@openhealth/oht-custom-parser-lib 0.5.53 → 0.5.54

package/dist/service/ohtReportMeasurementsExtractor.service.js

@@ -39,6 +39,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.ohtReportMeasurementsExtractor = ohtReportMeasurementsExtractor;
 const crypto_1 = __importDefault(require("crypto"));
 const dataUtils_1 = require("../util-ts/dataUtils");
+const loincMapping_1 = require("../util-ts/loincMapping");
 const extractionUtils_1 = require("../util-ts/extractionUtils");
 const processingLogger_service_1 = require("./processingLogger.service");
 const apiUtils_1 = require("../util-ts/apiUtils");
@@ -292,6 +293,7 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
     else {
         processingLogger_service_1.processingLogger.logInfo(`No biomarker mappings found in backend for partner: ${partnerId}`);
     }
+    const loincMappingByOhtBmId = (0, loincMapping_1.buildLoincMappingByOhtBmId)(mappedBiomarkers);
     // Assign UUIDs to exams for tracking through duplicate-labKey (double-hit) support.
     const examsWithIds = exams.map((exam) => ({
         ...exam,
@@ -588,8 +590,10 @@ async function ohtReportMeasurementsExtractor(isReportPreview, exams, sourceFile
             if (labKey.startsWith('GROUPED_') && !extractedAnnotation) {
                 continue;
             }
+            const loincMapping = loincMappingByOhtBmId.get(ohtBiomarker.id);
             let measurement = {
                 biomarkerId: ohtBiomarker.id,
+                ...(loincMapping ? { loincMapping } : {}),
                 valueType,
                 value: (0, dataUtils_1.isBiomarkerValueNumerical)(ohtBiomarker) ? numberValue : null,
                 alphanumericValue: alphaValue,

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

@@ -1 +1 @@
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package/dist/types/oht.types.d.ts

@@ -155,8 +155,13 @@ export type DataImportFileUpload = {
     labOrderId?: string;
     prescriberExternalId?: string;
 };
+export interface LoincMapping {
+    loincCode?: string;
+    bmObjectUuid?: string;
+}
 export interface Measurement {
     biomarkerId: number;
+    loincMapping?: LoincMapping;
     valueType: BiomarkerValueType;
     alphanumericValue: string | null;
     alphanumericRiskLevelId?: string;
@@ -546,6 +551,7 @@ export interface BackendBiomarkerMapping {
     keepAsUnmapped?: boolean;
     /** Optional tagged LOINC code */
     taggedLoincCode?: string;
+    loincMapping?: LoincMapping;
     /** all the following configurations will be deleted */
     /** Range extraction configuration */
     rangeExtraction: RangeExtractionConfig;

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

@@ -1 +1 @@
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package/dist/util-ts/loincMapping.d.ts

@@ -0,0 +1,5 @@
+import type { BackendBiomarkerMapping, LoincMapping } from '../types/oht.types';
+/** Prefer structured loincMapping; fall back to legacy taggedLoincCode. */
+export declare function getEffectiveLoincMapping(mapping: Pick<BackendBiomarkerMapping, 'loincMapping' | 'taggedLoincCode'> | null | undefined): LoincMapping | undefined;
+/** Build ohtBmId → effective loincMapping from fetched partner biomarker mappings. */
+export declare function buildLoincMappingByOhtBmId(mappedBiomarkers: Record<string, BackendBiomarkerMapping> | null | undefined): Map<number, LoincMapping>;

package/dist/util-ts/loincMapping.js

@@ -0,0 +1,81 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getEffectiveLoincMapping = getEffectiveLoincMapping;
+exports.buildLoincMappingByOhtBmId = buildLoincMappingByOhtBmId;
+const UUID_RE = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i;
+function trimField(value) {
+    return (value ?? '').trim();
+}
+function normalizeLoincCodeKey(code) {
+    return trimField(code).replace(/\s+/g, '');
+}
+function extractUuid(value) {
+    const trimmed = trimField(value);
+    if (!trimmed) {
+        return undefined;
+    }
+    const lower = trimmed.toLowerCase();
+    return UUID_RE.test(lower) ? lower : undefined;
+}
+function normalizeLoincMapping(lm) {
+    if (!lm) {
+        return undefined;
+    }
+    const loincCode = normalizeLoincCodeKey(lm.loincCode ?? '');
+    const bmObjectUuid = extractUuid(lm.bmObjectUuid);
+    if (!loincCode && !bmObjectUuid) {
+        return undefined;
+    }
+    const result = {};
+    if (loincCode) {
+        result.loincCode = loincCode;
+    }
+    if (bmObjectUuid) {
+        result.bmObjectUuid = bmObjectUuid;
+    }
+    return result;
+}
+/** Prefer structured loincMapping; fall back to legacy taggedLoincCode. */
+function getEffectiveLoincMapping(mapping) {
+    if (!mapping) {
+        return undefined;
+    }
+    const fromStructured = normalizeLoincMapping(mapping.loincMapping);
+    if (fromStructured) {
+        return fromStructured;
+    }
+    const tagged = trimField(mapping.taggedLoincCode);
+    if (!tagged) {
+        return undefined;
+    }
+    const uuid = extractUuid(tagged);
+    if (uuid && uuid === tagged.toLowerCase()) {
+        return { bmObjectUuid: uuid };
+    }
+    const codeKey = normalizeLoincCodeKey(tagged);
+    if (codeKey) {
+        return { loincCode: codeKey };
+    }
+    return undefined;
+}
+/** Build ohtBmId → effective loincMapping from fetched partner biomarker mappings. */
+function buildLoincMappingByOhtBmId(mappedBiomarkers) {
+    const index = new Map();
+    if (!mappedBiomarkers) {
+        return index;
+    }
+    for (const mapping of Object.values(mappedBiomarkers)) {
+        if (!mapping || mapping.isIgnored || mapping.ohtBmId <= 0) {
+            continue;
+        }
+        const effective = getEffectiveLoincMapping(mapping);
+        if (!effective) {
+            continue;
+        }
+        if (!index.has(mapping.ohtBmId)) {
+            index.set(mapping.ohtBmId, effective);
+        }
+    }
+    return index;
+}
+//# sourceMappingURL=loincMapping.js.map

