@openhealth/oht-custom-parser-lib 0.5.34 → 0.5.36

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 };

package/dist/service/ohtAgnosticMeasurementsExtractor.service.js

@@ -0,0 +1,603 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ohtAgnosticMeasurementsExtractor = ohtAgnosticMeasurementsExtractor;
+exports.agnosticCheckValueForPlausibleValues = agnosticCheckValueForPlausibleValues;
+exports.agnosticExtractReferenceRanges = agnosticExtractReferenceRanges;
+exports.agnosticExtractReferenceAnnotation = agnosticExtractReferenceAnnotation;
+exports.agnosticParseExamValue = agnosticParseExamValue;
+exports.agnosticExtractUnit = agnosticExtractUnit;
+exports.agnosticExtractValueFromGreaterLowerThan = agnosticExtractValueFromGreaterLowerThan;
+const dataUtils_1 = require("../util-ts/dataUtils");
+const regexUtils_1 = require("../util-ts/regexUtils");
+const extractionUtils_1 = require("../util-ts/extractionUtils");
+const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
+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 = '';
+/**
+ * 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
+ */
+function agnosticExtractUnit(rawData, ohtBiomarker, synonymUnits = null, partnerId = null) {
+    if (!(0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)) {
+        return { unit: "None", isUnitParsedCorrectly: true, originalUnit: "", isArbitraryUnit: false, unknownUnit: '' };
+    }
+    const isArbitraryUnit = ohtBiomarker.acf.standardUnitArbUnitLogic === 'default';
+    let originalUnit = '';
+    // Use unit directly from ohtExam
+    const unit = rawData?.unit ?? '';
+    let unitLowerCase = unit?.toLowerCase();
+    unitLowerCase = unitLowerCase?.replaceAll(/ /g, '') ?? '';
+    const standardUnit = ohtBiomarker.acf.standardUnit;
+    const allBmOhtUnits = [
+        standardUnit?.toLowerCase(),
+        ...ohtBiomarker.acf?.alternativeUnits
+            ?.map((bmAlternative) => bmAlternative.name.toLowerCase()) ?? []
+    ];
+    // If the biomarker uses an arbitrary unit, return standard unit and set the original unit as the unit extracted from the data
+    if (isArbitraryUnit) {
+        originalUnit = unit;
+        return { unit: standardUnit, isUnitParsedCorrectly: true, originalUnit: originalUnit, isArbitraryUnit: isArbitraryUnit, unknownUnit: '' };
+    }
+    // First test if the biomarker has the unit explicit in the 'unity' field
+    const allUnitContainsJsonUnit = allBmOhtUnits.includes(unitLowerCase);
+    if (unitLowerCase?.length > 0 && allUnitContainsJsonUnit) {
+        // Find the original case version from standardUnit or alternativeUnits
+        let matchedUnit = standardUnit?.toLowerCase().replaceAll(/ /g, '') === unitLowerCase
+            ? standardUnit?.replaceAll(/ /g, '')
+            : ohtBiomarker.acf?.alternativeUnits?.find((bmAlternative) => bmAlternative.name.toLowerCase().replaceAll(/ /g, '') === unitLowerCase)?.name?.replaceAll(/ /g, '');
+        // Fallback to original unit if no match found (shouldn't happen, but safety check)
+        matchedUnit = matchedUnit || unit?.replaceAll(/ /g, '');
+        return {
+            unit: matchedUnit,
+            isUnitParsedCorrectly: true,
+            originalUnit: originalUnit,
+            isArbitraryUnit: isArbitraryUnit,
+            unknownUnit: ''
+        };
+    }
+    // Check if there are any Synonym configured
+    if (unitLowerCase?.length > 0) {
+        let resolvedUnit = null;
+        if (synonymUnits && synonymUnits.length > 0) {
+            const resolved = (0, dataUtils_1.resolveUnitFromSynonyms)(unitLowerCase, ohtBiomarker.id, partnerId, synonymUnits);
+            if (resolved.found && resolved.targetUnit) {
+                resolvedUnit = resolved.targetUnit;
+            }
+        }
+        if (resolvedUnit) {
+            const allUnitContainsJsonUnitSynonyms = allBmOhtUnits.includes(resolvedUnit.toLowerCase());
+            if (allUnitContainsJsonUnitSynonyms) {
+                return { unit: resolvedUnit, isUnitParsedCorrectly: true, originalUnit: originalUnit, isArbitraryUnit: isArbitraryUnit, unknownUnit: '' };
