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

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

@@ -0,0 +1 @@
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package/dist/util-ts/extractionUtils.d.ts

@@ -1,10 +1,69 @@
-import { LabToOhtMapper, RangeExtractionResponse } from "../types/custom-parser.types";
-import { OhtExam, PatientInfo } from "../types/oht.types";
+import { RangeExtractionResponse, SynonymUnit } from "../types/custom-parser.types";
+import { AnnotationLabKey, BackendBiomarkerMapping, OhtExam, PatientInfo, Biomarker, BiomarkerValueType, MeasurementValueComparator, AnnotationConfig, Exam } 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 };
+declare function parseRange(exam: OhtExam, patientInfo: PatientInfo): RangeExtractionResponse;
+/**
+* Converts backend biomarker id to know if it should be mapped or unmapped
+* @param backendMapping - The backend mapping configuration
+* @param labKey - The lab key identifier
+* @returns The final ohtBmId and annotationConfig
+*/
+declare function handleBiomarkerId(backendMapping: BackendBiomarkerMapping, labKey: string): {
+    ohtBmId: number;
+    annotationConfig: {
+        enabled: boolean;
+        labKeys: AnnotationLabKey[];
+    };
+};
+/**
+ * Extracts unit from ohtExam (OhtExam object)
+ * @param ohtExam - 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 ohtReportExtractUnit(ohtExam: OhtExam, ohtBiomarker: Biomarker, synonymUnits: SynonymUnit[] | null, partnerId: string): {
+    unit: string;
+    isUnitParsedCorrectly: boolean;
+    originalUnit: string;
+    isArbitraryUnit: boolean;
+    unknownUnit: string;
+};
+/**
+ * Extracts reference annotation from ohtExam (OhtExam object)
+ * @param annotationConfig - Annotation configuration for appended biomarkers
+ * @param ohtExam - OhtExam object (not a JSON string)
+ * @param patientInfo - Patient information
+ * @param documentDate - Document date
+ * @param exams - Array of exams for appended mappings
+ * @param filename - Current filename being processed (for error reporting)
+ */
+declare function ohtReportExtractReferenceAnnotation(annotationConfig: AnnotationConfig | undefined, ohtExam: OhtExam, patientInfo: PatientInfo, documentDate: Date | undefined, exams: Exam[] | undefined, filename: string): string;
+/**
+ * Extracts reference ranges from ohtExam (OhtExam object)
+ * Always uses parseRange function from extractionUtils for range extraction
+ */
+declare function ohtReportExtractReferenceRanges(ohtExam: OhtExam, patientInfo: PatientInfo): RangeExtractionResponse;
+declare function ohtReportExtractValueFromGreaterLowerThan(value: string): {
+    extractedValue: number | null;
+    extractedValueComparator: MeasurementValueComparator | null;
+    valueParsedCorrectly: boolean;
+};
+/**
+ * Parses exam value from ohtExam (OhtExam object)
+ * Now uses value directly from ohtExam
+ */
+declare function ohtReportParseExamValue(ohtExam: OhtExam, ohtBiomarker: Biomarker): {
+    valueType: BiomarkerValueType;
+    alphanumericalValue: string | null;
+    numberValue: number | null;
+    valueComparator: MeasurementValueComparator;
+    isValueParsedCorrectly: boolean;
+};
+declare function ohtReportCheckValueForPlausibleValues(ohtBmId: number, labKey: string, ohtBiomarker: Biomarker, unit: string, value: number, isUnitParsedCorrectly: boolean, filename: string): boolean;
+export { parseRange, handleBiomarkerId, ohtReportExtractUnit, ohtReportExtractReferenceAnnotation, ohtReportExtractReferenceRanges, ohtReportExtractValueFromGreaterLowerThan, ohtReportParseExamValue, ohtReportCheckValueForPlausibleValues, };

