@openhealth/oht-custom-parser-lib 0.2.76 → 0.2.78

package/dist/index.d.ts

@@ -1,12 +1,11 @@
 export { postDataImportFileUploadToCore, postReportPreviewToCore } from './service/reportCreator.service';
 export { parseExternalPatientId, parseGender, isPatientAgeValid, handleRejection, queryFileUploadsWithFilters, postFileUploadSetStatus, DigitalizationUpdateFields } from './service/auxiliaryFunctions.service';
-export { ohtReportMeasurementsExtractor, } from './service/ohtReportMeasurementsExtractor.service';
 export { ohtMeasurementsExtractor, checkValueForPlausibleValues, extractReferenceRanges, extractReferenceAnnotation, parseExamValue, getRangeFromPositionAndRegex, extractUnit, extractValueFromGreaterLowerThan } from './service/ohtMeasurementsExtractor.service';
 export { getSlackFileIssueNotificationMessage, sendMessageToSlack } from './service/slackMessages.service';
 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, UnmappedLabKey, 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, } 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';
@@ -15,4 +14,3 @@ export { readFileFromBucket, uploadFileBufferToGCS } from './util-ts/googleStora
 export { default as pinoLogger } from './util-ts/pinoLogger';
 export { getGreaterThanPatterns, getLowerThanPatterns } from './util-ts/regexUtils';
 export { getMappedBiomarkers, } from './util-ts/dataUtils';
-export { parseRange } from './util-ts/extractionUtils';

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.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.ohtReportMeasurementsExtractor = exports.postFileUploadSetStatus = exports.queryFileUploadsWithFilters = exports.handleRejection = exports.isPatientAgeValid = exports.parseGender = exports.parseExternalPatientId = exports.postReportPreviewToCore = exports.postDataImportFileUploadToCore = void 0;
-exports.parseRange = exports.getMappedBiomarkers = exports.getLowerThanPatterns = exports.getGreaterThanPatterns = void 0;
+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;
 // ### SERVICES ###
 var reportCreator_service_1 = require("./service/reportCreator.service");
 Object.defineProperty(exports, "postDataImportFileUploadToCore", { enumerable: true, get: function () { return reportCreator_service_1.postDataImportFileUploadToCore; } });
@@ -16,8 +16,6 @@ Object.defineProperty(exports, "isPatientAgeValid", { enumerable: true, get: fun
 Object.defineProperty(exports, "handleRejection", { enumerable: true, get: function () { return auxiliaryFunctions_service_1.handleRejection; } });
 Object.defineProperty(exports, "queryFileUploadsWithFilters", { enumerable: true, get: function () { return auxiliaryFunctions_service_1.queryFileUploadsWithFilters; } });
 Object.defineProperty(exports, "postFileUploadSetStatus", { enumerable: true, get: function () { return auxiliaryFunctions_service_1.postFileUploadSetStatus; } });
-var ohtReportMeasurementsExtractor_service_1 = require("./service/ohtReportMeasurementsExtractor.service");
-Object.defineProperty(exports, "ohtReportMeasurementsExtractor", { enumerable: true, get: function () { return ohtReportMeasurementsExtractor_service_1.ohtReportMeasurementsExtractor; } });
 var ohtMeasurementsExtractor_service_1 = require("./service/ohtMeasurementsExtractor.service");
 Object.defineProperty(exports, "ohtMeasurementsExtractor", { enumerable: true, get: function () { return ohtMeasurementsExtractor_service_1.ohtMeasurementsExtractor; } });
 Object.defineProperty(exports, "checkValueForPlausibleValues", { enumerable: true, get: function () { return ohtMeasurementsExtractor_service_1.checkValueForPlausibleValues; } });
@@ -76,6 +74,4 @@ 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; } });
-var extractionUtils_1 = require("./util-ts/extractionUtils");
-Object.defineProperty(exports, "parseRange", { enumerable: true, get: function () { return extractionUtils_1.parseRange; } });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

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package/dist/service/reportCreator.service.js

