@openhealth/oht-custom-parser-lib 0.2.78 → 0.2.80

package/dist/index.d.ts

@@ -5,12 +5,12 @@ export { getSlackFileIssueNotificationMessage, sendMessageToSlack } from './serv
 export { aggregateMessages, aggregateBiMessages, publishToTopic, generateBIMessages } from './service/errorHandling.service';
 export { applyRules as applyTransformationRules, validateJsonataExpression as validateTransformationRuleExpression, } from './service/transformationRules.service';
 export { LabToOhtContract, LabToOhtMapper, UnknownMeasurementExtraction, ReferenceAsAnnotation, UnitExtraction, RangeExtraction, RangeExtractionResponse, ValueExtraction, unitSynonyms, ValueExtractionResponse, SynonymUnit, UnknownUnits, } from './types/custom-parser.types';
-export { AcfBiomarkerRangeAnnotationCheck, AcfBiomarkerGenericDisclaimerLogic, ManualCheck, BiomarkerCompatibility, ReferenceRangeType, AcfReferenceRange, VisualRange, NameAlias, AlternativeUnit, BiomarkerAcf, Biomarker, PipelineStep, DigitizationStatus, MeasurementValueComparator, BiomarkerValueType, DataImportFileUploadStatus, Sex, Digitization, PatientInfo, UnknownMeasurement, Measurement, DataImportFileUpload, MessagePayload, SignedUpload, ReportStyleConfig, LanguageCode, BiomarkerCustomisation, PartnerCustomPanel, ReportDisplaySettings, ReportCustomisation, OHTPartner, UploadType, RejectReason, } from './types/oht.types';
+export { AcfBiomarkerRangeAnnotationCheck, AcfBiomarkerGenericDisclaimerLogic, ManualCheck, BiomarkerCompatibility, ReferenceRangeType, AcfReferenceRange, VisualRange, NameAlias, AlternativeUnit, BiomarkerAcf, Biomarker, PipelineStep, DigitizationStatus, MeasurementValueComparator, BiomarkerValueType, DataImportFileUploadStatus, Sex, Digitization, PatientInfo, UnknownMeasurement, Measurement, DataImportFileUpload, MessagePayload, SignedUpload, ReportStyleConfig, LanguageCode, BiomarkerCustomisation, PartnerCustomPanel, ReportDisplaySettings, ReportCustomisation, OHTPartner, UploadType, RejectReason, AnnotationLabKey, ExtractionPath, AnnotationConfig, } from './types/oht.types';
 export { ErrorMessage } from './types/error.types';
 export type { TransformationRule, TransformationContext, ApplyRulesResult as TransformationApplyRulesResult, ApplyRulesOptions as TransformationApplyRulesOptions, ValidationResult as TransformationValidationResult, } from './types/transformationRules.types';
 export { makeApiCallWithRetry, parseErrorObj } from './util-ts/apiUtils';
-export { extractValue, isBiomarkerValueNumerical, isBiomarkerExternalNoVisualRange, processAppendedMappings, fetchSynonymUnits, resolveUnitFromSynonyms } from './util-ts/dataUtils';
+export { extractValue, isBiomarkerValueNumerical, isBiomarkerExternalNoVisualRange, processAppendedMappings, fetchSynonymUnits, resolveUnitFromSynonyms, extractFromPath, applyFormat } from './util-ts/dataUtils';
 export { readFileFromBucket, uploadFileBufferToGCS } from './util-ts/googleStorageUtils';
 export { default as pinoLogger } from './util-ts/pinoLogger';
 export { getGreaterThanPatterns, getLowerThanPatterns } from './util-ts/regexUtils';
-export { getMappedBiomarkers, } from './util-ts/dataUtils';
+export { getMappedBiomarkers, getMappedBiomarkersLatest } from './util-ts/dataUtils';

