) now receive OhtExam object
- */
 declare function parseExamValue(rawExamObj: any, valueExtraction: ValueExtraction | undefined, ohtBiomarker: Biomarker): {
     valueType: BiomarkerValueType;
     alphanumericalValue: string | null;

package/dist/service/ohtMeasurementsExtractor.service.js

@@ -21,14 +21,6 @@ const auxiliaryFunctions_service_1 = require("./auxiliaryFunctions.service");
 const logger = (0, pinoLogger_1.default)();
 const OHT_CORE_URL = process.env.OHT_CORE_URL;
 let filename = '';
-/**
- * Extracts unit from rawData (OhtExam object)
- * @param unitExtraction - Unit extraction configuration
- * @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
- */
 function extractUnit(unitExtraction, rawData, ohtBiomarker, synonymUnits = null, partnerId = null) {
     if (!(0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)) {
         return { unit: "None", isUnitParsedCorrectly: true, originalUnit: "", isArbitraryUnit: false, unknownUnit: '' };
@@ -93,12 +85,8 @@ function extractUnit(unitExtraction, rawData, ohtBiomarker, synonymUnits = null,
         return { unit: unitExtraction?.predefinedUnit, isUnitParsedCorrectly: allUnitContainsUnitFromOhtMap, originalUnit: originalUnit, isArbitraryUnit: isArbitraryUnit, unknownUnit: '' };
     }
     if (unitExtraction?.extractionRegex) {
-        // CHANGED: Extract value first, then apply regex to the extracted string value
-        // rawData is now OhtExam object, not a string, so we need to extract the value first
-        const extractedValue = (0, dataUtils_1.extractValue)(rawData, unitExtraction?.unitPosition);
-        const valueString = extractedValue ? String(extractedValue) : '';
         const regex = new RegExp(unitExtraction.extractionRegex);
-        const match = valueString.match(regex);
+        const match = rawData.match(regex);
         const allUnitContainsUnitMatch = allBmOhtUnits.includes(match?.[1]?.toLowerCase());
         if (match?.[1] && allUnitContainsUnitMatch) {
             return { unit: match?.[1], isUnitParsedCorrectly: true, originalUnit: originalUnit, isArbitraryUnit: isArbitraryUnit, unknownUnit: '' };
@@ -107,14 +95,6 @@ function extractUnit(unitExtraction, rawData, ohtBiomarker, synonymUnits = null,
     // if the unit didnt match any of the cases, add the unit to an unknownUnit list
     return { unit: '', isUnitParsedCorrectly: false, originalUnit: '', isArbitraryUnit: false, unknownUnit: unit };
 }
-/**
- * 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
- */
 function extractReferenceAnnotation(labToOhtMapper, rawExam, patientInfo, documentDate, exams) {
     const annotationExtractionFunc = labToOhtMapper?.referenceAsAnnotation?.extractionFunc;
     let annotation = '';
@@ -145,16 +125,11 @@ function extractReferenceAnnotation(labToOhtMapper, rawExam, patientInfo, docume
     }
     return annotation || undefined;
 }
-/**
- * Extracts range from rawData (OhtExam object) using position and regex
- */
 const getRangeFromPositionAndRegex = (rangeExtraction, rawData) => {
     const extractionRegex = rangeExtraction.extractionRegex;
     const rangePosition = rangeExtraction.rangePosition;
     const regex = typeof extractionRegex === 'string' ? new RegExp(extractionRegex) : extractionRegex;
-    // CHANGED: extractValue returns any, convert to string for regex.exec()
-    const extractedValue = (0, dataUtils_1.extractValue)(rawData, rangePosition);
-    const value = extractedValue ? String(extractedValue) : '';
+    const value = (0, dataUtils_1.extractValue)(rawData, rangePosition);
     if (regex) {
         let match = regex.exec(value);
         if (match) {
@@ -175,10 +150,6 @@ const getRangeFromPositionAndRegex = (rangeExtraction, rawData) => {
     };
 };
 exports.getRangeFromPositionAndRegex = getRangeFromPositionAndRegex;
-/**
- * Extracts reference ranges from rawData (OhtExam object)
- * Custom extraction functions (extractionFunc, defaultRangeExtractionFunc) now receive OhtExam object
- */
 function extractReferenceRanges(labToOhtMapper, rawData, patientInfo, documentDate) {
     // WIP
     const nullRangeNotParsedCorrectly = { from: null, to: null, isRangeParsedCorrectly: false };
@@ -251,21 +222,10 @@ function extractValueFromGreaterLowerThan(value) {
     // If no pattern is found, return the value as is and the comparator as EQUAL and isValueParsedCorrectly as false
     return { extractedValue: null, extractedValueComparator: null, valueParsedCorrectly: false };
 }
-/**
- * Parses exam value from rawExamObj (OhtExam object)
- * Custom extraction functions (extractionFunc) now receive OhtExam object
- */
 function parseExamValue(rawExamObj, valueExtraction, ohtBiomarker) {
     let value = (0, dataUtils_1.extractValue)(rawExamObj, valueExtraction?.valuePosition);
     // try default extraction function or return the value as is
     value = valueExtraction?.extractionFunc ? valueExtraction?.extractionFunc(rawExamObj) : value;
-    // extractValue can return any type, so we normalize to string for parseFloat
-    if (value != null) {
-        value = String(value);
-    }
-    else {
-        value = '';
-    }
     // If is parse float nan, the value is alphanumerical
     const valueType = (0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)
         ? oht_types_1.BiomarkerValueType.NUMERICAL
@@ -336,7 +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.ohtExam.labKey}", filename: ${filename}`);