@@ -160,13 +160,20 @@ async function postDataImportFileUploadToCore(dataImportFileUpload, unknownMeasu
     catch (error) {
         const errorDetail = (0, apiUtils_1.parseErrorObj)(error);
         logger.error({ patchStatus, resp: errorDetail }, `ERROR: on report generation url:${ohtCoreIngestionUrl} filename: ${filename}`);
-        // set digitalization error
-        await (0, apiUtils_1.makeApiCallWithRetry)('patch', ohtCoreDigitalizationUrl, {
-            status: oht_types_1.DigitizationStatus.ERROR,
-            pipelineStep: oht_types_1.PipelineStep.EXTRACTING_BIOMARKERS,
-            pipelineStepData: rejectReason,
-        }, ohtCoreApiKey);
-        return null;
+        // Set digitalization error for tracking
+        try {
+            await (0, apiUtils_1.makeApiCallWithRetry)('patch', ohtCoreDigitalizationUrl, {
+                status: oht_types_1.DigitizationStatus.ERROR,
+                pipelineStep: oht_types_1.PipelineStep.SENDING_RESULTS,
+                pipelineStepData: rejectReason,
+            }, ohtCoreApiKey);
+        }
+        catch (digitalizationError) {
+            logger.error({ digitalizationError: (0, apiUtils_1.parseErrorObj)(digitalizationError) }, `Failed to update digitalization status, filename: ${filename}`);
+        }
+        // Re-throw error so it can be handled by the error handler in agnostic-parser
+        // The error handler will detect 409 conflicts and update file upload status appropriately
+        throw error;
     }
 }
 //# sourceMappingURL=reportCreator.service.js.map

package/dist/service/reportCreator.service.js.map

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

@@ -73,7 +73,7 @@ export interface OriginalExam {
 export interface LabToOhtMapper {
     ohtBmId?: number;
     biomarkerName?: string;
-    labKey?: string;
+    labKey: string;
     rawExam?: string;
     material?: string;
     method?: string;

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

@@ -182,7 +182,6 @@ export interface OhtRange {
     text: string;
     age?: string;
     sex?: string;
-    noSourceRanges?: boolean;
 }
 export interface OriginalExam {
     contentType: string;
@@ -445,9 +444,6 @@ export interface BackendBiomarkerMapping {
     jsonBlob?: any;
     isIgnored?: boolean;
     keepAsUnmapped?: boolean;
-    /** Optional tagged LOINC code */
-    taggedLoincCode?: string;
-    /** all the following configurations will be deleted */
     /** Range extraction configuration */
     rangeExtraction: RangeExtractionConfig;
     /** Unit extraction configuration */
@@ -457,7 +453,9 @@ export interface BackendBiomarkerMapping {
     /** Reference as annotation configuration */
     referenceAsAnnotation: ReferenceAsAnnotationConfig;
     /** Annotation configuration for appended biomarkers */
-    annotationConfig: AnnotationConfig;
+    annotationConfig?: AnnotationConfig;
+    /** Optional tagged LOINC code */
+    taggedLoincCode?: string;
 }
 /** Custom parser transformation rules */
 export type TransformationRule = {

