@openhealth/oht-custom-parser-lib 0.5.8 → 0.5.9

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/ohtMeasurementsExtractor.service.js

@@ -296,9 +296,10 @@ function checkValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, value,
     const isPlausibleValue = value >= plausibleLowerValue && value <= plausibleUpperValue;
     // Log if the value is not plausible
     if (!isPlausibleValue) {
-        processingLogger_service_1.processingLogger.addWarning(`Value "${value} ${standardUnit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${labToOhtMapper.ohtBmId}" | "${labToOhtMapper.labKey}"`, 'plausibility_check', {
+        processingLogger_service_1.processingLogger.addWarning(`Value "${value} ${unit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${labToOhtMapper.ohtBmId}" | "${labToOhtMapper.labKey}"`, 'plausibility_check', {
             labToOhtMapper,
             value,
+            unit,
             standardUnit,
             plausibleLowerValue,
             plausibleUpperValue,

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

@@ -1 +1 @@
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package/dist/util-ts/extractionUtils.js

@@ -656,10 +656,11 @@ function ohtReportCheckValueForPlausibleValues(ohtBmId, labKey, ohtBiomarker, un
     const isPlausibleValue = value >= plausibleLowerValue && value <= plausibleUpperValue;
     // Log if the value is not plausible
     if (!isPlausibleValue) {
-        processingLogger_service_1.processingLogger.addWarning(`Value "${value} ${standardUnit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${ohtBmId}" | "${labKey}"`, 'plausibility_check', {
+        processingLogger_service_1.processingLogger.addWarning(`Value "${value} ${unit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${ohtBmId}" | "${labKey}"`, 'plausibility_check', {
             ohtBmId,
             labKey,
             value,
+            unit,
             standardUnit,
             plausibleLowerValue,
             plausibleUpperValue,

package/dist/util-ts/extractionUtils.js.map

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

@@ -1,36 +1,36 @@
-{
-  "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.5.8",
-  "description": "Shared nodejs lib with with reusable functions",
-  "main": "dist/index.js",
-  "types": "dist/index.d.ts",
-  "files": [
-    "/dist"
-  ],
-  "scripts": {
-    "test": "jest"
-  },
-  "keywords": [],
-  "author": "",
-  "license": "ISC",
-  "dependencies": {
-    "@google-cloud/pubsub": "^4.10.0",
-    "@google-cloud/storage": "^7.7.0",
-    "axios": "^1.13.2",
-    "bottleneck": "^2.19.5",
-    "dayjs": "^1.11.13",
-    "dotenv": "^16.4.5",
-    "jsonata": "^2.1.0",
-    "moment": "^2.30.1",
-    "mongodb": "^6.3.0",
-    "pino": "^8.19.0",
-    "pino-pretty": "^11.3.0"
-  },
-  "devDependencies": {
-    "@types/jest": "^29.5.14",
-    "axios-mock-adapter": "^2.1.0",
-    "jest": "^29.7.0",
-    "ts-jest": "^29.2.5",
-    "typescript": "^5.0.0"
-  }
-}
+{
+  "name": "@openhealth/oht-custom-parser-lib",
+  "version": "0.5.9",
+  "description": "Shared nodejs lib with with reusable functions",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "files": [
+    "/dist"
+  ],
+  "scripts": {
+    "test": "jest"
+  },
+  "keywords": [],
+  "author": "",
+  "license": "ISC",
+  "dependencies": {
+    "@google-cloud/pubsub": "^4.10.0",
+    "@google-cloud/storage": "^7.7.0",
+    "axios": "^1.13.2",
+    "bottleneck": "^2.19.5",
+    "dayjs": "^1.11.13",
+    "dotenv": "^16.4.5",
+    "jsonata": "^2.1.0",
+    "moment": "^2.30.1",
+    "mongodb": "^6.3.0",
+    "pino": "^8.19.0",
+    "pino-pretty": "^11.3.0"
+  },
+  "devDependencies": {
+    "@types/jest": "^29.5.14",
+    "axios-mock-adapter": "^2.1.0",
+    "jest": "^29.7.0",
+    "ts-jest": "^29.2.5",
+    "typescript": "^5.0.0"
+  }
+}