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

@@ -0,0 +1 @@
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package/package.json

@@ -1,40 +1,40 @@
-{
-  "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.5.53",
-  "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": "^1.13.2",
-    "bottleneck": "^2.19.5",
-    "csv-parse": "^6.2.1",
-    "dayjs": "^1.11.13",
-    "dotenv": "^16.4.5",
-    "jsonata": "^2.1.0",
-    "moment": "^2.30.1",
-    "mongodb": "^6.3.0",
-    "pino": "^8.19.0",
-    "pino-pretty": "^11.3.0",
-    "xml2js": "^0.6.2"
-  },
-  "devDependencies": {
-    "@types/jest": "^29.5.14",
-    "@types/xml2js": "^0.4.14",
-    "axios-mock-adapter": "^2.1.0",
-    "jest": "^29.7.0",
-    "ts-jest": "^29.2.5",
-    "tsx": "^4.19.2",
-    "typescript": "^5.0.0"
-  }
-}
+{
+  "name": "@openhealth/oht-custom-parser-lib",
+  "version": "0.5.54",
+  "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": "^1.13.2",
+    "bottleneck": "^2.19.5",
+    "csv-parse": "^6.2.1",
+    "dayjs": "^1.11.13",
+    "dotenv": "^16.4.5",
+    "jsonata": "^2.1.0",
+    "moment": "^2.30.1",
+    "mongodb": "^6.3.0",
+    "pino": "^8.19.0",
+    "pino-pretty": "^11.3.0",
+    "xml2js": "^0.6.2"
+  },
+  "devDependencies": {
+    "@types/jest": "^29.5.14",
+    "@types/xml2js": "^0.4.14",
+    "axios-mock-adapter": "^2.1.0",
+    "jest": "^29.7.0",
+    "ts-jest": "^29.2.5",
+    "tsx": "^4.19.2",
+    "typescript": "^5.0.0"
+  }
+}

package/readme.md

@@ -1,115 +1,115 @@
-# 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');
-```
-
-## Logging
-
-- **Production / GCP**: Logs are emitted as JSON (one line per log) for Cloud Logging.
-- **Local / development**: When `NODE_ENV !== 'production'`, logs are pretty-printed in the terminal (colors, timestamps, readable structure). You can override: `LOG_PRETTY=true` to force pretty output, or `LOG_PRETTY=false` to force JSON when not in production.
-
-### Processing logger: request-scoped state
-
-The processing logger (`processingLogger`, `runWithContextAsync`, `getRequestIdFromContext`) uses a **registry + facade** so each request has isolated state and logs never leak context between concurrent invocations (e.g. in Cloud Functions).
-
-- **Registry**: One `ProcessingState` per request, keyed by request id (`fileUploadId ?? messageId ?? cloudEventId ?? generatedId`). The same id is used for the whole request.
-- **AsyncLocalStorage**: Holds only the current request id; state is resolved via `registry.get(id)`.
-- **Entry point**: Wrap your handler in `runWithContextAsync(context, async () => { ... })`. The lib creates a registry entry, runs your callback with the id in AsyncLocalStorage, and removes the entry in a `finally` block.
-- **Clear-state rule**: If there is no request id or the id is not in the registry (e.g. logging outside `runWithContextAsync` or after teardown), the logger uses a **transient empty state** for that call only (never stored). That way one request never overwrites another’s context.
-
-Use `processingLogger.logInfo`, `logWarn`, `logError`, `logProgress`, etc. inside the callback so logs include the same context and are searchable by `fileUploadId` / filename.
-
-## 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');
+```
+
+## Logging
+
+- **Production / GCP**: Logs are emitted as JSON (one line per log) for Cloud Logging.
+- **Local / development**: When `NODE_ENV !== 'production'`, logs are pretty-printed in the terminal (colors, timestamps, readable structure). You can override: `LOG_PRETTY=true` to force pretty output, or `LOG_PRETTY=false` to force JSON when not in production.
+
+### Processing logger: request-scoped state
+
+The processing logger (`processingLogger`, `runWithContextAsync`, `getRequestIdFromContext`) uses a **registry + facade** so each request has isolated state and logs never leak context between concurrent invocations (e.g. in Cloud Functions).
+
+- **Registry**: One `ProcessingState` per request, keyed by request id (`fileUploadId ?? messageId ?? cloudEventId ?? generatedId`). The same id is used for the whole request.
+- **AsyncLocalStorage**: Holds only the current request id; state is resolved via `registry.get(id)`.
+- **Entry point**: Wrap your handler in `runWithContextAsync(context, async () => { ... })`. The lib creates a registry entry, runs your callback with the id in AsyncLocalStorage, and removes the entry in a `finally` block.
+- **Clear-state rule**: If there is no request id or the id is not in the registry (e.g. logging outside `runWithContextAsync` or after teardown), the logger uses a **transient empty state** for that call only (never stored). That way one request never overwrites another’s context.
+
+Use `processingLogger.logInfo`, `logWarn`, `logError`, `logProgress`, etc. inside the callback so logs include the same context and are searchable by `fileUploadId` / filename.
+
+## 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.