SCMCP

Instructions

Implementation Reference

• src/scmcp/schema/tl.py:155-207 (schema)

  Pydantic model defining the input schema for the draw_graph tool, including parameters like layout, init_pos, root, etc., with validation.
  class DrawGraphModel(JSONParsingModel): """Input schema for the force-directed graph drawing tool.""" layout: str = Field( default='fa', description="Graph layout algorithm ('fa', 'fr', 'kk', etc.)", ) init_pos: Optional[Union[str, bool]] = Field( default=None, description="Initial position for nodes ('paga'/True, False, or .obsm key)", ) root: Optional[int] = Field( default=None, description="Root node for tree layouts", ge=0 ) random_state: int = Field( default=0, description="Random seed for reproducibility" ) n_jobs: Optional[int] = Field( default=None, description="Number of jobs for parallel computation", gt=0 ) key_added_ext: Optional[str] = Field( default=None, description="Suffix for storing results in .obsm" ) neighbors_key: Optional[str] = Field( default=None, description="Key for neighbors settings in .uns" ) obsp: Optional[str] = Field( default=None, description="Key for adjacency matrix in .obsp" ) @field_validator('layout') def validate_layout(cls, v: str) -> str: """Validate layout is supported""" valid_layouts = ['fa', 'fr', 'grid_fr', 'kk', 'lgl', 'drl', 'rt'] if v.lower() not in valid_layouts: raise ValueError(f"layout must be one of {valid_layouts}") return v.lower() @field_validator('root', 'n_jobs') def validate_positive_integers(cls, v: Optional[int]) -> Optional[int]: """Validate positive integers where applicable""" if v is not None and v <= 0: raise ValueError("must be a positive integer") return v
• src/scmcp/tool/tl.py:26-31 (registration)

  Definition of the draw_graph Tool object with name, description, and input schema reference.
  # Add draw_graph tool draw_graph_tool = types.Tool( name="draw_graph", description="Force-directed graph drawing for visualization", inputSchema=DrawGraphModel.model_json_schema(), )
• src/scmcp/tool/tl.py:145-162 (registration)

  tl_tools dictionary registers the draw_graph_tool along with other tl tools for use in server.list_tools().
  tl_tools = { "tsne": tsne_tool, "umap": umap_tool, "draw_graph": draw_graph_tool, "diffmap": diffmap_tool, "embedding_density": embedding_density_tool, "leiden": leiden_tool, "louvain": louvain_tool, "dendrogram": dendrogram_tool, "dpt": dpt_tool, "paga": paga_tool, "ingest": ingest_tool, "rank_genes_groups": rank_genes_groups_tool, "filter_rank_genes_groups": filter_rank_genes_groups_tool, "marker_gene_overlap": marker_gene_overlap_tool, "score_genes": score_genes_tool, "score_genes_cell_cycle": score_genes_cell_cycle_tool, }
• src/scmcp/server.py:59-92 (handler)

  MCP server call_tool handler dispatches draw_graph (in tl_tools) to run_tl_func.
  @server.call_tool() async def call_tool( name: str, arguments ): try: logger.info(f"Running {name} with {arguments}") if name in io_tools.keys(): res = run_io_func(ads, name, arguments) elif name in pp_tools.keys(): res = run_pp_func(ads, name, arguments) elif name in tl_tools.keys(): res = run_tl_func(ads, name, arguments) elif name in pl_tools.keys(): res = run_pl_func(ads, name, arguments) elif name in util_tools.keys(): res = run_util_func(ads, name, arguments) elif name in ccc_tools.keys(): res = run_ccc_func(ads.adata_dic[ads.active], name, arguments) output = str(res) if res is not None else str(ads.adata_dic[ads.active]) return [ types.TextContent( type="text", text=str({"output": output}) ) ] except Exception as error: logger.error(f"{name} with {error}") return [ types.TextContent( type="text", text=str({"Error": error}) ) ]
• src/scmcp/tool/tl.py:164-177 (helper)

  Helper function that executes the tool by calling sc.tl.draw_graph(adata, **kwargs) for func='draw_graph'.
  def run_tl_func(ads, func, arguments): adata = ads.adata_dic[ads.active] if func not in tl_func: raise ValueError(f"Unsupported function: {func}") run_func = tl_func[func] parameters = inspect.signature(run_func).parameters kwargs = {k: arguments.get(k) for k in parameters if k in arguments} try: res = run_func(adata, **kwargs) add_op_log(adata, run_func, kwargs) except Exception as e: logger.error(f"Error running function {func}: {e}") raise return