@js4cytoscape/ndex-client 0.6.0-alpha.1 → 0.6.0-alpha.2

package/README.md

@@ -1,15 +1,13 @@
 # NDEx JavaScript Client
 
-A modern TypeScript/JavaScript client library for the NDEx (Network Data Exchange) API.
+A 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
 
@@ -48,35 +46,117 @@ console.log('User:', user.data);
 
 ## Documentation
 
-### Client Documentation
+### Documentation Architecture
 
-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/)
+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 site (API + narrative)
+# Build complete documentation (API + user guides)
 npm run docs:build
 
-# Build only API reference (TypeDoc)
+# Build only API reference (clean TypeDoc HTML)
 npm run docs:api
 
-# Serve documentation locally for development
+# 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
 
-# Clean documentation files
+```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/`;
 ```
 
-The documentation site will be available at `http://localhost:3000` when served locally.
+### Documentation Content Structure
 
-**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
+- **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
 
@@ -231,14 +311,25 @@ src/
 ├── types/                  # TypeScript definitions
 └── models/                 # Data models
 
-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
+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
+
+docs-site/                  # Legacy documentation (to be removed)
 
 __tests__/
 ├── unit/                   # Fast unit tests

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package/dist/index.d.mts

@@ -463,6 +463,14 @@ interface AccessKeyResponse {
  * Valid actions for updating access keys
  */
 declare type AccessKeyAction = 'enable' | 'disable';
+/**
+ * NDEx object update status - returned from network creation and update operations
+ * Corresponds to server-side NdexObjectUpdateStatus class
+ */
+interface NDExObjectUpdateStatus {
+    uuid: string;
+    modificationTime: number;
+}
 
 /**
  * HTTPService - Core HTTP client for NDEx API communication
@@ -470,6 +478,7 @@ declare type AccessKeyAction = 'enable' | 'disable';
  *
  * @note User-Agent header is set to 'NDEx-JS-Client/${version}' but only works in Node.js.
  *       Browsers will ignore custom User-Agent headers for security reasons.
+ * @internal
  */
 declare class HTTPService {
     private axiosInstance;
@@ -507,67 +516,7 @@ declare class HTTPService {
     delete<T = any>(endpoint: string, config?: AxiosRequestConfig & {
         version?: 'v2' | 'v3';
     }): Promise<T>;
-    /**
-     * Upload a file to the NDEx API with progress tracking support
-     *
-     * This method handles file uploads using multipart/form-data encoding and supports
-     * various input types for maximum flexibility across different environments.
-     *
-     * @template T - The expected response type from the API
-     * @param endpoint - API endpoint path (e.g., 'networks' for network upload)
-     * @param file - File data to upload. Supports multiple input types:
-     *   - `File` (browser): HTML5 File object from file input or drag-and-drop
-     *   - `Blob` (browser): Binary data as Blob object
-     *   - `Buffer` (Node.js): Binary data as Buffer for server-side uploads
-     *   - `string`: Text content that will be converted to Blob (useful for CX/CX2 JSON)
-     * @param options - Upload configuration options
-     * @param options.filename - Custom filename for the upload. Defaults:
-     *   - File objects: uses `file.name`
-     *   - Other types: 'file.cx2'
-     * @param options.contentType - MIME type for string content (default: 'application/json')
-     * @param options.onProgress - Progress callback that receives percentage (0-100)
-     *   Called periodically during upload with current progress
-     * @param options.version - API version to use ('v2' or 'v3', defaults to 'v2')
-     * @param options.config - Additional Axios configuration options
-     *
-     * @returns Promise resolving to upload result
-     *
-     * @example
-     * ```typescript
-     * // Upload a File object from file input (browser)
