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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.0.2] - 2026-05-25

  • Fix mcp app reload during restart of desktop to be consistent, it was susceptible to be skipped due to race conditions in osgi timing. . pull/8

[1.0.1] - 2026-05-25

  • Fixed app init after installing app into a running instance of desktop. The app init routine wasn't getting triggered to render the toolbar icon for mcp and start the etl service, had to restart desktop. This fixes the behavior to force app init to run after install on current desktop. pull/6

[1.0.0] - 2026-05-25

First GA release.

  • Added TableImportFile mcp tool, pull/5

[1.0.0-rc.4] - 2026-04-25

  • Add 3 new tools for using desktop commands from llm: CommandGatewayGetTool, CommandGatewayInvokeTool, CommandGatewaySearchTool, pull/3

[1.0.0-rc.3] - 2026-03-25

Added

  • Claude Desktop extension bundle (cytoscape-mcp.mcpb) added to enable stdio bridge configuration to Cytoscape's MCP HTTP server, use make build_claude_mcpb
  • 10 new tools added for visual style mapping and data column interrogation: get_mappable_properties, get_compatible_columns, get_styles, switch_current_style, get_column_range, get_column_distinct_values, create_continuous_mapping, create_discrete_mapping, create_discrete_mapping_generated, create_passthrough_mapping
  • refer to MCPManifest.md for detailed descriptions of each MCP tool.

Fixed / Changed

  • load_cytoscape_network_view refactored from optional parameters to a ConditionalParameter model for improved LLM input guidance and more reliable parameter resolution

  • Fixed conditional parameter processing on load_cytoscape_network_view to correctly handle waived vs. provided states

  • Added inferred data types on tabular file column inspection and enforced a maximum-size cap on column value retrievals

  • Revised tool descriptions across the manifest to remove direct tool-name self-references for cleaner LLM context

  • Discrete mapping generator color input made conditional; node size is now locked when a size-based style mapping is applied

  • Fixed stdio bridge timeout in the Claude Desktop extension

  • Updated to mcp sdk 1.1.0, updated McpTransportProvider to follow the latest from 1.1.0.

  • prompt activation examples

    • discrete mapping
      • > map edge shape to interaction
      • > map weight to node size
      • > generate green colors on edges based on discrete values of confidence
    • continous mapping
      • > set color gradient on nodes from blue to red based on eccentricity
    • pass through mapping
      • > set node label to gene1
    • manage styles
      • > switch network style
      • > switch network style to default

[1.0.0-rc.2] - 2026-03-11

Added

  • 2 new tools added for reading and updating properties of network default style: set_visual_default, get_visual_style_defaults
  • refer to MCPManifest.md for detailed descriptions of each MCP tool.
  • prompt activation examples
  • > increse the network edge width by 1
  • > change the network node color to green
  • > change node label to courier new
  • > what properties can I lock on network
  • > lock node width and height on network

[1.0.0-rc.1] - 2026-03-09

Added

  • Initial release of the Cytoscape MCP Server app
  • Embedded MCP (Model Context Protocol) server running inside Cytoscape Desktop CyRest HTTP (Streamable HTTP transport) — no separate server process required
  • 9 MCP tools initially added related to loading and analyzing a network on desktop: get_loaded_network_views, set_current_network_view, create_network_view, load_cytoscape_network_view, inspect_tabular_file, get_file_columns, analyze_network, get_layout_algorithms, apply_layout
  • refer to MCPManifest.md for detailed descriptions of each MCP tool.
  • prompt activation examples
  • > open a network using cytoscape desktop
  • > analyze the network
  • > change the network layout