@js4cytoscape/ndex-client 0.6.0-alpha.1 → 0.6.0-alpha.3

package/src/types/index.ts

@@ -1,515 +0,0 @@
-/**
- * Core type definitions for NDEx Client Library
- * Pragmatic TypeScript types allowing flexibility with any types where needed
- */
-
-// Export Cytoscape-related types
-export * from './cytoscape';
-
-// ============================================================================
-// Authentication Types
-// ============================================================================
-
-export interface BasicAuth {
-  type: 'basic';
-  username: string;
-  password: string;
-}
-
-export interface OAuthAuth {
-  type: 'oauth';
-  idToken: string;  // ID token from OAuth provider
-}
-
-export interface NDExAuthResponse {
-  token?: string;
-  userId?: string;
-  userName?: string;
-  isAdmin?: boolean;
-  permissions?: string[];
-  expirationTime?: number;
-}
-
-export interface NDExUser {
-  externalId: string;
-  userName: string;
-  firstName?: string;
-  lastName?: string;
-  emailAddress?: string;
-  website?: string;
-  description?: string;
-  image?: string;
-  isIndividual?: boolean;
-  isVerified?: boolean;
-  creationTime?: number;
-  modificationTime?: number;
-}
-
-// ============================================================================
-// Network Types
-// ============================================================================
-
-export interface CX1MetaDataItem {
-  name: string;
-  elementCount: number;
-  version: string;
-  idCounter?: number;
-  [key: string]: any; // Allow any additional properties
-}
-
-export interface CX1MetaDataResponse {
-  metaData: CX1MetaDataItem[];
-}
-
-export interface CX1NetworkProperty {
-  predicateString: string;
-  value: string;
-  dataType?: 'string' | 'integer' | 'double' | 'boolean' | 'list_of_string';
-}
-
-export interface CX2NetworkProperties {
-  [key: string]: {
-    t: string;  // type
-    v: any;     // value
-  };
-}
-
-export enum NetworkIndexLevel {
-  NONE = 'NONE',
-  BASIC = 'BASIC',
-  FULL = 'FULL'
-}
-
-export interface NetworkSummaryV2 {
-  externalId: string;
-  name: string;
-  description?: string;
-  nodeCount: number;
-  edgeCount: number;
-  visibility: 'PUBLIC' | 'PRIVATE';
-  owner: string;
-  ownerUUID: string;
-  creationTime: number;
-  modificationTime: number;
-  version?: string;
-  properties?: CX1NetworkProperty[];  // V2 uses CX1 array format
-  isReadOnly: boolean;
-  isValid: boolean;
-  warnings?: string[];
-  hasLayout: boolean;
-  hasSample: boolean;
-  
-  // Additional attributes for both V2 and V3
-  updatedBy: string;           // username who modified this network last
-  errorMessage?: string;
-  cxFormat?: string;
-  cxFileSize?: number;         // File size in bytes
-  cx2FileSize?: number;        // File size in bytes
-  isShowcase?: boolean;
-  isCompleted?: boolean;
-  doi?: string;
-  isCertified?: boolean;
-  indexLevel?: NetworkIndexLevel;
-  parentDirUUID?: string;
-  showInTrash?: boolean;
-  subnetworkIds?: string[];
-  reference?: string;
-  organism?: string;
-  disease?: string;
-  tissue?: string;
-  networkType?: string[];
-  rightsHolder?: string;
-  rights?: string;
-  sourceFormat?: string;
-}
-
-/**
- * NetworkSummaryV3 - Network summary for NDEx API v3
- * 
- * Extends NetworkSummaryV2 but uses CX2-style properties format instead of CX1 format.
