@openhealth/oht-custom-parser-lib 0.2.54 → 0.2.56

package/{readme.md → README.md}

@@ -1,99 +1,99 @@
-# 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');
-```
-
-## 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');
+```
+
+## 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.

package/dist/service/auxiliaryFunctions.service.d.ts

@@ -1,6 +1,8 @@
 import { ErrorMessage } from '../types/error.types';
 import { DataImportFileUpload, DataImportFileUploadStatus, Sex } from "../types/oht.types";
 import dayjs from 'dayjs';
+import { TransformationRulesChains } from "../types/custom-parser.types";
+declare function getPatientAge(documentDate?: Date, patientBirthdate?: Date): number | null;
 declare function isPatientAgeValid(documentDate?: Date, patientBirthdate?: Date): boolean;
 declare function parseExternalPatientId(patientExternalId?: string): boolean;
 declare function parseGender(patientGender?: string): {
@@ -23,4 +25,5 @@ declare function postFileUploadSetStatus(payload: {
         lastUpdated: dayjs.Dayjs;
     };
 }, fileUploadId: string, filename: string, ohtCoreApiKey: string): Promise<DataImportFileUpload>;
-export { parseExternalPatientId, parseGender, isPatientAgeValid, handleRejection, queryFileUploadsWithFilters, postFileUploadSetStatus };
+declare function getPartnerTransformationRules(partnerId: string, labKeys: string[], ohtCoreApiKey: string): Promise<TransformationRulesChains>;
+export { parseExternalPatientId, parseGender, isPatientAgeValid, getPatientAge, handleRejection, queryFileUploadsWithFilters, postFileUploadSetStatus, getPartnerTransformationRules, };

package/dist/service/auxiliaryFunctions.service.js

@@ -6,9 +6,11 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseExternalPatientId = parseExternalPatientId;
 exports.parseGender = parseGender;
 exports.isPatientAgeValid = isPatientAgeValid;
+exports.getPatientAge = getPatientAge;
 exports.handleRejection = handleRejection;
 exports.queryFileUploadsWithFilters = queryFileUploadsWithFilters;
 exports.postFileUploadSetStatus = postFileUploadSetStatus;
+exports.getPartnerTransformationRules = getPartnerTransformationRules;
 const moment_1 = __importDefault(require("moment/moment"));
 const apiUtils_1 = require("../util-ts/apiUtils");
 const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
@@ -19,10 +21,17 @@ const utc_1 = __importDefault(require("dayjs/plugin/utc"));
 dayjs_1.default.extend(customParseFormat_1.default);
 dayjs_1.default.extend(utc_1.default);
 const logger = (0, pinoLogger_1.default)();
-function isPatientAgeValid(documentDate, patientBirthdate) {
+const OHT_CORE_URL = process.env.OHT_CORE_URL;
+function getPatientAge(documentDate, patientBirthdate) {
     if (!patientBirthdate || !documentDate)
+        return null;
+    return (0, moment_1.default)(documentDate).diff(patientBirthdate, 'years');
+}
+function isPatientAgeValid(documentDate, patientBirthdate) {
+    const patientAge = getPatientAge(documentDate, patientBirthdate);
+    if (patientAge === null) {
         return false;
-    const patientAge = (0, moment_1.default)(documentDate).diff(patientBirthdate, 'years');
+    }
     return patientAge >= 18 && patientAge <= 130;
 }
 function parseExternalPatientId(patientExternalId) {
@@ -68,4 +77,47 @@ async function postFileUploadSetStatus(payload, fileUploadId, filename, ohtCoreA
     logger.info({ resp: processingResponse?.data }, `Resp: POST status: ${payload.status} /file-uploads/${fileUploadId}, filename: ${filename}`);
     return processingResponse?.data;
 }
+// getPartnerTransformationRules fetches all the available partner transformation rules
+async function getPartnerTransformationRules(partnerId, labKeys, ohtCoreApiKey) {
+    // Fetch every partner transformation rule
+    const ohtCoreTransformationRulesUrl = `${OHT_CORE_URL}/v1/customparser/partners/${partnerId}/transformation-rules`;
+    const rulesResponse = await (0, apiUtils_1.makeApiCallWithRetry)('GET', ohtCoreTransformationRulesUrl, null, ohtCoreApiKey);
+    const rulesMap = (rulesResponse?.data?.items ?? [])
+        .reduce((map, rule) => {
+        return map.set(rule.id, {
+            id: rule.id,
+            name: rule.name,
+            description: rule.description,
+            conditionExpression: rule.conditionExpression,
+            valueExpression: rule.valueExpression,
+            targetExpression: rule.targetExpression,
+            tags: [],
+            createdAt: dayjs_1.default.utc(rule.createdAt).toDate(),
+            updatedAt: dayjs_1.default.utc(rule.updatedAt).toDate(),
+        });
+    }, new Map());
+    // Fetch the rule chains for the requested labKeys
+    const ohtCoreTransformationRulesChainsUrl = `${OHT_CORE_URL}/v1/customparser/partners/${partnerId}/transformation-rules-chains/query`;
+    const rulesChainsResponse = await (0, apiUtils_1.makeApiCallWithRetry)('POST', ohtCoreTransformationRulesChainsUrl, {
+        filters: [
+            {
+                field: 'labKey',
+                multiSearch: labKeys,
+            }
+        ],
+    }, ohtCoreApiKey);
+    // Hydrate the rules chains with the actual rules
+    return (rulesChainsResponse?.data?.items ?? [])
+        .reduce((map, chainItem) => {
+        return map.set(chainItem.labKey, chainItem.ruleIds
+            .map((ruleId) => {
+            const rule = rulesMap.get(ruleId);
+            if (!rule) {
+                throw new Error(`Transformation rule with ID ${ruleId} for labKey ${chainItem.labKey} not found for partner ${partnerId}.`);
+            }
+            return rule;
+        })
+            .filter((rule) => rule !== undefined));
+    }, new Map());
+}
 //# sourceMappingURL=auxiliaryFunctions.service.js.map

