scmcp-shared 0.3.5__py3-none-any.whl → 0.3.7__py3-none-any.whl

scmcp_shared/__init__.py

@@ -1,3 +1,3 @@
 
-__version__ = "0.3.5"
+__version__ = "0.3.7"
 

scmcp_shared/schema/io.py

@@ -7,7 +7,7 @@ from typing import Optional, Literal
 
 
 
-class ReadModel(BaseModel):
+class ReadParams(BaseModel):
     """Input schema for the read tool."""
     filename: str = Field(
         ...,
@@ -30,9 +30,9 @@ class ReadModel(BaseModel):
         default=False,
         description="Assume the first column stores row names. This is only necessary if these are not strings: strings in the first column are automatically assumed to be row names."
     )
-    first_column_obs: bool = Field(
-        default=True,
-        description="If True, assume the first column stores observations (cell or barcode) names when provide text file. If False, the data will be transposed."
+    transpose: bool = Field(
+        default=False,
+        description="If True, the data will be transposed."
     )
     backup_url: str = Field(
         default=None,
@@ -82,7 +82,7 @@ class ReadModel(BaseModel):
         return v
 
 
-class WriteModel(BaseModel):
+class WriteParams(BaseModel):
     """Input schema for the write tool."""
     filename: str = Field(
         description="Path to save the file. If no extension is provided, the default format will be used."

scmcp_shared/schema/pl.py

@@ -72,12 +72,12 @@ class FigureSizeMixin:
 
 
 # 基础可视化模型，包含所有可视化工具共享的字段
-class BaseVisualizationModel(BaseModel, LegendMixin, ColorMappingMixin, FigureSizeMixin):
+class BaseVisualizationParams(BaseModel, LegendMixin, ColorMappingMixin, FigureSizeMixin):
     """基础可视化模型，包含所有可视化工具共享的字段"""    
     pass
 
 # 基础嵌入可视化模型，包含所有嵌入可视化工具共享的字段
-class BaseEmbeddingModel(BaseVisualizationModel):
+class BaseEmbeddingParams(BaseVisualizationParams):
     """基础嵌入可视化模型，包含所有嵌入可视化工具共享的字段"""
     
     color: Optional[Union[str, List[str]]] = Field(
@@ -176,8 +176,8 @@ class BaseEmbeddingModel(BaseVisualizationModel):
     )
 
 
-# 重构 ScatterModel 作为基础散点图模型
-class BaseScatterModel(BaseVisualizationModel):
+# 重构 ScatterParams 作为基础散点图模型
+class BaseScatterParams(BaseVisualizationParams):
     """基础散点图模型"""
     
     x: Optional[str] = Field(
@@ -211,8 +211,8 @@ class BaseScatterModel(BaseVisualizationModel):
     )
 
 
-# 使用继承关系重构 EnhancedScatterModel
-class EnhancedScatterModel(BaseScatterModel):
+# 使用继承关系重构 EnhancedScatterParams
+class EnhancedScatterParams(BaseScatterParams):
     """Input schema for the enhanced scatter plotting tool."""
     
     sort_order: bool = Field(
@@ -261,7 +261,7 @@ class EnhancedScatterModel(BaseScatterModel):
 
 
 # 创建基础统计可视化模型
-class BaseStatPlotModel(BaseVisualizationModel):
+class BaseStatPlotParams(BaseVisualizationParams):
     """基础统计可视化模型，包含统计图表共享的字段"""
     
     groupby: Optional[str] = Field(
@@ -328,8 +328,8 @@ class BaseStatPlotModel(BaseVisualizationModel):
             raise ValueError("size must be a positive integer")
         return v
 
-# 添加缺失的 BaseMatrixModel 类
-class BaseMatrixModel(BaseVisualizationModel):
+# 添加缺失的 BaseMatrixParams 类
+class BaseMatrixParams(BaseVisualizationParams):
     """基础矩阵可视化模型，包含所有矩阵可视化工具共享的字段"""
     
     var_names: Union[List[str], Mapping[str, List[str]]] = Field(
@@ -374,8 +374,8 @@ class BaseMatrixModel(BaseVisualizationModel):
     )
 
 
-# 重构 HeatmapModel
-class HeatmapModel(BaseMatrixModel):
+# 重构 HeatmapParams
+class HeatmapParams(BaseMatrixParams):
     """Input schema for the heatmap plotting tool."""
     
     num_categories: int = Field(
@@ -412,14 +412,14 @@ class HeatmapModel(BaseMatrixModel):
         return v
 
