@js4cytoscape/ndex-client 0.5.0-alpha.9 → 0.6.0-alpha.1

package/README.md

@@ -1,27 +1,262 @@
-# NDEx Javascript client
+# NDEx JavaScript Client
 
-A NDEx API Client written in JS.
+A modern TypeScript/JavaScript client library for the NDEx (Network Data Exchange) API.
+
+## Features
+
+- 🎯 **Modern TypeScript** - Full type safety and IntelliSense support
+- 🚀 **Multiple Formats** - ESM, CJS, and UMD builds
+- 🔒 **Authentication** - Basic auth and OAuth support
+- 🌐 **Version Support** - Compatible with NDEx API v2 and v3
+- 📦 **Lightweight** - Optimized bundle sizes
+- 🧪 **Well Tested** - Comprehensive unit and integration tests
+
+## Installation
+
+```bash
+npm install @js4cytoscape/ndex-client
+```
+
+## Quick Start
+
+```typescript
+import { NDExClient } from '@js4cytoscape/ndex-client';
+
+// Create client
+const client = new NDExClient({
+  baseURL: 'https://www.ndexbio.org',
+  timeout: 30000
+});
+
+// Authenticate (optional for public operations)
+client.updateConfig({
+  auth: {
+    type: 'basic',
+    username: 'your-username',
+    password: 'your-password'
+  }
+});
+
+// Get server status
+const status = await client.getServerStatus();
+console.log('Server status:', status.data);
+
+// Get current user (requires authentication)
+const user = await client.user.getCurrentUser();
+console.log('User:', user.data);
+```
 
 ## Documentation
 
+### Client Documentation
+
+This project uses a hybrid documentation approach combining:
+- **Narrative Documentation** - Guides, tutorials, and examples built with [Docusaurus](https://docusaurus.io/)
+- **API Reference** - Auto-generated from TypeScript source code using [TypeDoc](https://typedoc.org/)
+
+#### Building Documentation
+
+```bash
+# Build complete documentation site (API + narrative)
+npm run docs:build
+
+# Build only API reference (TypeDoc)
+npm run docs:api
+
+# Serve documentation locally for development
+npm run docs:serve
+
+# Clean documentation files
+npm run docs:clean
+```
+
+The documentation site will be available at `http://localhost:3000` when served locally.
+
+**Documentation Structure:**
+- **Getting Started** - Installation, authentication, first network
+- **User Guides** - Working with networks, user management, file operations  
+- **Examples** - Code examples and integration patterns
+- **API Reference** - Complete TypeScript API documentation
+
+#### Online Documentation
+
 - See the full [NDEx API documentation](https://home.ndexbio.org/using-the-ndex-server-api/)
 - Try out the [NDEx API](http://openapi.ndextools.org/)
 
-_Have in mind that you have to build your library before publishing. The files under the `dist` folder are the ones that should be distributed._
+## Development
+
+### Prerequisites
+
+- Node.js 16+ 
+- npm or yarn
+
+### Setup
+
+1. **Install dependencies**
+   ```bash
+   npm install
+   ```
+
+2. **Configure integration tests** (optional)
+   ```bash
+   # Edit test/testconfig.js with your NDEx credentials
+   # This is only needed if you want to run integration tests
+   ```
+
+### Building
+
+The library uses [tsup](https://tsup.egoist.dev/) for fast, modern bundling:
+
+```bash
+# Build for production
+npm run build
+
+# Build in watch mode during development  
+npm run dev
+```
+
+**Build outputs:**
+- `dist/index.js` - CommonJS build
+- `dist/index.mjs` - ES Module build
+- `dist/index.global.js` - UMD build for browsers
+- `dist/index.d.ts` - TypeScript declarations
+
+### Testing
+
+The project uses a modern two-tier testing approach:
+
+#### Unit Tests (Fast - Default)
+```bash
+# Run unit tests (default, ~0.5s)
+npm test
+# or
+npm run test:unit
+
+# Watch mode for development
+npm run test:watch
+
+# Unit tests with coverage
+npm run test:coverage
+```
+
+**Unit tests:**
+- ✅ Mock-based, isolated testing
+- ✅ Fast execution for development feedback
+- ✅ 70% coverage requirement
+- ✅ Focus on business logic and error handling
+
+#### Integration Tests (Real API)
+```bash
+# Run integration tests (~1-2s)
+npm run test:integration
+
+# Run all tests (unit + integration)  
+npm run test:all
+
+# CI command with full coverage
+npm run test:ci
+```
+
+**Integration tests:**
+- ✅ Real API calls to NDEx servers
+- ✅ Uses credentials from `test/testconfig.js`
+- ✅ Validates end-to-end functionality
+- ✅ 60% coverage requirement
+
+#### Test Configuration
+
+Integration tests use the configuration in `test/testconfig.js`:
+
+```javascript
+const integrationTestConfig = {
+  server: {
+    baseURL: 'https://dev1.ndexbio.org',  // Test server
+  },
+  testAccount: {
+    username: 'your-test-username',       // Update with your credentials
+    password: 'your-test-password'
+  }
+};
+```
+
+### Other Scripts
+
+```bash
+# Linting and formatting
+npm run lint          # ESLint with auto-fix
+npm run format        # Prettier formatting
+npm run type-check    # TypeScript checking
+
+# Documentation  
+npm run docs:build    # Build complete documentation (API + narrative)
+npm run docs:api      # Generate API reference only
+npm run docs:serve    # Serve documentation locally
+npm run docs:clean    # Clean documentation files
+
+# Cleanup
+npm run clean         # Remove dist and coverage folders
+```
+
+### Development Workflow
+
+1. **Fast development loop:**
+   ```bash
+   npm run dev          # Build in watch mode
+   npm run test:watch   # Tests in watch mode
+   ```
+
+2. **Pre-commit checks:**
+   ```bash
+   npm run test:all     # Full test suite
+   npm run lint         # Code quality
+   npm run type-check   # TypeScript validation
+   ```
+
+3. **Release preparation:**
+   ```bash
+   npm run clean
+   npm run build
+   npm run test:ci
+   ```
+
+## Project Structure
+
+```
+src/
+├── index.ts                 # Main exports
+├── services/               # Service layer
+│   ├── HTTPService.ts      # HTTP client
+│   ├── UserService.ts      # User operations
+│   └── ...
+├── types/                  # TypeScript definitions
+└── models/                 # Data models
 
-## Getting started
+docs-site/                  # Documentation site (Docusaurus)
+├── docs/                   # Narrative documentation
+│   ├── getting-started/    # Installation, auth, first network
+│   ├── guides/            # User guides and workflows
+│   ├── examples/          # Code examples
+│   └── api/               # API reference (generated)
+├── docusaurus.config.js   # Docusaurus configuration
+└── package.json           # Documentation dependencies
 
-1. Build your library
+__tests__/
+├── unit/                   # Fast unit tests
+├── integration/            # Real API tests  
+└── shared/                 # Test utilities
 
-- Modify the testconfig.js file with the credentials of test account.
-- Run `npm install` to get the project's dependencies
-- Run `npm run build` to produce a bundle
+dist/                       # Built library (generated)
+typedoc.json               # TypeDoc configuration
+```
 
-2. Running the tests
+## Contributing
 
-- Run `npm run test`
+1. Fork the repository
+2. Create a feature branch
+3. Make your changes with tests
+4. Run the full test suite: `npm run test:all`
+5. Submit a pull request
 
-## Scripts
+## License
 
-- `npm run build` - produces production version of your library under the `lib` folder
-- `npm run test` - well ... it runs the tests :)
+MIT License - see LICENSE file for details.

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