+            }
+        }
+    }
+    // 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 agnosticExtractReferenceAnnotation(labToOhtMapper, rawExam, patientInfo, documentDate, exams) {
+    let annotation = '';
+    // if it is an appended mapping, add the extracted values to annotation
+    if (labToOhtMapper?.annotationConfig?.enabled) {
+        const appendedResult = (0, dataUtils_1.processAppendedMappings)(exams, labToOhtMapper.annotationConfig.labKeys, filename, {
+            maxLength: labToOhtMapper.annotationConfig.maxLength,
+            fallbackValue: labToOhtMapper.annotationConfig.fallbackValue,
+            separator: labToOhtMapper.annotationConfig.separator
+        });
+        if (appendedResult.text?.length) {
+            annotation += appendedResult.text;
+        }
+    }
+    // Use annotation directly from ohtExam
+    const extractedReference = rawExam?.annotation ?? '';
+    if (extractedReference?.length) {
+        annotation += annotation ? `\n${extractedReference}` : extractedReference;
+    }
+    return annotation || undefined;
+}
+/**
+ * Extracts reference ranges from rawData (OhtExam object)
+ * Always uses parseRange function from extractionUtils for range extraction
+ */
+function agnosticExtractReferenceRanges(labToOhtMapper, rawData, patientInfo, documentDate) {
+    const nullRangeNotParsedCorrectly = { from: null, to: null, isRangeParsedCorrectly: false };
+    const nullRangeParsedCorrectly = { from: null, to: null, isRangeParsedCorrectly: true };
+    // if internalRange return null, but is parsed correctly
+    if (labToOhtMapper?.rangeExtraction?.useInternalRange) {
+        return nullRangeParsedCorrectly;
+    }
+    // Always use parseRange function from extractionUtils
+    const rangeExtractionResult = (0, extractionUtils_1.parseRange)(rawData, labToOhtMapper, patientInfo);
+    if (rangeExtractionResult.isRangeParsedCorrectly) {
+        return rangeExtractionResult;
+    }
+    return nullRangeNotParsedCorrectly;
+}
+function agnosticExtractValueFromGreaterLowerThan(value) {
+    // Checks first if any greater than pattern is present
+    const greaterThanPatterns = (0, regexUtils_1.getGreaterThanPatterns)();
+    const lowerThanPatterns = (0, regexUtils_1.getLowerThanPatterns)();
+    value = value.toLowerCase();
+    for (const pattern of greaterThanPatterns) {
+        const match = pattern.exec(value);
+        if (match) {
+            const value = parseFloat(match?.[1].replaceAll(',', '.'));
+            const valueComparator = oht_types_1.MeasurementValueComparator.GREATER_THAN;
+            return {
+                extractedValue: value,
+                extractedValueComparator: valueComparator,
+                valueParsedCorrectly: !Number.isNaN(value)
+            };
+        }
+    }
+    // Checks if any lower than pattern is present
+    for (const pattern of lowerThanPatterns) {
+        const match = pattern.exec(value);
+        if (match) {
+            const value = parseFloat(match?.[1].replaceAll(',', '.'));
+            const valueComparator = oht_types_1.MeasurementValueComparator.LESS_THAN;
+            return {
+                extractedValue: value,
+                extractedValueComparator: valueComparator,
+                valueParsedCorrectly: !Number.isNaN(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)
+ * Now uses value directly from ohtExam
+ */
+function agnosticParseExamValue(rawExamObj, ohtBiomarker) {
+    // Use value directly from ohtExam
+    let value = rawExamObj?.value ?? '';
+    // 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
+        : oht_types_1.BiomarkerValueType.ALPHANUMERICAL;
+    let alphanumericalValue = Number.isNaN(parseFloat(value))
+        ? value
+        : null;
+    if (valueType === oht_types_1.BiomarkerValueType.ALPHANUMERICAL
+        && !Number.isNaN(parseFloat(value))) {
+        // convert numberValue to string
+        alphanumericalValue = value.toString();
+    }