package/dist/util-ts/extractionUtils.js

@@ -4,14 +4,28 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseRange = parseRange;
+exports.handleBiomarkerId = handleBiomarkerId;
+exports.ohtReportExtractUnit = ohtReportExtractUnit;
+exports.ohtReportExtractReferenceAnnotation = ohtReportExtractReferenceAnnotation;
+exports.ohtReportExtractReferenceRanges = ohtReportExtractReferenceRanges;
+exports.ohtReportExtractValueFromGreaterLowerThan = ohtReportExtractValueFromGreaterLowerThan;
+exports.ohtReportParseExamValue = ohtReportParseExamValue;
+exports.ohtReportCheckValueForPlausibleValues = ohtReportCheckValueForPlausibleValues;
+const oht_types_1 = require("../types/oht.types");
 const moment_1 = __importDefault(require("moment"));
+const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
+const dataUtils_1 = require("./dataUtils");
+/**
+ * Logger instance for the application
+ */
+const logger = (0, pinoLogger_1.default)();
 /**
  * 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
  */
-function parseRange(exam, labToOhtMapper, patientInfo) {
+function parseRange(exam, patientInfo) {
     // Define document date with priority:
     // 1. collectionDate
     // 2. effectiveDate
@@ -184,7 +198,7 @@ function parseRange(exam, labToOhtMapper, patientInfo) {
                 }
             }
             // Try "less than" patterns
-            const lessThanPatterns = getLessThanPatterns();
+            const lessThanPatterns = getLessThanPatternsLocal();
             for (const pattern of lessThanPatterns) {
                 try {
                     const match = pattern.exec(textToSearch.toLowerCase());
@@ -200,7 +214,7 @@ function parseRange(exam, labToOhtMapper, patientInfo) {
                 }
             }
             // Try "greater than" patterns
-            const greaterThanPatterns = getGreaterThanPatterns();
+            const greaterThanPatterns = getGreaterThanPatternsLocal();
             for (const pattern of greaterThanPatterns) {
                 try {
                     const match = pattern.exec(textToSearch.toLowerCase());
@@ -358,8 +372,9 @@ function parsePtNumber(raw) {
 * Gets an array of regular expressions for matching "less than" patterns in various languages
 * @returns Array of RegExp objects for "less than" pattern matching
 */
-function getLessThanPatterns() {
+function getLessThanPatternsLocal() {
     const patterns = [
+        /<=\s*([\d\.,]+)/, // Universal: "<="
         /at[eé]\s*([\d\.,]+)/, // Portuguese: "até"
         /inferior\s+a\s+([\d\.,]+)/, // Portuguese: "inferior a"
         /<\s?([\d\.,]+)/, // Universal: "<"
@@ -371,7 +386,6 @@ function getLessThanPatterns() {
         /menor\s+ou\s+igual\s+a\s+([\d\.,]+)/, // Portuguese: "menor ou igual a"
         /inferior\s+ou\s+igual\s+(?:a\s+)?([\d\.,]+)/, // Portuguese: "inferior ou igual a"
         /less\s+than\s+or\s+equal\s+to\s+([\d\.,]+)/i, // English: "less than or equal to"
-        /<=\s*([\d\.,]+)/, // Universal: "<="
     ];
     return patterns;
 }
@@ -379,8 +393,9 @@ function getLessThanPatterns() {
  * Gets an array of regular expressions for matching "greater than" patterns in various languages
  * @returns Array of RegExp objects for "greater than" pattern matching
  */
-function getGreaterThanPatterns() {
+function getGreaterThanPatternsLocal() {
     const patterns = [
+        />=\s*([\d\.,]+)/, // Universal: ">="
         /superior\s+a\s+([\d\.,]+)/, // Spanish: "superior a"
         />\s?([\d\.,]+)/, // Universal: ">"
         /maior\s+que\s+([\d\.,]+)/, // Portuguese: "maior que"
@@ -391,8 +406,261 @@ function getGreaterThanPatterns() {
         /acima\s+de\s+([\d\.,]+)/, // Portuguese: "acima de"
         /maior\s+ou\s+igual\s+(?:a\s+)?([\d\.,]+)/, // Portuguese: "maior ou igual a"
         /greater\s+than\s+or\s+equal\s+to\s+([\d\.,]+)/i, // English: "greater than or equal to"
-        />=\s*([\d\.,]+)/, // Universal: ">="
     ];
     return patterns;
 }
+/**
+* Converts backend biomarker id to know if it should be mapped or unmapped
+* @param backendMapping - The backend mapping configuration
+* @param labKey - The lab key identifier
+* @returns The final ohtBmId and annotationConfig
+*/
+function handleBiomarkerId(backendMapping, labKey) {
+    // Handle unmapped biomarkers:
+    // 1. ohtBmId: -1 means already unmapped in backend
+    // 2. keepAsUnmapped: true means override to unmapped (ohtBmId becomes -1)
