Class CyNDExService

CyNDEx Service - Cytoscape-NDEx Bridge

Provides seamless integration between Cytoscape desktop application and NDEx, enabling import/export of networks with support for CX and CX2 formats.

This service communicates with Cytoscape via its REST API and handles NDEx authentication parameters that are passed to Cytoscape for NDEx operations.

Example

// Basic usage
const cyNDEx = new CyNDExService();

// Configure NDEx server
cyNDEx.setNDExBaseURL('https://www.ndexbio.org');

// Set authentication
cyNDEx.setBasicAuth('username', 'password');
// or
cyNDEx.setAuthToken('oauth-id-token');

// Import network from NDEx to Cytoscape
await cyNDEx.postNDExNetworkToCytoscape('network-uuid', 'access-key');

// Export network from Cytoscape to NDEx
await cyNDEx.postCytoscapeNetworkToNDEx('current');

// Import CX2 data to Cytoscape
await cyNDEx.postCX2NetworkToCytoscape(cx2String, 'My Network', 'My Collection');

Index

Constructors

constructor

new CyNDExService(port?: number, config?: CyNDExConfig): CyNDExService
Create a new CyNDEx service instance
Parameters
- port: number = 1234
  Port number for Cytoscape REST API (default: 1234)
- Optionalconfig: CyNDExConfig
  Optional configuration object
Returns CyNDExService
- Defined in services/CyNDExService.ts:57

Accessors

port

get port(): number
Get the port number for Cytoscape REST API

Returns number
- Defined in services/CyNDExService.ts:75

`Static`cyRestBaseURL

get cyRestBaseURL(): string
Get the base URL for Cytoscape REST API

Returns string
- Defined in services/CyNDExService.ts:82

Methods

setNDExBaseURL

setNDExBaseURL(ndexBaseURL: string): void
Set NDEx server base URL
Parameters
- ndexBaseURL: string
  Complete base URL for NDEx server (e.g., 'https://www.ndexbio.org') Must include protocol (https:// or http://)
Returns void
Example
```
cyNDEx.setNDExBaseURL('https://www.ndexbio.org');
cyNDEx.setNDExBaseURL('https://test.ndexbio.org');
```
- Defined in services/CyNDExService.ts:98

getNDExBaseURL

getNDExBaseURL(): string
Get the current NDEx server base URL

Returns string
Complete NDEx server base URL
- Defined in services/CyNDExService.ts:109

setBasicAuth

setBasicAuth(username: string, password: string): void
Set basic authentication credentials for NDEx operations
Parameters
- username: string
  NDEx username
- password: string
  NDEx password
Returns void
- Defined in services/CyNDExService.ts:120

setAuthToken

setAuthToken(idToken: string): void
Set OAuth ID token for NDEx operations
Parameters
- idToken: string
  OAuth ID token from authentication provider
Returns void
- Defined in services/CyNDExService.ts:135

clearAuth

clearAuth(): void
Clear authentication credentials

Returns void
- Defined in services/CyNDExService.ts:147

cyRestURL

cyRestURL(): string
Get the complete Cytoscape REST API URL

Returns string
Complete URL for Cytoscape REST API
- Defined in services/CyNDExService.ts:156

getCyNDExStatus

getCyNDExStatus(): Promise<CyNDExStatusResponse>
Get CyNDEx plugin status from Cytoscape

Returns Promise<CyNDExStatusResponse>
Promise resolving to CyNDEx status information
- Defined in services/CyNDExService.ts:234

getCytoscapeNetworkSummary

getCytoscapeNetworkSummary(suid?: string): Promise<CytoscapeNetworkSummary>
Get network summary information from Cytoscape
Parameters
- suid: string = 'current'
  Network SUID or 'current' for current network (default: 'current')
Returns Promise<CytoscapeNetworkSummary>
Promise resolving to network summary
- Defined in services/CyNDExService.ts:244

postNDExNetworkToCytoscape

postNDExNetworkToCytoscape(
    uuid: string,
    accessKey?: string,
    createView?: boolean,
): Promise<any>
Import network from NDEx to Cytoscape
Parameters
- uuid: string
  NDEx network UUID
- OptionalaccessKey: string
  Optional access key for private networks
- OptionalcreateView: boolean
  Whether to create a network view (default: undefined)
Returns Promise<any>
Promise resolving to import result
- Defined in services/CyNDExService.ts:256

postCXNetworkToCytoscape

postCXNetworkToCytoscape(cx: any): Promise<any>
Import CX network data to Cytoscape
Parameters
- cx: any
  CX format network data
Returns Promise<any>
Promise resolving to import result
- Defined in services/CyNDExService.ts:284

postCX2NetworkToCytoscape

postCX2NetworkToCytoscape(
    cx2_string: string,
    title: string,
    collection_name: string,
): Promise<any>
Import CX2 network data to Cytoscape
Parameters
- cx2_string: string
  CX2 format network data as string
- title: string
  Network title
- collection_name: string
  Collection name
Returns Promise<any>
Promise resolving to import result
- Defined in services/CyNDExService.ts:296

postCytoscapeNetworkToNDEx

postCytoscapeNetworkToNDEx(suid?: string): Promise<any>
Export network from Cytoscape to NDEx (create new network)
Parameters
- suid: string = 'current'
  Network SUID or 'current' for current network (default: 'current')
Returns Promise<any>
Promise resolving to export result
- Defined in services/CyNDExService.ts:316

putCytoscapeNetworkInNDEx

putCytoscapeNetworkInNDEx(suid?: string, uuid: string): Promise<any>
Update existing network in NDEx with data from Cytoscape
Parameters
- suid: string = 'current'
  Network SUID or 'current' for current network (default: 'current')
- uuid: string
  Target NDEx network UUID to update
Returns Promise<any>
Promise resolving to update result
- Defined in services/CyNDExService.ts:332

Class CyNDExService

Example

Index

Constructors

Accessors

Methods

Constructors

constructor

Parameters

Returns CyNDExService

Accessors

port

Returns number

StaticcyRestBaseURL

Returns string

Methods

setNDExBaseURL

Parameters

Returns void

Example

getNDExBaseURL

Returns string

setBasicAuth

Parameters

Returns void

setAuthToken

Parameters

Returns void

clearAuth

Returns void

cyRestURL

Returns string

getCyNDExStatus

Returns Promise<CyNDExStatusResponse>

getCytoscapeNetworkSummary

Parameters

Returns Promise<CytoscapeNetworkSummary>

postNDExNetworkToCytoscape

Parameters

Returns Promise<any>

postCXNetworkToCytoscape

Parameters

Returns Promise<any>

postCX2NetworkToCytoscape

Parameters

Returns Promise<any>

postCytoscapeNetworkToNDEx

Parameters

Returns Promise<any>

putCytoscapeNetworkInNDEx

Parameters

Returns Promise<any>

Settings

On This Page

`Static`cyRestBaseURL