package/readme.md

@@ -1,115 +1,115 @@
-# oht-custom-parser-lib
-
-`oht-custom-parser-lib` is a shared library designed for use across multiple Node.js cloud functions. It contains common MongoDB connectors and data utilities that can be reused to avoid code duplication and ensure consistency.
-
-## Table of Contents
-
-- [Installation](#installation)
-- [Usage](#usage)
-- [Development](#development)
-    - [Patch Versions](#patch-versions)
-    - [Publish to npm Registry](#publish-to-npm-registry)
-- [Using the Library in Cloud Functions](#using-the-library-in-cloud-functions)
-
-## Installation
-
-To install `oht-custom-parser-lib`, you can add it as a dependency in your project using npm:
-
-```bash
-npm install oht-custom-parser-lib
-```
-
-Or, if you want to install a specific version:
-
-```bash
-npm install oht-custom-parser-lib@<version>
-```
-
-## Usage
-
-After installing, you can import and use the library in your cloud functions:
-
-```javascript
-const { connectToMongoDB } = require('oht-custom-parser-lib');
-```
-
-## Logging
-
-- **Production / GCP**: Logs are emitted as JSON (one line per log) for Cloud Logging.
-- **Local / development**: When `NODE_ENV !== 'production'`, logs are pretty-printed in the terminal (colors, timestamps, readable structure). You can override: `LOG_PRETTY=true` to force pretty output, or `LOG_PRETTY=false` to force JSON when not in production.
-
-### Processing logger: request-scoped state
-
-The processing logger (`processingLogger`, `runWithContextAsync`, `getRequestIdFromContext`) uses a **registry + facade** so each request has isolated state and logs never leak context between concurrent invocations (e.g. in Cloud Functions).
-
-- **Registry**: One `ProcessingState` per request, keyed by request id (`fileUploadId ?? messageId ?? cloudEventId ?? generatedId`). The same id is used for the whole request.
-- **AsyncLocalStorage**: Holds only the current request id; state is resolved via `registry.get(id)`.
-- **Entry point**: Wrap your handler in `runWithContextAsync(context, async () => { ... })`. The lib creates a registry entry, runs your callback with the id in AsyncLocalStorage, and removes the entry in a `finally` block.
-- **Clear-state rule**: If there is no request id or the id is not in the registry (e.g. logging outside `runWithContextAsync` or after teardown), the logger uses a **transient empty state** for that call only (never stored). That way one request never overwrites another’s context.
-
-Use `processingLogger.logInfo`, `logWarn`, `logError`, `logProgress`, etc. inside the callback so logs include the same context and are searchable by `fileUploadId` / filename.
-
-## Development
-
-### Patch Versions
-
-When making changes to the `oht-custom-parser-lib`, you need to update the version number before publishing. Follow these steps:
-
-1. **Update the version number**: Use npm's version command to bump the version:
-    - **Patch** for bug fixes:
-      ```bash
-      npm version patch
-      ```
-    - **Minor** for new features:
-      ```bash
-      npm version minor
-      ```
-    - **Major** for breaking changes:
-      ```bash
-      npm version major
-      ```
-
-   This command will automatically update the version in the `package.json` and create a git tag.
-
-2. **Commit Changes**: Ensure your changes and the version bump are committed to the repository.
-
-### Publish to npm Registry
-
-After updating the version, you can publish the library to the npm registry:
-
-1. **Login to npm** (if you haven't already):
-   ```bash
-   npm login
-   ```
-
-2. **Publish the package**:
-   ```bash
-   npm publish
-   ```
-
-   If this is a private package, use:
-   ```bash
-   npm publish --access restricted
-   ```
-
-3. **Verify the publish**: You can check the package on [npmjs.com](https://www.npmjs.com/) to verify that the new version is available.
-
-## Using the Library in Cloud Functions
-
-To use `oht-custom-parser-lib` in your cloud functions:
-
-1. **Install the Library**: Add `oht-custom-parser-lib` as a dependency in the cloud function's `package.json`:
-
-   ```json
-   {
-     "dependencies": {
-       "oht-custom-parser-lib": "^1.0.0"
-     }
-   }
-   ```
-
-   Replace `^1.0.0` with the appropriate version as needed.
-
-2. **Install Dependencies**: Run `npm install` to install the library along with other dependencies.
-
-3. **Deploy Your Function**: Deploy your cloud function as usual, ensuring that the updated dependencies are included.