+    if (valueType === oht_types_1.BiomarkerValueType.NUMERICAL
+        && Number.isNaN(parseFloat(value))) {
+        // convert numberValue to string
+        const { extractedValue, extractedValueComparator, valueParsedCorrectly } = agnosticExtractValueFromGreaterLowerThan(value);
+        return {
+            valueType,
+            alphanumericalValue,
+            numberValue: extractedValue,
+            valueComparator: extractedValueComparator ?? oht_types_1.MeasurementValueComparator.EQUAL,
+            isValueParsedCorrectly: valueParsedCorrectly
+        };
+    }
+    if (valueType === 'NUMERICAL') {
+        return {
+            valueType,
+            alphanumericalValue,
+            numberValue: parseFloat(value),
+            valueComparator: oht_types_1.MeasurementValueComparator.EQUAL,
+            isValueParsedCorrectly: !Number.isNaN(parseFloat(value))
+        };
+    }
+    if (valueType === 'ALPHANUMERICAL') {
+        return {
+            valueType,
+            alphanumericalValue,
+            numberValue: parseFloat(value),
+            valueComparator: oht_types_1.MeasurementValueComparator.EQUAL,
+            isValueParsedCorrectly: Boolean(alphanumericalValue)
+        };
+    }
+    return {
+        valueType,
+        alphanumericalValue,
+        numberValue: null,
+        valueComparator: oht_types_1.MeasurementValueComparator.EQUAL,
+        isValueParsedCorrectly: false
+    };
+}
+function agnosticCheckValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, value, isUnitParsedCorrectly) {
+    if (!(0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker) && isUnitParsedCorrectly) {
+        return true;
+    }
+    const standardUnit = ohtBiomarker.acf.standardUnit;
+    const plausibleLowerValue = ohtBiomarker.acf.plausibilityRangeCheck;
+    const plausibleUpperValue = ohtBiomarker.acf.plausibilityRangeCheckHigh;
+    const biomarkerStdValueDecimals = ohtBiomarker.acf?.displayDecimals ?? 2;
+    if (unit !== standardUnit) {
+        const alternativeUnit = (Array.isArray(ohtBiomarker.acf?.alternativeUnits)
+            ? ohtBiomarker.acf?.alternativeUnits
+            : [])?.find((altUnit) => altUnit.name === unit);
+        if (alternativeUnit) {
+            const conversionFactor = alternativeUnit.conversionFactor;
+            value = +(value * conversionFactor).toFixed(biomarkerStdValueDecimals);
+        }
+    }
+    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}`);
+    }
+    return isPlausibleValue;
+}
+/**
+ * Apply transformation rules to exams
+ * This function applies transformation rules chain to each exam, passing all exams as context
+ *
+ * @param exams - Array of original exam objects
+ * @param transformationRules - Mapping of labKey to transformation rule chains
+ * @param labToOhtContract - The contract containing patient info and other context
+ * @returns Promise<Exam[]> - Array of transformed exams
+ */
+async function applyTransformationRulesToExams(exams, transformationRules, patientInfo, documentDate) {
+    if (transformationRules.size === 0) {
+        return {
+            transformedExams: exams,
+            applicationErrorMessages: []
+        };
+    }
+    const transformedExams = [];
+    // Prepare context for transformation rules
+    const reportContext = {
+        patient: {
+            sex: patientInfo.sex,
+            birthdate: patientInfo.birthdate,
+            age: (0, auxiliaryFunctions_service_1.getPatientAge)(documentDate, patientInfo.birthdate),
+        }
+    };
+    // Prepare the OHT exam data
+    const ohtReport = {
+        exams: exams.map(e => e.ohtExam),
+    };
+    logger.info({ examsCount: exams.length, chainsCount: transformationRules.size, filename }, 'Applying transformation rules to exams...');
+    let labKeysWithRulesCount = 0;
+    let transformedLabKeysCount = 0;
+    const applicationErrorMessages = [];
+    for (const exam of exams) {
+        const labKey = exam.ohtExam.labKey;
+        const rulesChain = transformationRules.get(labKey);