package/dist/types/oht.types.js.map

@@ -1 +1 @@
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+{"version":3,"file":"oht.types.js","sourceRoot":"","sources":["../../types/oht.types.ts"],"names":[],"mappings":";;;AA8OA,IAAY,GAIX;AAJD,WAAY,GAAG;IACb,oBAAa,CAAA;IACb,wBAAiB,CAAA;IACjB,sBAAe,CAAA;AACjB,CAAC,EAJW,GAAG,mBAAH,GAAG,QAId;AAED,IAAY,UAGX;AAHD,WAAY,UAAU;IACpB,qDAAuC,CAAA;IACvC,6BAAe,CAAA;AACjB,CAAC,EAHW,UAAU,0BAAV,UAAU,QAGrB;AAED,IAAY,0BAYX;AAZD,WAAY,0BAA0B;IACpC,mDAAqB,CAAA;IACrB,iDAAmB,CAAA;IACnB,uDAAyB,CAAA;IACzB,uDAAyB,CAAA;IACzB,qDAAuB,CAAA;IACvB,qDAAuB,CAAA;IACvB,6CAAe,CAAA;IACf,iDAAmB,CAAA;IACnB,mDAAqB,CAAA;IACrB,mDAAqB,CAAA;IACrB,2DAA6B,CAAA;AAC/B,CAAC,EAZW,0BAA0B,0CAA1B,0BAA0B,QAYrC;AAED,IAAY,kBAGX;AAHD,WAAY,kBAAkB;IAC5B,uDAAiC,CAAA;IACjC,6CAAuB,CAAA;AACzB,CAAC,EAHW,kBAAkB,kCAAlB,kBAAkB,QAG7B;AAED,IAAY,0BAIX;AAJD,WAAY,0BAA0B;IACpC,6CAAe,CAAA;IACf,2DAA6B,CAAA;IAC7B,qDAAuB,CAAA;AACzB,CAAC,EAJW,0BAA0B,0CAA1B,0BAA0B,QAIrC;AAED,IAAY,kBAOX;AAPD,WAAY,kBAAkB;IAC5B,yCAAmB,CAAA;IACnB,yCAAmB,CAAA;IACnB,+CAAyB,CAAA;IACzB,mCAAa,CAAA;IACb,qCAAe,CAAA;IACf,2CAAqB,CAAA;AACvB,CAAC,EAPW,kBAAkB,kCAAlB,kBAAkB,QAO7B;AAED,IAAY,YASX;AATD,WAAY,YAAY;IACtB,6CAA6B,CAAA;IAC7B,mDAAmC,CAAA;IACnC,yDAAyC,CAAA;IACzC,2DAA2C,CAAA;IAC3C,2DAA2C,CAAA;IAC3C,+DAA+C,CAAA;IAC/C,2DAA2C,CAAA;IAC3C,mDAAmC,CAAA;AACrC,CAAC,EATW,YAAY,4BAAZ,YAAY,QASvB;AAED,IAAY,YAgBX;AAhBD,WAAY,YAAY;IACtB,mFAAmE,CAAA;IACnE,uDAAuC,CAAA;IACvC,+DAA+C,CAAA;IAC/C,mDAAmC,CAAA;IACnC,iEAAiD,CAAA;IACjD,uDAAuC,CAAA;IACvC,uDAAuC,CAAA;IACvC,6DAA6C,CAAA;IAC7C,2EAA2D,CAAA;IAC3D,2DAA2C,CAAA;IAC3C,uEAAuD,CAAA;IACvD,yDAAyC,CAAA;IACzC,uEAAuD,CAAA;IACvD,iEAAiD,CAAA;IACjD,oHAAoG,CAAA;AACtG,CAAC,EAhBW,YAAY,4BAAZ,YAAY,QAgBvB;AA6CD,IAAY,YAIX;AAJD,WAAY,YAAY;IACtB,+BAAe,CAAA;IACf,iCAAiB,CAAA;IACjB,2BAAW,CAAA;AACb,CAAC,EAJW,YAAY,4BAAZ,YAAY,QAIvB;AAsCD,IAAY,kBAIX;AAJD,WAAY,kBAAkB;IAC5B,6CAAuB,CAAA;IACvB,2CAAqB,CAAA;IACrB,uDAAiC,CAAA;AACnC,CAAC,EAJW,kBAAkB,kCAAlB,kBAAkB,QAI7B;AAED,IAAY,sBAOX;AAPD,WAAY,sBAAsB;IAChC,+CAAqB,CAAA;IACrB,+CAAqB,CAAA;IACrB,4EAAkD,CAAA;IAClD,4EAAkD,CAAA;IAClD,4DAAkC,CAAA;IAClC,2CAAiB,CAAA;AACnB,CAAC,EAPW,sBAAsB,sCAAtB,sBAAsB,QAOjC;AAED,IAAY,WAGX;AAHD,WAAY,WAAW;IACrB,wBAAS,CAAA;IACT,sCAAuB,CAAA;AACzB,CAAC,EAHW,WAAW,2BAAX,WAAW,QAGtB;AAED,IAAY,kCAGX;AAHD,WAAY,kCAAkC;IAC5C,6DAAuB,CAAA;IACvB,iEAA2B,CAAA;AAC7B,CAAC,EAHW,kCAAkC,kDAAlC,kCAAkC,QAG7C;AAED,IAAY,gCAMX;AAND,WAAY,gCAAgC;IAC1C,2DAAuB,CAAA;IACvB,6EAAyC,CAAA;IACzC,+EAA2C,CAAA;IAC3C,2FAAuD,CAAA;IACvD,uFAAmD,CAAA;AACrD,CAAC,EANW,gCAAgC,gDAAhC,gCAAgC,QAM3C"}

package/package.json

@@ -1,34 +1,34 @@
-{
-  "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.2.76",
-  "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": "0.2.78",
+  "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"
+  }
+}

