@openhealth/oht-custom-parser-lib 0.4.3 → 0.5.3

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

@@ -1 +1 @@
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package/dist/util-ts/pinoLogger.js

@@ -16,6 +16,14 @@ const SeverityLookup = {
     warn: 'WARNING',
     error: 'ERROR',
 };
+/** True when logs should be pretty-printed for terminal (local/dev). GCP/production keeps JSON. */
+function usePrettyLogs() {
+    if (process.env.LOG_PRETTY === 'true')
+        return true;
+    if (process.env.LOG_PRETTY === 'false')
+        return false;
+    return process.env.NODE_ENV !== 'production';
+}
 // Define the default Pino configuration
 const defaultPinoConfig = {
     messageKey: 'message',
@@ -46,8 +54,27 @@ const defaultPinoConfig = {
         }
     },
 };
+/** Options for pino-pretty when running locally (readable terminal output). */
+const prettyTransportOptions = {
+    target: 'pino-pretty',
+    options: {
+        colorize: true,
+        translateTime: 'SYS:HH:MM:ss',
+        messageKey: 'message',
+        singleLine: false,
+        errorLikeObjectKeys: ['err', 'error'],
+        ignore: 'pid,hostname',
+    },
+};
 // Export a function that creates a Pino logger instance with the provided configuration overrides
 exports.default = (pinoConfigOverrides = {}) => {
-    return (0, pino_1.default)({ ...defaultPinoConfig, ...pinoConfigOverrides });
+    const baseConfig = { ...defaultPinoConfig, ...pinoConfigOverrides };
+    if (usePrettyLogs()) {
+        return (0, pino_1.default)({
+            ...baseConfig,
+            transport: prettyTransportOptions,
+        });
+    }
+    return (0, pino_1.default)(baseConfig);
 };
 //# sourceMappingURL=pinoLogger.js.map

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

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package/package.json

@@ -1,34 +1,36 @@
-{
-  "name": "@openhealth/oht-custom-parser-lib",
-  "version": "0.4.3",
-  "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": "0.5.3",
+  "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",
+    "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"
+  },
+  "devDependencies": {
+    "@types/jest": "^29.5.14",
+    "axios-mock-adapter": "^2.1.0",
+    "jest": "^29.7.0",
+    "ts-jest": "^29.2.5",
+    "typescript": "^5.0.0"
+  }
+}

package/readme.md

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

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 };