- * The main difference is in how network properties are structured:
- * 
- * | Aspect | NetworkSummaryV2 | NetworkSummaryV3 |
- * |--------|------------------|------------------|
- * | **Properties Format** | `CX1NetworkProperty[]` (array) | `CX2NetworkProperties` (object) |
- * | **Structure** | CX1-style array of property objects | CX2-style key-value map |
- * | **Example** | `[{predicateString: "name", value: "My Network"}]` | `{name: {t: "string", v: "My Network"}}` |
- * 
- * @example
- * ```typescript
- * // V2 properties format (array of objects)
- * const v2Summary: NetworkSummaryV2 = {
- *   externalId: "12345",
- *   name: "Sample Network",
- *   properties: [
- *     { predicateString: "description", value: "A sample network", dataType: "string" },
- *     { predicateString: "nodeCount", value: "100", dataType: "integer" }
- *   ]
- * };
- * 
- * // V3 properties format (object map)
- * const v3Summary: NetworkSummaryV3 = {
- *   externalId: "12345", 
- *   name: "Sample Network",
- *   properties: {
- *     description: { t: "string", v: "A sample network" },
- *     nodeCount: { t: "integer", v: 100 }
- *   }
- * };
- * ```
- */
-export interface NetworkSummaryV3 extends Omit<NetworkSummaryV2, 'properties'> {
-  properties?: CX2NetworkProperties;  // V3 uses CX2 object/map format
-  // V3-specific additional attributes can be added here as needed
-}
-
-
-export interface NetworkPermission {
-  uuid: string;
-  permission: 'READ' | 'WRITE' | 'ADMIN';
-  memberUUID: string;
-  memberAccountName?: string;
-  resourceUUID: string;
-}
-
-// NetworkSet interface removed - deprecated in NDEx v3, replaced by folders with network shortcuts
-
-// ============================================================================
-// CX2 Network Types
-// ============================================================================
-
-export interface CX2Network {
-  CXVersion: string;
-  hasFragments: boolean;
-  metaData: CX2MetaData[];
-  attributeDeclarations?: CX2AttributeDeclarations;
-  networkAttributes?: CX2NetworkAttribute[];
-  nodes?: CX2Node[];
-  edges?: CX2Edge[];
-  nodeBypass?: CX2NodeBypass[];
-  edgeBypass?: CX2EdgeBypass[];
-  visualProperties?: CX2VisualProperty;
-  status?: CX2Status[];
-}
-
-export interface CX2MetaData {
-  name: string;
-  elementCount?: number;
-}
-
-export interface CX2AttributeDeclarations {
-  [aspectName: string]: {
-    [attributeName: string]: {
-      d: string;  // datatype
-      a?: string; // alias
-      v?: any;    // default value
-    };
-  };
-}
-
-export interface CX2AttributeSpec {
-  d: string; // data type
-  v?: any; // default value
-  s?: boolean; // is single
-}
-
-export interface CX2NetworkAttribute {
-  [key: string]: any;
-}
-
-export interface CX2Node {
-  id: number;
-  x?: number; // x coordinate
-  y?: number; // y coordinate  
-  z?: number; // z coordinate (optional)
-  v?: Record<string, any>; // attributes
-}
-
-export interface CX2Edge {
-  id: number;
-  s: number; // source node id
-  t: number; // target node id
-  v?: Record<string, any>; // attributes
-}
-
-export interface CX1Edge {
-  // CX1 edge structure varies - can be any array structure
-  [key: string]: any;
-}
-
-export interface CX2NodeBypass {
-  id: number; // node id
-  v: VisualPropertyTable; // visual properties
-}
-
-export interface CX2EdgeBypass {
-  id: number; // edge id
-  v: VisualPropertyTable; // visual properties
-}
-
-// ============================================================================
-// CX2 Visual Property Types - Based on server-side CxVisualProperty class
-// ============================================================================
-
-/**
- * Visual Property Mapping Types
- */
-export type VPMappingType = 'DISCRETE' | 'CONTINUOUS' | 'PASSTHROUGH';
-
-/**
- * Mapping Definition for visual property mappings
- * Note: Using flexible typing for mapping definitions as they vary by type
- */
-export interface MappingDefinition {
-  mapppingList?: Array<Record<string, any>>; // Note: server has typo "mapppingList"
-  [key: string]: any; // Allow other mapping definition properties
-}
-
-/**
- * Visual Property Mapping structure
- */
-export interface VisualPropertyMapping {
-  type: VPMappingType;
-  definition: MappingDefinition;
-}
-
-/**
- * Visual Property Table - holds visual property values
- * Equivalent to server-side VisualPropertyTable class
- */
-export interface VisualPropertyTable {
-  [visualPropertyName: string]: any; // Maps visual property names to their values
-}
-
-/**
- * Table Column Visual Style - for individual visual properties
- */
-export interface TableColumnVisualStyle {
-  default?: any; // Default value for the visual property
-  mapping?: VisualPropertyMapping; // Optional mapping definition
-}
-
-/**
- * Default Visual Properties structure
- */
-export interface DefaultVisualProperties {
-  edge?: VisualPropertyTable; // Default edge visual properties
-  network?: Record<string, any>; // Default network visual properties  
-  node?: VisualPropertyTable; // Default node visual properties
-}
-
-/**
- * CX2 Visual Property - Main visual properties aspect
- * Equivalent to server-side CxVisualProperty class
- */
-export interface CX2VisualProperty {
-  default?: DefaultVisualProperties; // Default visual properties
-  edgeMapping?: Record<string, VisualPropertyMapping>; // Edge visual property mappings