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.

package/dist/service/ohtAgnosticMeasurementsExtractor.service.d.ts

@@ -1,59 +0,0 @@
-import { LabToOhtContract, LabToOhtMapper, RangeExtractionResponse, SynonymUnit, UnknownUnits, TransformationRulesChains } from "../types/custom-parser.types";
-import { Biomarker, BiomarkerValueType, Measurement, MeasurementValueComparator, PatientInfo, UnknownMeasurement, Exam } from "../types/oht.types";
-/**
- * Extracts unit from rawData (OhtExam object)
- * @param rawData - OhtExam object (not a JSON string)
- * @param ohtBiomarker - Biomarker information
- * @param synonymUnits - Synonym units for unit resolution
- * @param partnerId - Partner ID for synonym resolution
- */
-declare function agnosticExtractUnit(rawData: any, ohtBiomarker: Biomarker, synonymUnits?: SynonymUnit[] | null, partnerId?: string | null | undefined): {
-    unit: string;
-    isUnitParsedCorrectly: boolean;
-    originalUnit: string;
-    isArbitraryUnit: boolean;
-    unknownUnit: string;
-};
-/**
- * Extracts reference annotation from rawExam (OhtExam object)
- * @param labToOhtMapper - Lab to OHT mapper configuration
- * @param rawExam - OhtExam object (not a JSON string)
- * @param patientInfo - Patient information
- * @param documentDate - Document date
- * @param exams - Array of exams for appended mappings
- */
-declare function agnosticExtractReferenceAnnotation(labToOhtMapper: LabToOhtMapper, rawExam: any, patientInfo: PatientInfo, documentDate?: Date, exams?: Exam[]): string;
-/**
- * Extracts reference ranges from rawData (OhtExam object)
- * Always uses parseRange function from extractionUtils for range extraction
- */
-declare function agnosticExtractReferenceRanges(labToOhtMapper: LabToOhtMapper, rawData: any, patientInfo: PatientInfo, documentDate?: Date): RangeExtractionResponse;
-declare function agnosticExtractValueFromGreaterLowerThan(value: string): {
-    extractedValue: number | null;
-    extractedValueComparator: MeasurementValueComparator | null;
-    valueParsedCorrectly: boolean;
-};
-/**
- * Parses exam value from rawExamObj (OhtExam object)
- * Now uses value directly from ohtExam
- */
-declare function agnosticParseExamValue(rawExamObj: any, ohtBiomarker: Biomarker): {
-    valueType: BiomarkerValueType;
-    alphanumericalValue: string | null;
-    numberValue: number | null;
-    valueComparator: MeasurementValueComparator;
-    isValueParsedCorrectly: boolean;
-};
-declare function agnosticCheckValueForPlausibleValues(labToOhtMapper: LabToOhtMapper, ohtBiomarker: Biomarker, unit: string, value: number, isUnitParsedCorrectly: boolean): boolean;
-type ApplyTransformationRulesResult = {
-    transformedExams: Exam[];
-    applicationErrorMessages: string[];
-};
-declare function ohtAgnosticMeasurementsExtractor(labToOhtContract: LabToOhtContract, exams: Exam[], transformationRules: TransformationRulesChains, ohtCoreApiKey: string, partnerId?: string | null | undefined): Promise<{
-    measurements: Measurement[];
-    unknownMeasurements: UnknownMeasurement[];
-    unknownUnits: UnknownUnits[];
-    isReportCorrectlyParsed: boolean;
-    transformationRulesErrors: string[];
-}>;
-export { ApplyTransformationRulesResult, ohtAgnosticMeasurementsExtractor, agnosticCheckValueForPlausibleValues, agnosticExtractReferenceRanges, agnosticExtractReferenceAnnotation, agnosticParseExamValue, agnosticExtractUnit, agnosticExtractValueFromGreaterLowerThan };