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

@@ -1,4 +1,4 @@
-import { LabToOhtContract, LabToOhtMapper, RangeExtraction, RangeExtractionResponse, UnitExtraction, ValueExtraction, SynonymUnit, UnknownUnits } from "../types/custom-parser.types";
+import { LabToOhtContract, LabToOhtMapper, RangeExtraction, RangeExtractionResponse, UnitExtraction, ValueExtraction, SynonymUnit, UnknownUnits, TransformationRulesChains } from "../types/custom-parser.types";
 import { Biomarker, BiomarkerValueType, Measurement, MeasurementValueComparator, PatientInfo, UnknownMeasurement, Exam } from "../types/oht.types";
 declare function extractUnit(unitExtraction: UnitExtraction | undefined, rawData: any, ohtBiomarker: Biomarker, synonymUnits?: SynonymUnit[] | null, partnerId?: string | null | undefined): {
     unit: string;
@@ -26,10 +26,15 @@ declare function parseExamValue(rawExamObj: any, valueExtraction: ValueExtractio
     isValueParsedCorrectly: boolean;
 };
 declare function checkValueForPlausibleValues(labToOhtMapper: LabToOhtMapper, ohtBiomarker: Biomarker, unit: string, value: number, isUnitParsedCorrectly: boolean): boolean;
-declare function ohtMeasurementsExtractor(labToOhtContract: LabToOhtContract, exams: Exam[], ohtCoreApiKey: string, partnerId?: string | null | undefined): Promise<{
+type ApplyTransformationRulesResult = {
+    transformedExams: Exam[];
+    applicationErrorMessages: string[];
+};
+declare function ohtMeasurementsExtractor(labToOhtContract: LabToOhtContract, exams: Exam[], transformationRules: TransformationRulesChains, ohtCoreApiKey: string, partnerId?: string | null | undefined): Promise<{
     measurements: Measurement[];
     unknownMeasurements: UnknownMeasurement[];
     unknownUnits: UnknownUnits[];
     isReportCorrectlyParsed: boolean;
+    transformationRulesErrors: string[];
 }>;
-export { ohtMeasurementsExtractor, checkValueForPlausibleValues, extractReferenceRanges, extractReferenceAnnotation, parseExamValue, getRangeFromPositionAndRegex, extractUnit, extractValueFromGreaterLowerThan };
+export { ApplyTransformationRulesResult, ohtMeasurementsExtractor, checkValueForPlausibleValues, extractReferenceRanges, extractReferenceAnnotation, parseExamValue, getRangeFromPositionAndRegex, extractUnit, extractValueFromGreaterLowerThan };