-     * const fileInput = document.getElementById('file') as HTMLInputElement;
-     * const file = fileInput.files[0];
-     * const result = await httpService.uploadFile('networks', file, {
-     *   filename: 'my-network.cx2',
-     *   onProgress: (progress) => console.log(`Upload: ${progress}%`),
-     *   version: 'v3'
-     * });
-     *
-     * // Upload CX2 network data as string
-     * const cx2Data = JSON.stringify({ CXVersion: '2.0', networks: [...] });
-     * const result = await httpService.uploadFile('networks', cx2Data, {
-     *   filename: 'network.cx2',
-     *   contentType: 'application/json',
-     *   version: 'v3'
-     * });
-     *
-     * // Upload with progress tracking
-     * const result = await httpService.uploadFile('networks', file, {
-     *   onProgress: (progress) => {
-     *     progressBar.style.width = `${progress}%`;
-     *     console.log(`Uploading: ${progress}%`);
-     *   }
-     * });
-     * ```
-     *
-     * @throws Will throw NDExError on network errors,
-     *         server errors, or invalid file data
-     *
-     * @note The Content-Type header is automatically set to 'multipart/form-data'
-     *       and Axios will handle the boundary parameter automatically
-     */
     uploadFile<T = any>(endpoint: string, file: File | Blob | Buffer | string, options?: {
-        filename?: string;
         contentType?: string;
         onProgress?: (progress: number) => void;
         version?: 'v2' | 'v3';
@@ -818,14 +767,12 @@ declare class NetworkServiceV3 {
      */
     createNetworkFromCX2(cx2Data: CX2Network$1 | CX2Network, options?: {
         visibility?: 'PUBLIC' | 'PRIVATE';
-        name?: string;
-    }): Promise<{
-        uuid: string;
-    }>;
+        folderId?: string;
+    }): Promise<NDExObjectUpdateStatus>;
     /**
      * Update network with CX2 data
      */
-    updateNetworkCX2(networkUUID: string, cx2Data: CX2Network$1 | CX2Network): Promise<void>;
+    updateNetworkCX2(networkUUID: string, cx2Data: CX2Network$1 | CX2Network): Promise<NDExObjectUpdateStatus>;
     /**
      * Upload network file (CX2, CX, or other formats)
      */
@@ -1303,28 +1250,33 @@ declare class UnifiedNetworkService {
     /**
      * Create network from raw CX2 data (migrated from original NDEx.js)
      *
-     * Creates a new network in NDEx from raw CX2 network data. This is an unstable function
-     * for uploading CX2 format networks directly to NDEx using the V3 API. The function
-     * extracts the network UUID from the response location header.
+     * Creates a new network on NDEx from raw CX2 data using the V3 API.
+     * This function delegates to the NetworkServiceV3 implementation.
      *
-     * @param rawCX2 - Raw CX2 network data as an object or CX2Network instance
-     * @param makePublic - Whether to make the network public (default: false = private)
-     * @returns Promise resolving to an object containing the UUID of the created network
+     * @param cx2Data - Raw CX2 network data as an object or CX2Network instance
+     * @param options - Creation options including visibility and folderId
+     * @param options.visibility - Network visibility: 'PUBLIC' or 'PRIVATE' (default: 'PRIVATE')
+     * @param options.folderId - UUID of the folder to create the network in. If omitted, network is created in user's home directory
+     * @returns Promise resolving to NDExObjectUpdateStatus with uuid and modificationTime
      *
      * @example
      * ```typescript
-     * // Create private network from raw CX2 data
+     * // Create private network from raw CX2 data in user's home directory
      * const result = await client.networks.createNetworkFromRawCX2(cx2Data);
      * console.log(result.uuid); // "12345678-1234-1234-1234-123456789abc"
      *
-     * // Create public network from raw CX2 data
-     * const publicResult = await client.networks.createNetworkFromRawCX2(cx2Data, true);
+     * // Create public network from raw CX2 data in a specific folder
+     * const publicResult = await client.networks.createNetworkFromRawCX2(cx2Data, {
+     *   visibility: 'PUBLIC',