+        logger.warn({ labToOhtMapper, value, standardUnit, plausibleLowerValue, plausibleUpperValue, filename }, `Value "${value} ${standardUnit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${labToOhtMapper.ohtBmId}" | "${labToOhtMapper.labKey}", filename: ${filename}`);
     }
     return isPlausibleValue;
 }
@@ -474,16 +434,19 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
     }
     labToOhtContract.labToOhtList.forEach((labToOhtMapper) => {
         let isMeasurementCorrectlyParsed = true;
-        if (!labToOhtMapper.ohtExam) {
+        if (!labToOhtMapper.rawExam) {
             labToOhtContract.errorMessages.push({
                 destination: { slack: true, notes: false, bi: false },
-                message: `Missing ohtExam for labKey: ${labToOhtMapper.ohtExam?.labKey || 'unknown'} filename: ${filename}`,
+                message: `Missing rawExam for labKey: ${labToOhtMapper.labKey} filename: ${filename}`,
             });
             return;
         }
-        // Get the transformed exam for this labKey, or use the original ohtExam
-        const transformedExam = transformedExamsMap.get(labToOhtMapper.ohtExam.labKey);
-        const examObj = transformedExam ? transformedExam.ohtExam : labToOhtMapper.ohtExam;
+        let examObj = JSON.parse(labToOhtMapper.rawExam);
+        // Get the transformed exam for this labKey
+        const transformedExam = transformedExamsMap.get(labToOhtMapper.labKey);
+        if (transformedExam) {
+            examObj = transformedExam.ohtExam;
+        }
         if (labToOhtMapper?.ohtBmId && labToOhtMapper?.ohtBmId !== -1) {
             // if BM is already in measurements, continue to the next one
             if (measurements.some(measurement => measurement.biomarkerId === labToOhtMapper.ohtBmId)) {
@@ -491,30 +454,30 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
                 labToOhtContract.errorMessages.push({
                     destination: { slack: false, notes: false, bi: true },
                     message: `Biomarkers Duplicated keys:[PLACEHOLDER]`,
-                    item: `bmId:${labToOhtMapper.ohtBmId}, labKey:${examObj.labKey}`
+                    item: `bmId:${labToOhtMapper.ohtBmId}, labKey:${labToOhtMapper.labKey}`
                 });
                 return;
             }
             const ohtBiomarker = biomarkers?.data?.items.find((bm) => bm.id === labToOhtMapper.ohtBmId);
             // Used for error messages
             const bmInfo = ohtBiomarker?.acf?.shortName ?
-                `name:${ohtBiomarker.acf.shortName}, bmId:${labToOhtMapper.ohtBmId}, labKey:${examObj.labKey}` :
-                `bmId:${labToOhtMapper.ohtBmId}, labKey:${examObj.labKey}`;
+                `name:${ohtBiomarker.acf.shortName}, bmId:${labToOhtMapper.ohtBmId}, labKey:${labToOhtMapper.labKey}` :
+                `bmId:${labToOhtMapper.ohtBmId}, labKey:${labToOhtMapper.labKey}`;
             const { unit, isUnitParsedCorrectly, originalUnit, isArbitraryUnit, unknownUnit } = extractUnit(labToOhtMapper.unitExtraction, examObj, ohtBiomarker, synonymUnits, partnerId);
             if (unknownUnit.length > 0) {
                 unknownUnits.push({
                     biomarkerId: ohtBiomarker.id,
                     unit: unknownUnit,
                     partnerId: partnerId,
-                    labKey: examObj.labKey,
+                    labKey: labToOhtMapper.labKey,
                     ohtExam: labToOhtMapper.ohtExam,
                     originalExam: labToOhtMapper.originalExam,
-                    biomarkerName: examObj.mnemonic || '',
+                    biomarkerName: labToOhtMapper.biomarkerName,
                     dataImportFileUploadId: null, // is null it will be set later in the structParser.service.ts
                 });
             }
             if (!isUnitParsedCorrectly) {
-                logger.warn({ labToOhtMapper }, `Unit not extracted correctly for "${labToOhtMapper.ohtBmId}|${examObj.labKey}", filename: ${filename}`);
+                logger.warn({ labToOhtMapper }, `Unit not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
                 labToOhtContract.errorMessages.push({
                     destination: { slack: true, notes: true, bi: true },
                     message: `Unit not extracted correctly for:[PLACEHOLDER]`,
@@ -524,7 +487,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
             }
             let { valueType, alphanumericalValue, numberValue, valueComparator, isValueParsedCorrectly } = parseExamValue(examObj, labToOhtMapper.valueExtraction, ohtBiomarker);
             if (!isValueParsedCorrectly) {
-                logger.warn({ labToOhtMapper }, `Value not extracted correctly for "${labToOhtMapper.ohtBmId}|${examObj.labKey}", filename: ${filename}`);
+                logger.warn({ labToOhtMapper }, `Value not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
                 labToOhtContract.errorMessages.push({
                     destination: { slack: true, notes: true, bi: true },
                     message: `Value not extracted correctly for:[PLACEHOLDER]`,
@@ -535,7 +498,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
             if ((0, dataUtils_1.isNumericalWithoutValidResult)(valueType, numberValue, alphanumericalValue)) {
                 const alphanumericalValueTrimmed = alphanumericalValue?.trim() ?? '';
                 const unknownMeasurement = {
-                    labKey: examObj.labKey,
+                    labKey: labToOhtMapper.labKey,