package/dist/service/ohtMeasurementsExtractor.service.js

@@ -16,6 +16,8 @@ const regexUtils_1 = require("../util-ts/regexUtils");
 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 = '';
@@ -291,12 +293,113 @@ function checkValueForPlausibleValues(labToOhtMapper, ohtBiomarker, unit, value,
     }
     return isPlausibleValue;
 }
-async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey, partnerId) {
+/**
+ * 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 ohtMeasurementsExtractor(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) => `  - ${e}`).join("\n\n")}`,
+        });
+    }
+    const transformedExams = transformedExamsResult.transformedExams;
+    const transformedExamsMap = transformedExams.reduce((map, exam) => map.set(exam.ohtExam.labKey, exam), new Map());
     const allPossibleOHTBmIds = [];
     [
         ...Object.values(labToOhtContract.labToOhtList)
@@ -331,7 +434,12 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey,
             });
             return;
         }
-        const rawExamObj = JSON.parse(labToOhtMapper.rawExam);
+        let examObj = JSON.parse(labToOhtMapper.rawExam);
+        // Get the transformed exam for this labKey
+        const transformedExam = transformedExamsMap.get(labToOhtMapper.labKey);
+        if (transformedExam) {
+            examObj = transformedExam.ohtExam;
+        }
         if (labToOhtMapper?.ohtBmId && labToOhtMapper?.ohtBmId !== -1) {
             // if BM is already in measurements, continue to the next one
             if (measurements.some(measurement => measurement.biomarkerId === labToOhtMapper.ohtBmId)) {
@@ -348,7 +456,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey,
             const bmInfo = ohtBiomarker?.acf?.shortName ?
                 `name:${ohtBiomarker.acf.shortName}, bmId:${labToOhtMapper.ohtBmId}, labKey:${labToOhtMapper.labKey}` :
                 `bmId:${labToOhtMapper.ohtBmId}, labKey:${labToOhtMapper.labKey}`;
-            const { unit, isUnitParsedCorrectly, originalUnit, isArbitraryUnit, unknownUnit } = extractUnit(labToOhtMapper.unitExtraction, rawExamObj, ohtBiomarker, synonymUnits, partnerId);
+            const { unit, isUnitParsedCorrectly, originalUnit, isArbitraryUnit, unknownUnit } = extractUnit(labToOhtMapper.unitExtraction, examObj, ohtBiomarker, synonymUnits, partnerId);
             if (unknownUnit.length > 0) {
                 unknownUnits.push({
                     biomarkerId: ohtBiomarker.id,
@@ -370,7 +478,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey,
                 });
                 isMeasurementCorrectlyParsed = false;
             }
-            let { valueType, alphanumericalValue, numberValue, valueComparator, isValueParsedCorrectly } = parseExamValue(rawExamObj, labToOhtMapper.valueExtraction, ohtBiomarker);
+            let { valueType, alphanumericalValue, numberValue, valueComparator, isValueParsedCorrectly } = parseExamValue(examObj, labToOhtMapper.valueExtraction, ohtBiomarker);
             if (!isValueParsedCorrectly) {
                 logger.warn({ labToOhtMapper }, `Value not extracted correctly for "${labToOhtMapper.ohtBmId}|${labToOhtMapper.labKey}", filename: ${filename}`);
                 labToOhtContract.errorMessages.push({
@@ -397,7 +505,7 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey,
             let isRangeParsedCorrectly = true;
             // If the biomarker is numerical, extract the reference range
             if ((0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker)) {
-                const extractedRange = extractReferenceRanges(labToOhtMapper, rawExamObj, labToOhtContract.patientInfo, labToOhtContract.documentDate);
+                const extractedRange = extractReferenceRanges(labToOhtMapper, examObj, labToOhtContract.patientInfo, labToOhtContract.documentDate);
                 from = extractedRange.from ?? null;
                 to = extractedRange.to ?? null;
                 isRangeParsedCorrectly = extractedRange.isRangeParsedCorrectly;
@@ -413,16 +521,16 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey,
             }
             let extractedAnnotation;
             if (labToOhtMapper?.referenceAsAnnotation?.use || labToOhtMapper?.annotationConfig?.enabled) {
-                extractedAnnotation = extractReferenceAnnotation(labToOhtMapper, rawExamObj, labToOhtContract.patientInfo, labToOhtContract.documentDate, exams);
+                extractedAnnotation = extractReferenceAnnotation(labToOhtMapper, examObj, labToOhtContract.patientInfo, labToOhtContract.documentDate, transformedExams);
             }
-            const material = (0, dataUtils_1.extractValue)(rawExamObj, labToOhtMapper.material);
-            const method = (0, dataUtils_1.extractValue)(rawExamObj, labToOhtMapper.method);
+            const material = (0, dataUtils_1.extractValue)(examObj, labToOhtMapper.material);
+            const method = (0, dataUtils_1.extractValue)(examObj, labToOhtMapper.method);
             let alphaValue = !(0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker) && alphanumericalValue
                 ? alphanumericalValue.trim()
                 : '';
             // adding unit for alphanumerical values as number.
             if (!Number.isNaN(parseFloat(alphaValue))) {
-                let originalUnit = (0, dataUtils_1.extractValue)(rawExamObj, labToOhtMapper?.unitExtraction?.unitPosition);
+                let originalUnit = (0, dataUtils_1.extractValue)(examObj, labToOhtMapper?.unitExtraction?.unitPosition);
                 originalUnit = originalUnit?.replaceAll(/ /g, '') ?? '';
                 alphaValue = alphaValue && unit?.length > 0 ? `${alphaValue} ${originalUnit}`.trim() : alphaValue;
             }
@@ -506,7 +614,8 @@ async function ohtMeasurementsExtractor(labToOhtContract, exams, ohtCoreApiKey,
         measurements,
         unknownMeasurements,
         unknownUnits,
-        isReportCorrectlyParsed
+        isReportCorrectlyParsed,
+        transformationRulesErrors,
     };
 }
 //# sourceMappingURL=ohtMeasurementsExtractor.service.js.map