package/dist/index.js

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getGreaterThanPatterns = exports.pinoLogger = exports.uploadFileBufferToGCS = exports.readFileFromBucket = exports.resolveUnitFromSynonyms = exports.fetchSynonymUnits = exports.processAppendedMappings = exports.isBiomarkerExternalNoVisualRange = exports.isBiomarkerValueNumerical = exports.extractValue = exports.parseErrorObj = exports.makeApiCallWithRetry = exports.RejectReason = exports.UploadType = exports.Sex = exports.DataImportFileUploadStatus = exports.BiomarkerValueType = exports.MeasurementValueComparator = exports.DigitizationStatus = exports.PipelineStep = exports.ReferenceRangeType = exports.BiomarkerCompatibility = exports.ManualCheck = exports.AcfBiomarkerGenericDisclaimerLogic = exports.AcfBiomarkerRangeAnnotationCheck = exports.unitSynonyms = exports.validateTransformationRuleExpression = exports.applyTransformationRules = exports.generateBIMessages = exports.publishToTopic = exports.aggregateBiMessages = exports.aggregateMessages = exports.sendMessageToSlack = exports.getSlackFileIssueNotificationMessage = exports.extractValueFromGreaterLowerThan = exports.extractUnit = exports.getRangeFromPositionAndRegex = exports.parseExamValue = exports.extractReferenceAnnotation = exports.extractReferenceRanges = exports.checkValueForPlausibleValues = exports.ohtMeasurementsExtractor = exports.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.postReportPreviewToCore = exports.postDataImportFileUploadToCore = void 0;
-exports.getMappedBiomarkers = exports.getLowerThanPatterns = void 0;
+exports.uploadFileBufferToGCS = exports.readFileFromBucket = exports.applyFormat = exports.extractFromPath = exports.resolveUnitFromSynonyms = exports.fetchSynonymUnits = exports.processAppendedMappings = exports.isBiomarkerExternalNoVisualRange = exports.isBiomarkerValueNumerical = exports.extractValue = exports.parseErrorObj = exports.makeApiCallWithRetry = exports.RejectReason = exports.UploadType = exports.Sex = exports.DataImportFileUploadStatus = exports.BiomarkerValueType = exports.MeasurementValueComparator = exports.DigitizationStatus = exports.PipelineStep = exports.ReferenceRangeType = exports.BiomarkerCompatibility = exports.ManualCheck = exports.AcfBiomarkerGenericDisclaimerLogic = exports.AcfBiomarkerRangeAnnotationCheck = exports.unitSynonyms = exports.validateTransformationRuleExpression = exports.applyTransformationRules = exports.generateBIMessages = exports.publishToTopic = exports.aggregateBiMessages = exports.aggregateMessages = exports.sendMessageToSlack = exports.getSlackFileIssueNotificationMessage = exports.extractValueFromGreaterLowerThan = exports.extractUnit = exports.getRangeFromPositionAndRegex = exports.parseExamValue = exports.extractReferenceAnnotation = exports.extractReferenceRanges = exports.checkValueForPlausibleValues = exports.ohtMeasurementsExtractor = exports.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.postReportPreviewToCore = exports.postDataImportFileUploadToCore = void 0;
+exports.getMappedBiomarkersLatest = exports.getMappedBiomarkers = exports.getLowerThanPatterns = exports.getGreaterThanPatterns = exports.pinoLogger = void 0;
 // ### SERVICES ###
 var reportCreator_service_1 = require("./service/reportCreator.service");
 Object.defineProperty(exports, "postDataImportFileUploadToCore", { enumerable: true, get: function () { return reportCreator_service_1.postDataImportFileUploadToCore; } });
@@ -64,6 +64,8 @@ Object.defineProperty(exports, "isBiomarkerExternalNoVisualRange", { enumerable:
 Object.defineProperty(exports, "processAppendedMappings", { enumerable: true, get: function () { return dataUtils_1.processAppendedMappings; } });
 Object.defineProperty(exports, "fetchSynonymUnits", { enumerable: true, get: function () { return dataUtils_1.fetchSynonymUnits; } });
 Object.defineProperty(exports, "resolveUnitFromSynonyms", { enumerable: true, get: function () { return dataUtils_1.resolveUnitFromSynonyms; } });
+Object.defineProperty(exports, "extractFromPath", { enumerable: true, get: function () { return dataUtils_1.extractFromPath; } });
+Object.defineProperty(exports, "applyFormat", { enumerable: true, get: function () { return dataUtils_1.applyFormat; } });
 var googleStorageUtils_1 = require("./util-ts/googleStorageUtils");
 Object.defineProperty(exports, "readFileFromBucket", { enumerable: true, get: function () { return googleStorageUtils_1.readFileFromBucket; } });
 Object.defineProperty(exports, "uploadFileBufferToGCS", { enumerable: true, get: function () { return googleStorageUtils_1.uploadFileBufferToGCS; } });
@@ -74,4 +76,5 @@ Object.defineProperty(exports, "getGreaterThanPatterns", { enumerable: true, get
 Object.defineProperty(exports, "getLowerThanPatterns", { enumerable: true, get: function () { return regexUtils_1.getLowerThanPatterns; } });
 var dataUtils_2 = require("./util-ts/dataUtils");
 Object.defineProperty(exports, "getMappedBiomarkers", { enumerable: true, get: function () { return dataUtils_2.getMappedBiomarkers; } });
+Object.defineProperty(exports, "getMappedBiomarkersLatest", { enumerable: true, get: function () { return dataUtils_2.getMappedBiomarkersLatest; } });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

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package/dist/util-ts/dataUtils.d.ts

