SCMCP

Instructions

Implementation Reference

• src/scmcp/tool/tl.py:164-177 (handler)

  Handler function that executes the tool logic for 'diffmap' by dispatching to sc.tl.diffmap with input arguments, adds operation log, and handles errors.

  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 

• src/scmcp/schema/tl.py:209-237 (schema)

  Pydantic model defining the input schema and validation rules for the 'diffmap' tool.

  class DiffMapModel(JSONParsingModel):
      """Input schema for the Diffusion Maps dimensionality reduction tool."""
      
      n_comps: int = Field(
          default=15,
          description="The number of dimensions of the representation.",
          gt=0
      )
      neighbors_key: Optional[str] = Field(
          default=None,
          description=(
              "If not specified, diffmap looks .uns['neighbors'] for neighbors settings "
              "and .obsp['connectivities'], .obsp['distances'] for connectivities and "
              "distances respectively. If specified, diffmap looks .uns[neighbors_key] for "
              "neighbors settings and uses the corresponding connectivities and distances."
          )
      )
      random_state: int = Field(
          default=0,
          description="Random seed for reproducibility."
      )
      
      @field_validator('n_comps')
      def validate_positive_integers(cls, v: int) -> int:
          """Validate positive integers"""
          if v <= 0:
              raise ValueError("n_comps must be a positive integer")
          return v

• src/scmcp/tool/tl.py:33-38 (registration)

  Registration of the 'diffmap' tool as an MCP Tool object with name, description, and reference to the input schema.

  # Add diffmap tool
  diffmap_tool = types.Tool(
      name="diffmap",
      description="Diffusion Maps for dimensionality reduction",
      inputSchema=DiffMapModel.model_json_schema(),
  )

• src/scmcp/tool/tl.py:125-142 (helper)

  Mapping from tool name 'diffmap' to the underlying scanpy function sc.tl.diffmap used by the handler.

  tl_func = {
      "tsne": sc.tl.tsne,
      "umap": sc.tl.umap,
      "draw_graph": sc.tl.draw_graph,
      "diffmap": sc.tl.diffmap,
      "embedding_density": sc.tl.embedding_density,
      "leiden": sc.tl.leiden,
      "louvain": sc.tl.louvain,
      "dendrogram": sc.tl.dendrogram,
      "dpt": sc.tl.dpt,
      "paga": sc.tl.paga,
      "ingest": sc.tl.ingest,
      "rank_genes_groups": sc.tl.rank_genes_groups,
      "filter_rank_genes_groups": sc.tl.filter_rank_genes_groups,
      "marker_gene_overlap": sc.tl.marker_gene_overlap,
      "score_genes": sc.tl.score_genes,
      "score_genes_cell_cycle": sc.tl.score_genes_cell_cycle,
  }

• src/scmcp/server.py:35-56 (registration)

  MCP server list_tools method that includes tl_tools.values(), thereby registering the 'diffmap' tool when MODULE includes 'tl'.

  @server.list_tools()
  async def list_tools() -> list[types.Tool]:
      if MODULE == "io":
          tools = io_tools.values()
      elif MODULE == "pp":
          tools = pp_tools.values()
      elif MODULE == "tl":
          tools = tl_tools.values()
      elif MODULE == "pl":
          tools = pl_tools.values()
      elif MODULE == "util":
          tools = util_tools.values()
      else:
          tools = [
              *io_tools.values(),
              *pp_tools.values(),
              *tl_tools.values(),
              *pl_tools.values(),
              *util_tools.values(),
              *ccc_tools.values(),
          ]
      return tools