                     biomarkerName: examObj.description ?? '',
                     value: alphanumericalValueTrimmed,
                     unit: unit ?? '',
@@ -546,10 +509,10 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
                             methodVersion: 'oht-custom-parser-lib',
                             path: 'exams',
                         }],
-                    originalName: examObj.examName ?? '',
+                    originalName: labToOhtMapper?.originalName ?? '',
                     originalExam: {
                         contentType: 'application/json',
-                        exam: JSON.stringify(examObj)
+                        exam: labToOhtMapper.rawExam ?? ''
                     },
                     ohtExam: examObj
                 };
@@ -560,7 +523,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
             if (isValueParsedCorrectly && valueType === 'NUMERICAL') {
                 const isPlausibleValue = numberValue !== null && checkValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, numberValue, isUnitParsedCorrectly);
                 if (!isPlausibleValue) {
-                    logger.warn({ labToOhtMapper }, `Value [${numberValue} ${unit}] is not plausible for "${labToOhtMapper.ohtBmId}|${examObj.labKey}", filename: ${filename}`);
+                    logger.warn({ labToOhtMapper }, `Value [${numberValue} ${unit}] is not plausible for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
                     labToOhtContract.errorMessages.push({
                         destination: { slack: true, notes: true, bi: true },
                         message: `Value is not plausible for:[PLACEHOLDER]`,
@@ -578,7 +541,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
                 to = extractedRange.to ?? null;
                 isRangeParsedCorrectly = extractedRange.isRangeParsedCorrectly;
                 if (!isRangeParsedCorrectly) {
-                    logger.warn({ labToOhtMapper }, `Range not extracted correctly for "${labToOhtMapper.ohtBmId}|${examObj.labKey}", filename: ${filename}`);
+                    logger.warn({ labToOhtMapper }, `Range not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
                     labToOhtContract.errorMessages.push({
                         destination: { slack: true, notes: true, bi: true },
                         message: `Range not extracted correctly for:[PLACEHOLDER]`,
@@ -603,12 +566,12 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
                 alphaValue = alphaValue && unit?.length > 0 ? `${alphaValue} ${originalUnit}`.trim() : alphaValue;
             }
             // adding dates for measurements in ISO 8601 format
-            const collectionDate = examObj.collectionDate ? new Date(examObj.collectionDate).toISOString() : null;
-            const effectiveDate = examObj.effectiveDate ? new Date(examObj.effectiveDate).toISOString() : null;
-            const examCollectionDate = examObj.examCollectionDate ? new Date(examObj.examCollectionDate).toISOString() : null;
-            const examEffectiveDate = examObj.examEffectiveDate ? new Date(examObj.examEffectiveDate).toISOString() : null;
+            const collectionDate = labToOhtMapper?.collectionDate ? new Date(labToOhtMapper.collectionDate).toISOString() : null;
+            const effectiveDate = labToOhtMapper?.effectiveDate ? new Date(labToOhtMapper.effectiveDate).toISOString() : null;
+            const examCollectionDate = labToOhtMapper?.examCollectionDate ? new Date(labToOhtMapper.examCollectionDate).toISOString() : null;
+            const examEffectiveDate = labToOhtMapper?.examEffectiveDate ? new Date(labToOhtMapper.examEffectiveDate).toISOString() : null;
             // add original name for document search
-            const originalName = examObj.examName ?? '';
+            const originalName = labToOhtMapper?.originalName ?? '';
             let measurement = {
                 biomarkerId: ohtBiomarker.id,
                 valueType,
@@ -635,18 +598,18 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, transformationR
             measurements.push(measurement);
         }
         else {
-            const labKey = examObj.labKey;
-            logger.warn(`Created an ungroupedBiomarker for id: ${labKey}, filename: ${filename}`);
+            logger.warn(`Created an ungroupedBiomarker for id: ${labToOhtMapper.labKey}, filename: ${filename}`);
             labToOhtContract.errorMessages.push({
                 destination: { slack: false, notes: false, bi: true },
                 message: `Created ungroupedBiomarkers for:[PLACEHOLDER]`,
-                item: `labKey:${labKey}`
+                item: `labKey:${labToOhtMapper.labKey}`
             });
             const biomarkerName = labToOhtMapper?.unknownMeasurement?.biomarkerName ?? '';
             const value = labToOhtMapper?.unknownMeasurement?.value ?? '';
             const unit = labToOhtMapper?.unknownMeasurement?.unit ?? '';
             const annotation = labToOhtMapper?.unknownMeasurement?.annotation ?? '';
             const originalName = labToOhtMapper?.unknownMeasurement?.originalName ?? '';
+            const labKey = labToOhtMapper.labKey;
             const originalExam = labToOhtMapper?.unknownMeasurement?.originalExam
                 ? {
                     contentType: typeof labToOhtMapper.unknownMeasurement.originalExam.contentType === 'string'

