npm - @openhealth/oht-custom-parser-lib - Versions diffs - 0.2.55 → 0.2.56 - Mend

@openhealth/oht-custom-parser-lib 0.2.55 → 0.2.56

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (13) hide show

package/{readme.md → README.md} +99 -99
package/dist/service/auxiliaryFunctions.service.d.ts +4 -1
package/dist/service/auxiliaryFunctions.service.js +54 -2
package/dist/service/auxiliaryFunctions.service.js.map +1 -1
package/dist/service/ohtMeasurementsExtractor.service.d.ts +8 -3
package/dist/service/ohtMeasurementsExtractor.service.js +119 -10
package/dist/service/ohtMeasurementsExtractor.service.js.map +1 -1
package/dist/service/transformationRules.service.js +21 -4
package/dist/service/transformationRules.service.js.map +1 -1
package/dist/types/custom-parser.types.d.ts +2 -0
package/dist/types/custom-parser.types.js.map +1 -1
package/dist/types/oht.types.d.ts +21 -0
package/package.json +34 -34

package/{readme.md → README.md} RENAMED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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

package/dist/service/auxiliaryFunctions.service.js.map CHANGED Viewed

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

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

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

@@ -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/package.json CHANGED Viewed

@@ -1,34 +1,34 @@
-{
-  "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.2.55",
-  "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"
+  }
+}