@js4cytoscape/ndex-client 0.5.0-alpha.9 → 0.6.0-alpha.2

package/README.md

@@ -1,27 +1,353 @@
-# NDEx Javascript client
+# NDEx JavaScript Client
 
-A NDEx API Client written in JS.
+A TypeScript/JavaScript client library for the NDEx (Network Data Exchange) API.
+
+## Features
+
+- 🚀 **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
+
+## 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
 
+### Documentation Architecture
+
+This project uses a **hybrid documentation architecture** that separates concerns for optimal user experience:
+
+```
+docs-root/
+├── index.html                   # Main landing page with navigation
+├── api/                         # TypeDoc HTML output (standalone)
+│   ├── index.html               # API reference home
+│   ├── classes/                 # Class documentation
+│   ├── interfaces/              # Interface documentation
+│   └── enums/                   # Enum documentation
+├── guide/                       # Docusaurus site (user guides)
+│   ├── docs/                    # Narrative documentation source
+│   ├── build/                   # Built Docusaurus site
+│   └── docusaurus.config.js    # Docusaurus configuration
+└── assets/                      # Shared resources
+```
+
+**Key Benefits:**
+- 🎯 **No MDX Escaping Issues** - TypeDoc generates clean HTML directly
+- 🔧 **Independent Tools** - Each tool works in its optimal format
+- 🚀 **Better Performance** - Static HTML for API docs, optimized React for guides
+- 🛠️ **Easier Maintenance** - Tool updates don't break each other
+
+### Local Development
+
+#### Building Documentation
+
+```bash
+# Build complete documentation (API + user guides)
+npm run docs:build
+
+# Build only API reference (clean TypeDoc HTML)
+npm run docs:api
+
+# Build only user guides (Docusaurus)
+npm run docs:site
+
+# Clean all documentation build artifacts
+npm run docs:clean
+```
+
+#### Serving Locally
+
+```bash
+# Option 1: Serve complete documentation site (recommended for testing)
+cd docs-root && python3 -m http.server 8000
+# Visit: http://localhost:8000/
+
+# Option 2: Serve only Docusaurus in development mode
+npm run docs:serve
+# Visit: http://localhost:3000/ (Docusaurus dev server)
+```
+
+**Local Documentation URLs:**
+- **Main Landing Page**: `http://localhost:8000/`
+- **User Guides**: `http://localhost:8000/guide/build/` 
+- **API Reference**: `http://localhost:8000/api/`
+
+#### Development Workflow
+
+```bash
+# 1. Clean previous builds
+npm run docs:clean
+
+# 2. Generate API documentation
+npm run docs:api
+
+# 3. Build user guides with local API links
+cd docs-root/guide && npm run build:local
+
+# 4. Serve complete site for testing
+cd .. && python3 -m http.server 8000
+```
+
+### GitHub Pages Deployment
+
+Documentation is automatically deployed via GitHub Actions on pushes to `main` or `ndex3-major-refactor` branches.
+
+**Live Documentation**: [https://cytoscape.org/js4cytoscape/ndex-client/](https://cytoscape.org/js4cytoscape/ndex-client/)
+
+#### Deployment Workflow
+
+1. **Package Detection** - Auto-detects packages with `docs-root/` directories
+2. **API Documentation** - Generates clean TypeDoc HTML (no MDX processing needed)
+3. **User Guides** - Builds Docusaurus with production API links
+4. **Site Assembly** - Combines both into unified documentation site
+5. **GitHub Pages** - Deploys to `gh-pages` branch
+
+#### Environment-Aware Configuration
+
+The system automatically uses the correct API reference URLs:
+- **Local**: `http://localhost:8000/api/` 
+- **Production**: `https://cytoscape.org/js4cytoscape/ndex-client/api/`
+
+```javascript
+// docs-root/guide/docusaurus.config.js
+const isLocal = process.env.DOCUSAURUS_LOCAL === 'true';
+const siteUrl = isLocal ? 'http://localhost:8000' : 'https://cytoscape.org';
+const basePath = isLocal ? '' : '/js4cytoscape/ndex-client';
+const apiUrl = `${siteUrl}${basePath}/api/`;
+```
+
+### Documentation Content Structure
+
+- **Landing Page** (`docs-root/index.html`) - Professional overview with navigation
+- **Getting Started** - Installation, authentication, first network (serves as Docusaurus home)
+- **User Guides** - Working with networks, user management
+- **Examples** - Code examples and integration patterns  
+- **API Reference** - Complete TypeScript API documentation (TypeDoc HTML)
+
+#### 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
+
+docs-root/                  # New hybrid documentation architecture
+├── index.html             # Main landing page with navigation
+├── api/                   # TypeDoc HTML output (generated)
+│   ├── index.html         # API reference home
+│   ├── classes/           # Class documentation
+│   ├── interfaces/        # Interface documentation
+│   └── enums/             # Enum documentation
+├── guide/                 # Docusaurus site for user guides
+│   ├── docs/              # Narrative documentation source
+│   │   ├── getting-started.md    # Installation, auth (serves as home)
+│   │   ├── getting-started/      # Authentication, first network
+│   │   ├── guides/               # User guides and workflows  
+│   │   └── examples/             # Code examples
+│   ├── build/             # Built Docusaurus site (generated)
+│   ├── docusaurus.config.js     # Docusaurus configuration
+│   └── package.json       # Documentation dependencies
+└── assets/                # Shared documentation resources
 
-## Getting started
+docs-site/                  # Legacy documentation (to be removed)
 
-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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