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

@@ -1 +1 @@
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package/dist/service/transformationRules.service.js

@@ -6,6 +6,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.validateJsonataExpression = exports.applyRules = void 0;
 const jsonata_1 = __importDefault(require("jsonata"));
 const transformationRules_1 = require("../util-ts/transformationRules");
+const pinoLogger_1 = __importDefault(require("../util-ts/pinoLogger"));
+const logger = (0, pinoLogger_1.default)();
 /**
  * JSON Transformation Rules Engine
  *
@@ -38,7 +40,10 @@ const evaluateCondition = async (condition, context) => {
         return Boolean(result);
     }
     catch (error) {
-        console.error('Error evaluating condition:', error);
+        logger.error({
+            error: error instanceof Error ? error.message : String(error),
+            condition,
+        }, 'Error evaluating condition.');
         return false;
     }
 };
@@ -57,7 +62,10 @@ const evaluateValueExpression = async (valueExpression, context) => {
         return result;
     }
     catch (error) {
-        console.error('Error evaluating value expression:', error);
+        logger.error({
+            error: error instanceof Error ? error.message : String(error),
+            valueExpression,
+        }, 'Error evaluating value expression.');
         throw error;
     }
 };
@@ -139,11 +147,20 @@ const applyRules = async (rules, inputData, options = {}) => {
         appliedRules: [],
         errors: [],
     }));
+    // In case of errors, do not return partial transformed input.
+    if (result.errors.length > 0) {
+        return {
+            success: false,
+            data: inputData,
+            appliedRules: [],
+            errors: result.errors,
+        };
+    }
     return {
-        success: result.errors.length === 0,
+        success: true,
         data: result.data,
         appliedRules: result.appliedRules,
-        errors: result.errors,
+        errors: [],
     };
 };
 exports.applyRules = applyRules;

package/dist/service/transformationRules.service.js.map

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

@@ -1,5 +1,6 @@
 import { ErrorMessage } from "./error.types";
 import { AnnotationConfig, DataOrigin, MeasurementValueComparator, OhtExam, PatientInfo } from "./oht.types";
+import { TransformationRule } from "./transformationRules.types";
 export interface SynonymUnit {
     id: string;
     partnerId: string | null;
@@ -98,3 +99,4 @@ export interface LabToOhtContract {
     sourceFilename: string;
     externalPatientId: string;
 }
+export type TransformationRulesChains = Map<string, TransformationRule[]>;

package/dist/types/custom-parser.types.js.map

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

@@ -432,3 +432,24 @@ export interface BackendBiomarkerMapping {
     /** Optional tagged LOINC code */
     taggedLoincCode?: string;
 }
+/** Custom parser transformation rules */
+export type TransformationRule = {
+    id: string;
+    partnerId: string;
+    name: string;
+    description: string;
+    conditionExpression: string;
+    targetExpression: string;
+    valueExpression: string;
+    createdAt: string;
+    updatedAt: string;
+};
+/** Custom parser transformation rules chain for a labkey */
+export type TransformationRuleChain = {
+    id: string;
+    partnerId: string;
+    labKey: string;
+    ruleIds: string[];
+    createdAt: string;
+    updatedAt: string;
+};