@@ -14,6 +14,7 @@ export declare function isBiomarkerValueNumerical(biomarker: any): boolean;
 export declare function isBiomarkerExternalNoVisualRange(biomarker: any): boolean;
 export declare const extractValue: (obj: any, position?: string) => any;
 export declare const getMappedBiomarkers: (partnerId: string, ohtCoreApiKey: string) => Promise<any>;
+export declare const getMappedBiomarkersLatest: (partnerId: string, ohtCoreApiKey: string) => Promise<any>;
 export declare const updatePartnerCustomParserUnmappedLabKeys: (partnerId: string, unknownMeasurementsBulk: UnknownMeasurementsBulk, ohtCoreApiKey: string) => Promise<void>;
 export declare const bulkCreateCustomParserUnknownUnits: (partnerId: string, unknownUnits: UnknownUnits[], ohtCoreApiKey: string) => Promise<void>;
 /**
@@ -47,4 +48,20 @@ export declare function processAppendedMappings(exams: any[], labKeys: Annotatio
         used: boolean;
     }>;
 };
+/**
+ * Extract value from object using dot notation path
+ * Supports array indexing and wildcard expansion similar to AnnotationPreviewService
+ * @param obj - Object to extract value from
+ * @param path - Dot notation path (e.g., "description", "value", "unit", "range[*].field", "array[0].field")
+ * @returns Extracted value or null
+ */
+export declare function extractFromPath(obj: any, path: string): string | null;
+/**
+ * Apply format string to value similar to AnnotationPreviewService
+ * Supports %s placeholder and \n for line breaks
+ * @param value - Value to format
+ * @param format - Format string with %s placeholder
+ * @returns Formatted value
+ */
+export declare function applyFormat(value: string, format?: string): string;
 export declare function isNumericalWithoutValidResult(valueType: BiomarkerValueType, numberValue: number | null, alphanumericalValue: string | null): boolean;

package/dist/util-ts/dataUtils.js

@@ -3,11 +3,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.fetchSynonymUnits = exports.bulkCreateCustomParserUnknownUnits = exports.updatePartnerCustomParserUnmappedLabKeys = exports.getMappedBiomarkers = exports.extractValue = void 0;
+exports.fetchSynonymUnits = exports.bulkCreateCustomParserUnknownUnits = exports.updatePartnerCustomParserUnmappedLabKeys = exports.getMappedBiomarkersLatest = exports.getMappedBiomarkers = exports.extractValue = void 0;
 exports.resolveUnitFromSynonyms = resolveUnitFromSynonyms;
 exports.isBiomarkerValueNumerical = isBiomarkerValueNumerical;
 exports.isBiomarkerExternalNoVisualRange = isBiomarkerExternalNoVisualRange;
 exports.processAppendedMappings = processAppendedMappings;
+exports.extractFromPath = extractFromPath;
+exports.applyFormat = applyFormat;
 exports.isNumericalWithoutValidResult = isNumericalWithoutValidResult;
 const oht_types_1 = require("../types/oht.types");
 const apiUtils_1 = require("./apiUtils");
@@ -85,6 +87,21 @@ const getMappedBiomarkers = async (partnerId, ohtCoreApiKey) => {
     }
 };
 exports.getMappedBiomarkers = getMappedBiomarkers;
+// function that uses GET request at /v1/customparser/partner/{partnerId}/latest to get the latest mapping version for the biomarker
+// Used when reportPreview is true to get the latest version regardless of active status
+const getMappedBiomarkersLatest = async (partnerId, ohtCoreApiKey) => {
+    try {
+        const response = await (0, apiUtils_1.makeApiCallWithRetry)('get', `${OHT_CORE_URL}/v1/customparser/partners/${partnerId}/mappings/latest`, null, ohtCoreApiKey);
+        return response?.data?.biomarkerMappings ?? {};
+    }
+    catch (error) {
+        if (error.response?.status === 404) {
+            return {};
+        }
+        throw new Error(`Failed to fetch latest mapped biomarkers: ${error.message}`);
+    }
+};
+exports.getMappedBiomarkersLatest = getMappedBiomarkersLatest;
 // function that uses POST request at /v1/customparser/partners/{partnerId}/unmapped/bulk to send the unknownMeasurements to the server
 const updatePartnerCustomParserUnmappedLabKeys = async (partnerId, unknownMeasurementsBulk, ohtCoreApiKey) => {
     const response = await (0, apiUtils_1.makeApiCallWithRetry)('post', `${OHT_CORE_URL}/v1/customparser/partners/${partnerId}/unmapped/bulk`, {
@@ -265,6 +282,7 @@ function extractFromPath(obj, path) {
 }
 /**
  * Apply format string to value similar to AnnotationPreviewService
+ * Supports %s placeholder and \n for line breaks
  * @param value - Value to format
  * @param format - Format string with %s placeholder
  * @returns Formatted value
@@ -273,7 +291,10 @@ function applyFormat(value, format) {
     if (!format || !value)
         return value;
     try {
-        return format.replace(/%s/g, value);
+        let result = format.replace(/%s/g, value);
+        // Convert \n to actual newlines
+        result = result.replace(/\\n/g, '\n');
+        return result;
     }
     catch {
         return value;

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

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

@@ -1,34 +1,34 @@
-{
-  "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.2.78",
-  "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": "0.2.80",
+  "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"
+  }
+}

package/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.