package/dist/service/ohtMeasurementsExtractor.service.js.map

@@ -1 +1 @@
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package/dist/types/custom-parser.types.d.ts

@@ -72,16 +72,24 @@ export interface OriginalExam {
 }
 export interface LabToOhtMapper {
     ohtBmId?: number;
+    biomarkerName?: string;
+    labKey?: string;
+    rawExam?: string;
     material?: string;
     method?: string;
+    collectionDate?: string;
+    effectiveDate?: string;
+    examCollectionDate?: string;
+    examEffectiveDate?: string;
     valueExtraction?: ValueExtraction;
     unitExtraction?: UnitExtraction;
     rangeExtraction?: RangeExtraction;
     referenceAsAnnotation?: ReferenceAsAnnotation;
     unknownMeasurement?: UnknownMeasurementExtraction;
     annotationConfig?: AnnotationConfig;
+    originalName?: string;
     originalExam?: OriginalExam;
-    ohtExam: OhtExam;
+    ohtExam?: OhtExam;
 }
 export interface LabToOhtContract {
     labToOhtList: LabToOhtMapper[];

package/dist/types/oht.types.d.ts

@@ -445,6 +445,9 @@ export interface BackendBiomarkerMapping {
     jsonBlob?: any;
     isIgnored?: boolean;
     keepAsUnmapped?: boolean;
+    /** Optional tagged LOINC code */
+    taggedLoincCode?: string;
+    /** all the following configurations will be deleted */
     /** Range extraction configuration */
     rangeExtraction: RangeExtractionConfig;
     /** Unit extraction configuration */
@@ -454,9 +457,7 @@ export interface BackendBiomarkerMapping {
     /** Reference as annotation configuration */
     referenceAsAnnotation: ReferenceAsAnnotationConfig;
     /** Annotation configuration for appended biomarkers */
-    annotationConfig?: AnnotationConfig;
-    /** Optional tagged LOINC code */
-    taggedLoincCode?: string;
+    annotationConfig: AnnotationConfig;
 }
 /** Custom parser transformation rules */
 export type TransformationRule = {

package/dist/util-ts/extractionUtils.d.ts

@@ -0,0 +1,10 @@
+import { LabToOhtMapper, RangeExtractionResponse } from "../types/custom-parser.types";
+import { OhtExam, PatientInfo } from "../types/oht.types";
+/**
+ * Default range parsing function that extracts range information from exam data
+ * @param exam - The OHT exam object containing range information
+ * @param labToOhtMapper - The lab to OHT mapper configuration
+ * @returns Range extraction response with parsed range bounds
+ */
+declare function parseRange(exam: OhtExam, labToOhtMapper: LabToOhtMapper, patientInfo: PatientInfo): RangeExtractionResponse;
+export { parseRange };