-  nodeMapping?: Record<string, VisualPropertyMapping>; // Node visual property mappings
-}
-
-export interface CX2Status {
-  error?: string;
-  success?: boolean;
-}
-
-// ============================================================================
-// Search Types
-// ============================================================================
-
-export interface SearchResult {
-  numFound: number;
-  start: number;
-  networks: NetworkSummaryV2[] | NetworkSummaryV3[];
-}
-
-export interface SearchParameters {
-  searchString?: string;
-  accountName?: string;
-  permission?: string;
-  includeGroups?: boolean;
-  admin?: string;
-  start?: number;
-  size?: number;
-  source?: string;
-}
-
-// ============================================================================
-// File/Export Types
-// ============================================================================
-
-export interface ExportFormat {
-  format: 'CX' | 'CX2' | 'XGMML' | 'SIF' | 'GRAPHML';
-  version?: string;
-}
-
-export interface ExportRequest {
-  networkUUID: string;
-  format: ExportFormat;
-  accesskey?: string;
-}
-
-// ============================================================================
-// Task/Status Types
-// ============================================================================
-
-export interface Task {
-  externalId: string;
-  taskType: string;
-  status: 'submitted' | 'processing' | 'completed' | 'failed';
-  progress?: number;
-  message?: string;
-  resource?: string;
-  startTime?: number;
-  finishTime?: number;
-  attributes?: Record<string, any>;
-}
-
-// ============================================================================
-// API Configuration Types
-// ============================================================================
-
-export interface NDExClientConfig {
-  baseURL?: string;
-  timeout?: number;
-  retries?: number;
-  retryDelay?: number;
-  debug?: boolean;
-  headers?: Record<string, string>;
-  auth?: BasicAuth | OAuthAuth;  // Simplified to 2 authentication options
-}
-
-export interface APIResponse<T = any> {
-  data?: T;
-  errorCode?: string;
-  message?: string;
-  description?: string;
-  stackTrace?: string;
-  timeStamp?: number;
-}
-
-export interface APIError {
-  errorCode: string;
-  message: string;
-  description?: string;
-  stackTrace?: string;
-  timeStamp?: number;
-}
-
-// ============================================================================
-// Service Types
-// ============================================================================
-
-
-/**
- * Base error class for all NDEx API errors
- */
-export class NDExError extends Error {
-  constructor(
-    message: string,
-    public statusCode?: number,
-    public errorCode?: string,
-    public description?: string
-  ) {
-    super(message);
-    this.name = 'NDExError';
-  }
-}
-
-/**
- * Error thrown when network or request fails
- */
-export class NDExNetworkError extends NDExError {
-  constructor(message: string, public originalError?: Error) {
-    super(message, undefined, 'NETWORK_ERROR');
-    this.name = 'NDExNetworkError';
-  }
-}
-
-/**
- * Error thrown when authentication fails
- */
-export class NDExAuthError extends NDExError {
-  constructor(message: string = 'Authentication failed', statusCode: number = 401) {
-    super(message, statusCode, 'AUTH_ERROR');
-    this.name = 'NDExAuthError';
-  }
-}
-
-/**
- * Error thrown when requested resource is not found
- */
-export class NDExNotFoundError extends NDExError {
-  constructor(message: string = 'Resource not found', statusCode: number = 404) {
-    super(message, statusCode, 'NOT_FOUND');
-    this.name = 'NDExNotFoundError';
-  }
-}
-
-/**
- * Error thrown when request validation fails
- */
-export class NDExValidationError extends NDExError {
-  constructor(message: string, statusCode: number = 400) {
-    super(message, statusCode, 'VALIDATION_ERROR');
-    this.name = 'NDExValidationError';
-  }
-}
-
-/**
- * Error thrown when server encounters an internal error
- */
-export class NDExServerError extends NDExError {
-  constructor(message: string = 'Internal server error', statusCode: number = 500) {
-    super(message, statusCode, 'SERVER_ERROR');
-    this.name = 'NDExServerError';
-  }
-}
-
-// ============================================================================
-// Utility Types
-// ============================================================================
-
-export type UUID = string;
-export type Timestamp = number;
-
-// Allow flexible typing for gradual migration
-export type NDExAny = any;
-
-// Common parameter types
-export interface PaginationParams {
-  start?: number;
-  size?: number;
-}
-
-export interface AccessParams {
-  accesskey?: string;
-}
-
-// ============================================================================
-// Workspace Types
-// ============================================================================
-
-/**
- * CyWeb workspace object structure
- */
-export interface CyWebWorkspace {
-  externalId?: string;
-  name: string;
-  description?: string;
-  networkIds?: string[];
-  [key: string]: any; // Allow additional properties
-}
-
-/**
- * Network access key response structure
- */
-export interface AccessKeyResponse {
-  accessKey: string | null;
-}
-
-/**
- * Valid actions for updating access keys
- */
-export type AccessKeyAction = 'enable' | 'disable';
-