SCMCP

Instructions

Implementation Reference

• src/scmcp/schema/pp.py:363-390 (schema)

  Pydantic model defining the input schema for the 'combat' tool, including batch key and covariates with validation.
  class CombatModel(JSONParsingModel): """Input schema for the combat batch effect correction tool.""" key: str = Field( default='batch', description="Key to a categorical annotation from adata.obs that will be used for batch effect removal." ) covariates: Optional[List[str]] = Field( default=None, description="Additional covariates besides the batch variable such as adjustment variables or biological condition." ) @field_validator('key') def validate_key(cls, v: str) -> str: """Validate key is not empty""" if not v.strip(): raise ValueError("key cannot be empty") return v @field_validator('covariates') def validate_covariates(cls, v: Optional[List[str]]) -> Optional[List[str]]: """Validate covariates are non-empty strings if provided""" if v is not None: if not all(isinstance(item, str) and item.strip() for item in v): raise ValueError("covariates must be non-empty strings") return v
• src/scmcp/tool/pp.py:69-73 (registration)

  Registers the 'combat' tool using mcp.types.Tool with name, description, and CombatModel schema.
  combat = types.Tool( name="combat", description="ComBat function for batch effect correction", inputSchema=CombatModel.model_json_schema(), )
• src/scmcp/tool/pp.py:120-137 (handler)

  Handler function that executes preprocessing tools including 'combat' by dispatching to sc.pp.combat with validated arguments and logging.
  def run_pp_func(ads, func, arguments): adata = ads.adata_dic[ads.active] if func not in pp_func: raise ValueError(f"不支持的函数: {func}") run_func = pp_func[func] parameters = inspect.signature(run_func).parameters arguments["inplace"] = True 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 KeyError as e: raise KeyError(f"Can not foud {e} column in adata.obs or adata.var") except Exception as e: raise e return res
• src/scmcp/tool/pp.py:88-101 (helper)

  Dictionary mapping tool names to Scanpy functions, with 'combat' mapped to sc.pp.combat for execution.
  pp_func = { "filter_genes": sc.pp.filter_genes, "filter_cells": sc.pp.filter_cells, "calculate_qc_metrics": partial(sc.pp.calculate_qc_metrics, inplace=True), "log1p": sc.pp.log1p, "normalize_total": sc.pp.normalize_total, "pca": sc.pp.pca, "highly_variable_genes": sc.pp.highly_variable_genes, "regress_out": sc.pp.regress_out, "scale": sc.pp.scale, "combat": sc.pp.combat, "scrublet": sc.pp.scrublet, "neighbors": sc.pp.neighbors, }
• src/scmcp/tool/pp.py:104-117 (registration)

  Dictionary registering all pp tools including 'combat' Tool object for use in server or init.
  pp_tools = { "filter_genes": filter_genes, "filter_cells": filter_cells, "calculate_qc_metrics": calculate_qc_metrics, "log1p": log1p, "normalize_total": normalize_total, "pca": pca, "highly_variable_genes": highly_variable_genes, "regress_out": regress_out, "scale": scale, "combat": combat, "scrublet": scrublet, "neighbors": neighbors, }