Add NDEx 3 folder, shortcut, file search, and network move support

[coleslaw481]

Summary

CyNDEx-2 needs initial support for NDEx 3 folders so Cytoscape users can browse their NDEx account folder hierarchy, import networks from folders, choose a destination folder when uploading a network, and create folders from the upload/browse workflows.

CyNDEx-2 currently uses ndex-java-client for NDEx network import/export/search operations. To avoid duplicating NDEx REST logic inside CyNDEx-2, the Java client should expose the needed NDEx 3 folder/file APIs first.

Motivation

CyNDEx-2 should not implement a separate long-lived NDEx V3 REST adapter for folders. Folder behavior, authentication, base URL handling, paging, request serialization, response parsing, user agent handling, and NDEx error handling should stay centralized in ndex-java-client.

The current ndex-object-model already appears to include useful model classes such as:

• NdexFolder
• FolderRequest
• NdexShortcut
• ShortcutRequest
• NetworkSummary.getFolderId()

But NdexRestClientModelAccessLayer does not currently expose folder/shortcut/file methods needed by CyNDEx-2.

Needed Client Methods

Please add Java client methods for the NDEx 3 APIs needed by the CyNDEx-2 folder MVP.

Suggested methods on NdexRestClientModelAccessLayer:

UserHomeContent getUserHome(UUID userId)
List<NdexFolder> listFolders()
NdexFolder getFolder(UUID folderId)
FolderContents listFolderContents(UUID folderId, int start, int size)
FolderItemCounts getFolderItemCounts(UUID folderId)
UUID createFolder(FolderRequest request)
MoveNetworksResult moveNetworksToFolder(UUID folderId, Collection<UUID> networkIds)
List<NdexShortcut> listShortcuts()
NdexShortcut getShortcut(UUID shortcutId)
FileSearchResult searchFiles(SimpleFileQuery query, int start, int size)