+        if (!rulesChain || rulesChain.length === 0) {
+            transformedExams.push(exam);
+            continue;
+        }
+        labKeysWithRulesCount++;
+        try {
+            const result = await (0, transformationRules_service_1.applyRules)(rulesChain, exam.ohtExam, {
+                ohtReportJson: ohtReport,
+                contextJson: reportContext,
+            });
+            if (result.errors.length > 0) {
+                logger.warn({ labKey, errors: result.errors, filename }, 'Errors applying transformation rule(s) for labKey.');
+                applicationErrorMessages.push(`${labKey}: ${result.errors.map(e => `(rule ID ${e.ruleId}) ${e.error}`).join('; ')}`);
+            }
+            else {
+                if (result.appliedRules.length > 0) {
+                    transformedLabKeysCount++;
+                }
+                logger.info({ labKey, appliedRules: result.appliedRules.length, filename }, 'Done applying transformation rule(s) for labKey.');
+                // Add the transformed exam to the result array only if there are no errors in the chain
+                transformedExams.push({
+                    ohtExam: result.data,
+                    originalExam: exam.originalExam
+                });
+            }
+        }
+        catch (error) {
+            logger.error({ labKey, error, filename }, 'Failed to apply transformation rules for labKey.');
+            applicationErrorMessages.push(`${labKey}: Unhandled error occurred.`);
+        }
+    }
+    logger.info({
+        filename,
+        examsCount: exams.length,
+        chainsCount: transformationRules.size,
+        transformedLabKeysCount,
+        labKeysWithRulesCount,
+    }, 'Done applying the transformation rules to exams.');
+    return {
+        transformedExams,
+        applicationErrorMessages
+    };
+}
+async function ohtAgnosticMeasurementsExtractor(labToOhtContract, exams, transformationRules, ohtCoreApiKey, partnerId) {
+    filename = labToOhtContract.sourceFilename;
+    const measurements = [];
+    const unknownMeasurements = [];
+    const unknownUnits = [];
+    let isReportCorrectlyParsed = true;
+    let transformationRulesErrors = [];
+    // Apply transformation rules to all exams
+    let transformedExamsResult = { transformedExams: [], applicationErrorMessages: [] };
+    try {
+        transformedExamsResult = await applyTransformationRulesToExams(exams, transformationRules, labToOhtContract.patientInfo, labToOhtContract.documentDate);
+    }
+    catch (error) {
+        logger.error({ error, filename }, 'Unhandled error while applying transformation rules to exams.');
+        labToOhtContract.errorMessages.push({
+            destination: { slack: true, notes: true, bi: false },
+            message: `Failed applying the transformation rules for filename ${filename}. ${error instanceof Error ? error.message : error}`,
+        });
+    }
+    if (transformedExamsResult.applicationErrorMessages.length > 0) {
+        transformationRulesErrors = transformedExamsResult.applicationErrorMessages;
+        labToOhtContract.errorMessages.push({
+            destination: { slack: false, notes: true, bi: false },
+            message: `Failed applying some transformation rules:\n${transformedExamsResult.applicationErrorMessages.map((e) => `  - ${e}`).join("\n\n")}`,
+        });
+    }
+    const transformedExams = transformedExamsResult.transformedExams;
+    const transformedExamsMap = transformedExams.reduce((map, exam) => map.set(exam.ohtExam.labKey, exam), new Map());
+    const allPossibleOHTBmIds = [];
+    [
+        ...Object.values(labToOhtContract.labToOhtList)
+    ].forEach(labToOhtMapper => {
+        if (labToOhtMapper.ohtBmId) {
+            allPossibleOHTBmIds.push(labToOhtMapper.ohtBmId);
+        }
+    });
+    // data to request api
+    const requestData = {
+        "biomarkerIds": allPossibleOHTBmIds,
+        "page": 1,
+        "pageSize": allPossibleOHTBmIds.length
+    };
+    // api call to ohtCore to find biomarkers.