+# oht-custom-parser-lib
+
+`oht-custom-parser-lib` is a shared library designed for use across multiple Node.js cloud functions. It contains common MongoDB connectors and data utilities that can be reused to avoid code duplication and ensure consistency.
+
+## Table of Contents
+
+- [Installation](#installation)
+- [Usage](#usage)
+- [Development](#development)
+    - [Patch Versions](#patch-versions)
+    - [Publish to npm Registry](#publish-to-npm-registry)
+- [Using the Library in Cloud Functions](#using-the-library-in-cloud-functions)
+
+## Installation
+
+To install `oht-custom-parser-lib`, you can add it as a dependency in your project using npm:
+
+```bash
+npm install oht-custom-parser-lib
+```
+
+Or, if you want to install a specific version:
+
+```bash
+npm install oht-custom-parser-lib@<version>
+```
+
+## Usage
+
+After installing, you can import and use the library in your cloud functions:
+
+```javascript
+const { connectToMongoDB } = require('oht-custom-parser-lib');
+```
+
+## Logging
+
+- **Production / GCP**: Logs are emitted as JSON (one line per log) for Cloud Logging.
+- **Local / development**: When `NODE_ENV !== 'production'`, logs are pretty-printed in the terminal (colors, timestamps, readable structure). You can override: `LOG_PRETTY=true` to force pretty output, or `LOG_PRETTY=false` to force JSON when not in production.
+
+### Processing logger: request-scoped state
+
+The processing logger (`processingLogger`, `runWithContextAsync`, `getRequestIdFromContext`) uses a **registry + facade** so each request has isolated state and logs never leak context between concurrent invocations (e.g. in Cloud Functions).
+
+- **Registry**: One `ProcessingState` per request, keyed by request id (`fileUploadId ?? messageId ?? cloudEventId ?? generatedId`). The same id is used for the whole request.
+- **AsyncLocalStorage**: Holds only the current request id; state is resolved via `registry.get(id)`.
+- **Entry point**: Wrap your handler in `runWithContextAsync(context, async () => { ... })`. The lib creates a registry entry, runs your callback with the id in AsyncLocalStorage, and removes the entry in a `finally` block.
+- **Clear-state rule**: If there is no request id or the id is not in the registry (e.g. logging outside `runWithContextAsync` or after teardown), the logger uses a **transient empty state** for that call only (never stored). That way one request never overwrites another’s context.
+
+Use `processingLogger.logInfo`, `logWarn`, `logError`, `logProgress`, etc. inside the callback so logs include the same context and are searchable by `fileUploadId` / filename.
+
+## Development
+
+### Patch Versions
+
+When making changes to the `oht-custom-parser-lib`, you need to update the version number before publishing. Follow these steps:
+
+1. **Update the version number**: Use npm's version command to bump the version:
+    - **Patch** for bug fixes:
+      ```bash
+      npm version patch
+      ```
+    - **Minor** for new features:
+      ```bash
+      npm version minor
+      ```
+    - **Major** for breaking changes:
+      ```bash
+      npm version major
+      ```
+
+   This command will automatically update the version in the `package.json` and create a git tag.
+
+2. **Commit Changes**: Ensure your changes and the version bump are committed to the repository.
+
+### Publish to npm Registry
+
+After updating the version, you can publish the library to the npm registry:
+
+1. **Login to npm** (if you haven't already):
+   ```bash
+   npm login
+   ```
+
+2. **Publish the package**:
+   ```bash
+   npm publish
+   ```
+
+   If this is a private package, use:
+   ```bash
+   npm publish --access restricted
+   ```
+
+3. **Verify the publish**: You can check the package on [npmjs.com](https://www.npmjs.com/) to verify that the new version is available.
+
+## Using the Library in Cloud Functions
+
+To use `oht-custom-parser-lib` in your cloud functions:
+
+1. **Install the Library**: Add `oht-custom-parser-lib` as a dependency in the cloud function's `package.json`:
+
+   ```json
+   {
+     "dependencies": {
+       "oht-custom-parser-lib": "^1.0.0"
+     }
+   }
+   ```
+
+   Replace `^1.0.0` with the appropriate version as needed.
+
+2. **Install Dependencies**: Run `npm install` to install the library along with other dependencies.
+
+3. **Deploy Your Function**: Deploy your cloud function as usual, ensuring that the updated dependencies are included.