+     *   folderId: '87654321-4321-4321-4321-876543210fed'
+     * });
      * console.log(publicResult.uuid);
      * ```
      */
-    createNetworkFromRawCX2(rawCX2: CX2Network$1 | any, makePublic?: boolean): Promise<{
-        uuid: string;
-    }>;
+    createNetworkFromRawCX2(cx2Data: CX2Network$1 | CX2Network, options?: {
+        visibility?: 'PUBLIC' | 'PRIVATE';
+        folderId?: string;
+    }): Promise<NDExObjectUpdateStatus>;
     /**
      * Update network from raw CX2 data (migrated from original NDEx.js)
      *
@@ -1926,6 +1878,29 @@ declare class NDExClient {
         networks: NetworkServiceV3;
     };
 }
+/**
+ * Library version string imported from package.json
+ *
+ * Provides programmatic access to the current library version for:
+ * - Runtime version checking and validation
+ * - Debugging and error reporting
+ * - Logging and telemetry
+ * - Version-dependent feature detection
+ *
+ * @example
+ * ```typescript
+ * import { NDExClient, version } from '@js4cytoscape/ndex-client';
+ *
+ * console.log(`Using NDEx Client v${version}`);
+ *
+ * // In error reports
+ * const errorReport = {
+ *   error: err.message,
+ *   libraryVersion: version,
+ *   timestamp: new Date().toISOString()
+ * };
+ * ```
+ */
 declare const version: string;
 
-export { type APIError, type APIResponse, type AccessKeyAction, type AccessKeyResponse, type AccessParams, AdminService, type BasicAuth, type CX1Edge, type CX1MetaDataItem, type CX1MetaDataResponse, type CX1NetworkProperty, type CX2AttributeDeclarations, type CX2AttributeSpec, type CX2Edge, type CX2EdgeBypass, type CX2ImportParams, type CX2MetaData, CX2Network, type CX2NetworkAttribute, type CX2NetworkProperties, type CX2Node, type CX2NodeBypass, type CX2Status, type CX2VisualProperty, CyNDExService as CyNDEx, type CyNDExAuthConfig, type CyNDExConfig, CyNDExService, type CyNDExStatusResponse, type CyWebWorkspace, type CytoscapeNetworkSummary, type DefaultVisualProperties, type ExportFormat, type ExportRequest, FilesService, HTTPService, type MappingDefinition, type NDExAny, NDExAuthError, type NDExAuthResponse, NDExClient, type NDExClientConfig, NDExError, type NDExExportParams, type NDExImportParams, NDExNetworkError, NDExNotFoundError, NDExServerError, type NDExUser, NDExValidationError, NetworkIndexLevel, type NetworkPermission, NetworkServiceV2, NetworkServiceV3, type NetworkSummaryV2, type NetworkSummaryV3, type OAuthAuth, type PaginationParams, type SearchParameters, type SearchResult, type TableColumnVisualStyle, type Task, type Timestamp, type UUID, UnifiedNetworkService, UserService, type VPMappingType, type VisualPropertyMapping, type VisualPropertyTable, WorkspaceService, version };
+export { type APIError, type APIResponse, type AccessKeyAction, type AccessKeyResponse, type AccessParams, AdminService, type BasicAuth, type CX1Edge, type CX1MetaDataItem, type CX1MetaDataResponse, type CX1NetworkProperty, type CX2AttributeDeclarations, type CX2AttributeSpec, type CX2Edge, type CX2EdgeBypass, type CX2ImportParams, type CX2MetaData, CX2Network, type CX2NetworkAttribute, type CX2NetworkProperties, type CX2Node, type CX2NodeBypass, type CX2Status, type CX2VisualProperty, CyNDExService as CyNDEx, type CyNDExAuthConfig, type CyNDExConfig, CyNDExService, type CyNDExStatusResponse, type CyWebWorkspace, type CytoscapeNetworkSummary, type DefaultVisualProperties, type ExportFormat, type ExportRequest, FilesService, type MappingDefinition, type NDExAny, NDExAuthError, type NDExAuthResponse, NDExClient, type NDExClientConfig, NDExError, type NDExExportParams, type NDExImportParams, NDExNetworkError, NDExNotFoundError, type NDExObjectUpdateStatus, NDExServerError, type NDExUser, NDExValidationError, NetworkIndexLevel, type NetworkPermission, NetworkServiceV2, NetworkServiceV3, type NetworkSummaryV2, type NetworkSummaryV3, type OAuthAuth, type PaginationParams, type SearchParameters, type SearchResult, type TableColumnVisualStyle, type Task, type Timestamp, type UUID, UnifiedNetworkService, UserService, type VPMappingType, type VisualPropertyMapping, type VisualPropertyTable, WorkspaceService, version };