+    const biomarkers = await (0, apiUtils_1.makeApiCallWithRetry)('post', `${OHT_CORE_URL}/v1/biomarker/biomarkers`, requestData, ohtCoreApiKey);
+    // Fetch synonym units from API if enabled
+    let synonymUnits = null;
+    if (partnerId) {
+        synonymUnits = await (0, dataUtils_1.fetchSynonymUnits)(partnerId, ohtCoreApiKey);
+        // If API fetch failed or returned empty, set to null to use hardcoded fallback
+        if (synonymUnits.length === 0) {
+            synonymUnits = null;
+        }
+    }
+    labToOhtContract.labToOhtList.forEach((labToOhtMapper) => {
+        let isMeasurementCorrectlyParsed = true;
+        if (!labToOhtMapper.ohtExam) {
+            labToOhtContract.errorMessages.push({
+                destination: { slack: true, notes: false, bi: false },
+                message: `Missing ohtExam for labKey: ${labToOhtMapper.ohtExam?.labKey || 'unknown'} 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;
+        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: ${filename}`);
+                labToOhtContract.errorMessages.push({
+                    destination: { slack: false, notes: false, bi: true },
+                    message: `Biomarkers Duplicated keys:[PLACEHOLDER]`,
+                    item: `bmId:${labToOhtMapper.ohtBmId}, labKey:${examObj.labKey}`
+                });
+                return;
+            }
+            const ohtBiomarker = biomarkers?.data?.items.find((bm) => bm.id === labToOhtMapper.ohtBmId);
+            // Used for error messages
+            const bmInfo = ohtBiomarker?.acf?.shortName ?
+                `name:${ohtBiomarker.acf.shortName}, bmId:${labToOhtMapper.ohtBmId}, labKey:${examObj.labKey}` :
+                `bmId:${labToOhtMapper.ohtBmId}, labKey:${examObj.labKey}`;
+            const { unit, isUnitParsedCorrectly, originalUnit, isArbitraryUnit, unknownUnit } = agnosticExtractUnit(examObj, ohtBiomarker, synonymUnits, partnerId);
+            if (unknownUnit.length > 0) {
+                unknownUnits.push({
+                    biomarkerId: ohtBiomarker.id,
+                    unit: unknownUnit,
+                    partnerId: partnerId,
+                    labKey: examObj.labKey,
+                    ohtExam: labToOhtMapper.ohtExam,
+                    originalExam: labToOhtMapper.originalExam,
+                    biomarkerName: examObj.mnemonic || '',
+                    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: ${filename}`);
+                labToOhtContract.errorMessages.push({
+                    destination: { slack: true, notes: true, bi: true },
+                    message: `Unit not extracted correctly for:[PLACEHOLDER]`,
+                    item: `${bmInfo}`
+                });
+                isMeasurementCorrectlyParsed = false;
+            }
+            let { valueType, alphanumericalValue, numberValue, valueComparator, isValueParsedCorrectly } = agnosticParseExamValue(examObj, ohtBiomarker);
+            if (!isValueParsedCorrectly) {
+                logger.warn({ labToOhtMapper }, `Value not extracted correctly for "${labToOhtMapper.ohtBmId}|${examObj.labKey}", filename: ${filename}`);
+                labToOhtContract.errorMessages.push({
+                    destination: { slack: true, notes: true, bi: true },
+                    message: `Value not extracted correctly for:[PLACEHOLDER]`,
+                    item: `${bmInfo}`
+                });
+                isMeasurementCorrectlyParsed = false;
+            }
+            if ((0, dataUtils_1.isNumericalWithoutValidResult)(valueType, numberValue, alphanumericalValue)) {
+                const alphanumericalValueTrimmed = alphanumericalValue?.trim() ?? '';
+                const unknownMeasurement = {
+                    labKey: examObj.labKey,
+                    biomarkerName: examObj.description ?? '',
+                    value: alphanumericalValueTrimmed,
+                    unit: unit ?? '',
+                    annotation: examObj.annotation ?? '',
+                    dataOrigin: [{
+                            itemExtracted: 'measurement',
+                            method: 'custom-parser',
+                            methodVersion: 'oht-custom-parser-lib',
+                            path: 'exams',
+                        }],
+                    originalName: examObj.examName ?? '',
+                    originalExam: {
+                        contentType: 'application/json',
+                        exam: JSON.stringify(examObj)
+                    },
+                    ohtExam: examObj
+                };
+                unknownMeasurements.push(unknownMeasurement);
+                return;
+            }
+            // Check if the value is plausible
+            if (isValueParsedCorrectly && valueType === 'NUMERICAL') {
+                const isPlausibleValue = numberValue !== null && agnosticCheckValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, numberValue, isUnitParsedCorrectly);