+    const isAlreadyUnmapped = backendMapping.ohtBmId === -1;
+    const shouldBeUnmapped = backendMapping.keepAsUnmapped === true;
+    const finalOhtBmId = shouldBeUnmapped ? -1 : backendMapping.ohtBmId;
+    if (isAlreadyUnmapped) {
+        logger.info(`Processing backend unmapped biomarker: ${labKey} (ohtBmId: -1)`);
+    }
+    else if (shouldBeUnmapped) {
+        logger.info(`Overriding biomarker to unmapped: ${labKey} (ohtBmId: ${backendMapping.ohtBmId} -> -1)`);
+    }
+    return {
+        ohtBmId: finalOhtBmId,
+        annotationConfig: {
+            enabled: backendMapping.annotationConfig?.enabled ?? false,
+            labKeys: backendMapping.annotationConfig?.labKeys ?? [],
+        },
+    };
+}
+/**
+ * Extracts unit from ohtExam (OhtExam object)
+ * @param ohtExam - 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 ohtReportExtractUnit(ohtExam, ohtBiomarker, synonymUnits = null, partnerId) {
+    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 = ohtExam?.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 ohtExam (OhtExam object)
+ * @param annotationConfig - Annotation configuration for appended biomarkers
+ * @param ohtExam - OhtExam object (not a JSON string)
+ * @param patientInfo - Patient information
+ * @param documentDate - Document date
+ * @param exams - Array of exams for appended mappings
+ * @param filename - Current filename being processed (for error reporting)
+ */
+function ohtReportExtractReferenceAnnotation(annotationConfig, ohtExam, patientInfo, documentDate, exams, filename) {
+    let annotation = '';
+    // if it is an appended mapping, add the extracted values to annotation
+    if (annotationConfig?.enabled && annotationConfig.labKeys) {
+        const appendedResult = (0, dataUtils_1.processAppendedMappings)(exams, annotationConfig.labKeys, filename, {
+            maxLength: annotationConfig.maxLength,
+            fallbackValue: annotationConfig.fallbackValue,
+            separator: annotationConfig.separator,
+        });
+        if (appendedResult.text?.length) {
+            annotation += appendedResult.text;
+        }
+    }
+    // Use annotation directly from ohtExam
+    const extractedReference = ohtExam?.annotation ?? '';
+    if (extractedReference?.length) {
+        annotation += annotation ? `\n${extractedReference}` : extractedReference;
+    }
+    return annotation || undefined;
+}
+/**
+ * Extracts reference ranges from ohtExam (OhtExam object)
+ * Always uses parseRange function from extractionUtils for range extraction
+ */
+function ohtReportExtractReferenceRanges(ohtExam, patientInfo) {
+    const nullRangeNotParsedCorrectly = { from: null, to: null, isRangeParsedCorrectly: false };
+    // Always use parseRange function from extractionUtils
+    const rangeExtractionResult = parseRange(ohtExam, patientInfo);
+    if (rangeExtractionResult.isRangeParsedCorrectly) {
+        return rangeExtractionResult;
+    }
+    return nullRangeNotParsedCorrectly;
+}
+function ohtReportExtractValueFromGreaterLowerThan(value) {
+    // Checks first if any greater than pattern is present
+    const greaterThanPatterns = getGreaterThanPatternsLocal(); // TODO: CAN USE THE SAME PATTERNS AS PARSE RANGE FUNCTION?
+    const lowerThanPatterns = getLessThanPatternsLocal();
+    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 ohtExam (OhtExam object)
+ * Now uses value directly from ohtExam
+ */
+function ohtReportParseExamValue(ohtExam, ohtBiomarker) {
+    // Use value directly from ohtExam
+    let value = ohtExam?.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 } = ohtReportExtractValueFromGreaterLowerThan(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 ohtReportCheckValueForPlausibleValues(ohtBmId, labKey, ohtBiomarker, unit, value, isUnitParsedCorrectly, filename) {
+    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({ ohtBmId, labKey, value, standardUnit, plausibleLowerValue, plausibleUpperValue, filename }, `Value "${value} ${standardUnit}" not plausible "${plausibleLowerValue} to ${plausibleUpperValue}" for "${ohtBmId}" | "${labKey}", filename: ${filename}`);
+    }
+    return isPlausibleValue;
+}
 //# sourceMappingURL=extractionUtils.js.map

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

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.2.75",
+  "version": "0.2.76",
   "description": "Shared nodejs lib with with reusable functions",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",