package/dist/util-ts/regexUtils.js

@@ -4,17 +4,35 @@ exports.getGreaterThanPatterns = getGreaterThanPatterns;
 exports.getLowerThanPatterns = getLowerThanPatterns;
 // utils/patterns.ts
 function getGreaterThanPatterns() {
-    const pattern1 = /superior\s+a\s+([\d,]+)/;
-    const pattern2 = />\s?([\d,]+)/;
-    const pattern3 = /maior\s+que\s+([\d,]+)/;
-    const pattern4 = /mais\s+que\s+([\d,]+)/;
-    return [pattern1, pattern2, pattern3, pattern4];
+    // Check >= pattern first to avoid partial matches with >
+    const pattern1 = />=\s*([\d,]+)/;
+    // Then check > patterns
+    const pattern2 = /superior\s+a\s+([\d,]+)/;
+    const pattern3 = />\s?([\d,]+)/;
+    const pattern4 = /maior\s+que\s+([\d,]+)/;
+    const pattern5 = /mais\s+que\s+([\d,]+)/;
+    return [
+        pattern1,
+        pattern2,
+        pattern3,
+        pattern4,
+        pattern5
+    ];
 }
 function getLowerThanPatterns() {
-    const pattern1 = /inferior\s+a\s+([\d,]+)/;
-    const pattern2 = /<\s*([\d,.]+)/;
-    const pattern3 = /menor\s+que\s+([\d,]+)/;
-    const pattern4 = /menos\s+que\s+([\d,]+)/;
-    return [pattern1, pattern2, pattern3, pattern4];
+    // Check <= pattern first to avoid partial matches with <
+    const pattern1 = /<=\s*([\d,.]+)/;
+    // Then check < patterns
+    const pattern2 = /inferior\s+a\s+([\d,]+)/;
+    const pattern3 = /<\s*([\d,.]+)/;
+    const pattern4 = /menor\s+que\s+([\d,]+)/;
+    const pattern5 = /menos\s+que\s+([\d,]+)/;
+    return [
+        pattern1,
+        pattern2,
+        pattern3,
+        pattern4,
+        pattern5
+    ];
 }
 //# sourceMappingURL=regexUtils.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"regexUtils.js","sourceRoot":"","sources":["../../util-ts/regexUtils.ts"],"names":[],"mappings":";;AACA,wDAiBC;AAED,oDAiBC;AArCD,oBAAoB;AACpB,SAAgB,sBAAsB;IAClC,yDAAyD;IACzD,MAAM,QAAQ,GAAG,eAAe,CAAC;IAEjC,wBAAwB;IACxB,MAAM,QAAQ,GAAG,yBAAyB,CAAC;IAC3C,MAAM,QAAQ,GAAG,cAAc,CAAC;IAChC,MAAM,QAAQ,GAAG,wBAAwB,CAAC;IAC1C,MAAM,QAAQ,GAAG,uBAAuB,CAAC;IAEzC,OAAO;QACH,QAAQ;QACR,QAAQ;QACR,QAAQ;QACR,QAAQ;QACR,QAAQ;KACX,CAAC;AACN,CAAC;AAED,SAAgB,oBAAoB;IAChC,yDAAyD;IACzD,MAAM,QAAQ,GAAG,gBAAgB,CAAC;IAElC,wBAAwB;IACxB,MAAM,QAAQ,GAAG,yBAAyB,CAAC;IAC3C,MAAM,QAAQ,GAAG,eAAe,CAAC;IACjC,MAAM,QAAQ,GAAG,wBAAwB,CAAC;IAC1C,MAAM,QAAQ,GAAG,wBAAwB,CAAC;IAE1C,OAAO;QACH,QAAQ;QACR,QAAQ;QACR,QAAQ;QACR,QAAQ;QACR,QAAQ;KACX,CAAC;AACN,CAAC"}

package/package.json

@@ -1,34 +1,34 @@
-{
-  "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.2.54",
-  "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": "^1.6.7",
-    "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"
-  },
-  "devDependencies": {
-    "@types/jest": "^29.5.14",
-    "axios-mock-adapter": "^2.1.0",
-    "jest": "^29.7.0",
-    "ts-jest": "^29.2.5"
-  }
-}
+{
+  "name": "@openhealth/oht-custom-parser-lib",
+  "version": "0.2.56",
+  "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": "^1.6.7",
+    "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"
+  },
+  "devDependencies": {
+    "@types/jest": "^29.5.14",
+    "axios-mock-adapter": "^2.1.0",
+    "jest": "^29.7.0",
+    "ts-jest": "^29.2.5"
+  }
+}