+                if (!isPlausibleValue) {
+                    logger.warn({ labToOhtMapper }, `Value [${numberValue} ${unit}] is not plausible for "${labToOhtMapper.ohtBmId}|${examObj.labKey}", filename: ${filename}`);
+                    labToOhtContract.errorMessages.push({
+                        destination: { slack: true, notes: true, bi: true },
+                        message: `Value is not plausible for:[PLACEHOLDER]`,
+                        item: `${bmInfo}, value:${numberValue}${unit}`
+                    });
+                    isMeasurementCorrectlyParsed = false;
+                }
+            }
+            let from = null, to = null;
+            let isRangeParsedCorrectly = true;
+            // If the biomarker is numerical, extract the reference range
+            if ((0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)) {
+                const extractedRange = agnosticExtractReferenceRanges(labToOhtMapper, examObj, labToOhtContract.patientInfo, labToOhtContract.documentDate);
+                from = extractedRange.from ?? null;
+                to = extractedRange.to ?? null;
+                isRangeParsedCorrectly = extractedRange.isRangeParsedCorrectly;
+                if (!isRangeParsedCorrectly) {
+                    logger.warn({ labToOhtMapper }, `Range not extracted correctly for "${labToOhtMapper.ohtBmId}|${examObj.labKey}", filename: ${filename}`);
+                    labToOhtContract.errorMessages.push({
+                        destination: { slack: true, notes: true, bi: true },
+                        message: `Range not extracted correctly for:[PLACEHOLDER]`,
+                        item: `${bmInfo}`
+                    });
+                    isMeasurementCorrectlyParsed = false;
+                }
+            }
+            let extractedAnnotation;
+            if (labToOhtMapper?.referenceAsAnnotation?.use || labToOhtMapper?.annotationConfig?.enabled) {
+                extractedAnnotation = agnosticExtractReferenceAnnotation(labToOhtMapper, examObj, labToOhtContract.patientInfo, labToOhtContract.documentDate, transformedExams);
+            }
+            // Use material and method directly from ohtExam
+            const material = examObj?.material ?? '';
+            const method = examObj?.method ?? '';
+            let alphaValue = !(0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker) && alphanumericalValue
+                ? alphanumericalValue.trim()
+                : '';
+            // adding unit for alphanumerical values as number.
+            if (!Number.isNaN(parseFloat(alphaValue))) {
+                // Use unit directly from ohtExam
+                let originalUnit = examObj?.unit ?? '';
+                originalUnit = originalUnit?.replaceAll(/ /g, '') ?? '';
+                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;
+            // add original name for document search
+            const originalName = examObj.examName ?? '';
+            let measurement = {
+                biomarkerId: ohtBiomarker.id,
+                valueType,
+                value: (0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker) ? numberValue : null,
+                alphanumericValue: alphaValue,
+                rangeAnnotation: extractedAnnotation ? extractedAnnotation : null,
+                showVisualisationIfAnnotated: false, // TODO: WHAT SHOULD BE THE DEFAULT VALUE?
+                comparator: valueComparator ?? oht_types_1.MeasurementValueComparator.EQUAL,
+                minNormalValue: from,
+                maxNormalValue: to,
+                unit,
+                originalUnit,
+                isArbitraryUnit,
+                material,
+                method,
+                isDigitalizationApproved: isMeasurementCorrectlyParsed,
+                isManualChecked: isMeasurementCorrectlyParsed,
+                collectionDate: collectionDate,
+                effectiveDate: effectiveDate,
+                examCollectionDate: examCollectionDate,
+                examEffectiveDate: examEffectiveDate,
+                originalName: originalName,
+            };
+            measurements.push(measurement);
+        }
+        else {
+            const labKey = examObj.labKey;
+            logger.warn(`Created an ungroupedBiomarker for id: ${labKey}, filename: ${filename}`);
+            labToOhtContract.errorMessages.push({
+                destination: { slack: false, notes: false, bi: true },
+                message: `Created ungroupedBiomarkers for:[PLACEHOLDER]`,
+                item: `labKey:${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 originalExam = labToOhtMapper?.unknownMeasurement?.originalExam
+                ? {
+                    contentType: typeof labToOhtMapper.unknownMeasurement.originalExam.contentType === 'string'
+                        ? labToOhtMapper.unknownMeasurement.originalExam.contentType
+                        : '',
+                    exam: typeof labToOhtMapper.unknownMeasurement.originalExam.exam === 'string'
+                        ? labToOhtMapper.unknownMeasurement.originalExam.exam
+                        : String(labToOhtMapper.unknownMeasurement.originalExam.exam || '')
+                }
+                : { contentType: '', exam: '' };
+            const ohtExam = labToOhtMapper?.unknownMeasurement?.ohtExam
+                ? labToOhtMapper.unknownMeasurement.ohtExam
+                : { labKey: '', value: '', unit: '', collectionDate: '', documentDate: '', description: '', mnemonic: '', examName: '', range: [], annotation: '' };
+            const dataOrigin = labToOhtMapper?.unknownMeasurement?.dataOrigin
+                ? [labToOhtMapper?.unknownMeasurement?.dataOrigin]
+                : [{ path: '' }];
+            const unknownMeasurement = {
+                labKey: labKey,
+                biomarkerName: biomarkerName,
+                value: value,
+                unit: unit,
+                annotation: annotation,
+                dataOrigin: dataOrigin,
+                originalName: originalName,
+                originalExam: originalExam,
+                ohtExam: ohtExam
+            };
+            unknownMeasurements.push(unknownMeasurement);
+        }
+        isReportCorrectlyParsed = isReportCorrectlyParsed && isMeasurementCorrectlyParsed;
+    });
+    return {
+        measurements,
+        unknownMeasurements,
+        unknownUnits,
+        isReportCorrectlyParsed,
+        transformationRulesErrors,
+    };
+}
+//# sourceMappingURL=ohtAgnosticMeasurementsExtractor.service.js.map

package/dist/service/ohtAgnosticMeasurementsExtractor.service.js.map

@@ -0,0 +1 @@
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package/dist/service/ohtReportMeasurementsExtractor.service.js

@@ -618,7 +618,42 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
                         message: `Value is not plausible for:[PLACEHOLDER]`,
                         item: `${bmInfo}, value:${numberValue}${unit}`
                     });
-                    isMeasurementCorrectlyParsed = false;
+                    // Resolve name with fallbacks
+                    const implausibleName = transformedExamObj.examName ||
+                        transformedExamObj.mnemonic ||
+                        transformedExamObj.description ||
+                        '';
+                    // Extract range inline (no error reporting) to include in annotation
+                    const implausibleAnnotationParts = [];
+                    if (transformedExamObj.annotation) {
+                        implausibleAnnotationParts.push(transformedExamObj.annotation);
+                    }
+                    if ((0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)) {
+                        const implausibleRange = (0, extractionUtils_1.getRangeForCompatibility)(ohtBiomarker, effectiveCompatibility, transformedExamObj, patientInfo, referenceRangeLogEntries);
+                        const implausibleFrom = implausibleRange.from ?? null;
+                        const implausibleTo = implausibleRange.to ?? null;
+                        if (implausibleFrom !== null || implausibleTo !== null) {
+                            implausibleAnnotationParts.push(`Report.UngroupedImplausibleRange ${implausibleFrom ?? 'n/a'} - ${implausibleTo ?? 'n/a'}`);
+                        }
+                    }
+                    implausibleAnnotationParts.push('Report.UngroupedImplausibleAnnotation');
+                    const implausibleUnknownMeasurement = {
+                        biomarkerName: implausibleName,
+                        value: numberValue !== null ? String(numberValue) : (transformedExamObj.value || ''),
+                        unit: unit ?? '',
+                        annotation: implausibleAnnotationParts.join('\n'),
+                        dataOrigin: [{
+                                itemExtracted: 'measurement',
+                                method: 'custom-parser',
+                                methodVersion: `oht-custom-parser-lib-v${ohtCustomParserLibVersion}`,
+                                path: 'exams',
+                            }],
+                        originalName: transformedExamObj.examName || labKey.split(':')[1] || '',
+                        originalExam: originalExam ? originalExam : undefined,
+                        ohtExam: transformedExamObj,
+                    };
+                    unknownMeasurements.push(implausibleUnknownMeasurement);
+                    continue;
                 }
             }
             let from = null, to = null;

package/dist/service/ohtReportMeasurementsExtractor.service.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.5.34",
+  "version": "0.5.36",
   "description": "Shared nodejs lib with with reusable functions",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",