 
-# 重构 TracksplotModel
-class TracksplotModel(BaseMatrixModel):
+# 重构 TracksplotParams
+class TracksplotParams(BaseMatrixParams):
     """Input schema for the tracksplot plotting tool."""
-    # 所有需要的字段已经在 BaseMatrixModel 中定义
+    # 所有需要的字段已经在 BaseMatrixParams 中定义
 
 
-# 重构 ViolinModel
-class ViolinModel(BaseStatPlotModel):
+# 重构 ViolinParams
+class ViolinParams(BaseStatPlotParams):
     """Input schema for the violin plotting tool."""
     
     keys: Union[str, List[str]] = Field(
@@ -477,8 +477,8 @@ class ViolinModel(BaseStatPlotModel):
         return v
 
 
-# 重构 MatrixplotModel
-class MatrixplotModel(BaseMatrixModel):
+# 重构 MatrixplotParams
+class MatrixplotParams(BaseMatrixParams):
     """Input schema for the matrixplot plotting tool."""
     
     num_categories: int = Field(
@@ -523,8 +523,8 @@ class MatrixplotModel(BaseMatrixModel):
         return v
 
 
-# 重构 DotplotModel
-class DotplotModel(BaseMatrixModel):
+# 重构 DotplotParams
+class DotplotParams(BaseMatrixParams):
     """Input schema for the dotplot plotting tool."""
     
     expression_cutoff: float = Field(
@@ -577,8 +577,8 @@ class DotplotModel(BaseMatrixModel):
     )
 
 
-# 重构 RankGenesGroupsModel
-class RankGenesGroupsModel(BaseVisualizationModel):
+# 重构 RankGenesGroupsParams
+class RankGenesGroupsParams(BaseVisualizationParams):
     """Input schema for the rank_genes_groups plotting tool."""
     
     n_genes: int = Field(
@@ -631,7 +631,7 @@ class RankGenesGroupsModel(BaseVisualizationModel):
 
 
 # 重构 ClusterMapModel
-class ClusterMapModel(BaseModel):
+class ClusterMapParams(BaseModel):
     """Input schema for the clustermap plotting tool."""
 
     obs_keys: Optional[str] = Field(
@@ -645,8 +645,8 @@ class ClusterMapModel(BaseModel):
 
 
 
-# 重构 StackedViolinModel
-class StackedViolinModel(BaseStatPlotModel):
+# 重构 StackedViolinParams
+class StackedViolinParams(BaseStatPlotParams):
     """Input schema for the stacked_violin plotting tool."""
     
     stripplot: bool = Field(
@@ -688,8 +688,8 @@ class StackedViolinModel(BaseStatPlotModel):
         return v
 
 
-# 重构 TrackingModel
-class TrackingModel(BaseVisualizationModel):
+# 重构 TrackingParams
+class TrackingParams(BaseVisualizationParams):
     """Input schema for the tracking plotting tool."""
     
     groupby: str = Field(
@@ -717,8 +717,8 @@ class TrackingModel(BaseVisualizationModel):
         return v
 
 
-# 重构 EmbeddingDensityModel
-class EmbeddingDensityModel(BaseEmbeddingModel):
+# 重构 EmbeddingDensityParams
+class EmbeddingDensityParams(BaseEmbeddingParams):
     """Input schema for the embedding_density plotting tool."""
     
     basis: str = Field(
@@ -751,7 +751,7 @@ class EmbeddingDensityModel(BaseEmbeddingModel):
         return v
 
 
-class PCAModel(BaseEmbeddingModel):
+class PCAParams(BaseEmbeddingParams):
     """Input schema for the PCA plotting tool."""
     
     annotate_var_explained: bool = Field(
@@ -761,22 +761,22 @@ class PCAModel(BaseEmbeddingModel):
 
 
 # 重构 UMAP 模型
-class UMAPModel(BaseEmbeddingModel):
+class UMAPParams(BaseEmbeddingParams):
     """Input schema for the UMAP plotting tool."""
-    # 所有需要的字段已经在 BaseEmbeddingModel 中定义
+    # 所有需要的字段已经在 BaseEmbeddingParams 中定义
 
 
 # 重构 TSNE 模型
-class TSNEModel(BaseEmbeddingModel):
+class TSNEParams(BaseEmbeddingParams):
     """Input schema for the TSNE plotting tool."""
-    # 所有需要的字段已经在 BaseEmbeddingModel 中定义
+    # 所有需要的字段已经在 BaseEmbeddingParams 中定义
 
-# 重构 DiffusionMapModel
-class DiffusionMapModel(BaseEmbeddingModel):
+# 重构 DiffusionMapParams
+class DiffusionMapParams(BaseEmbeddingParams):
     """Input schema for the diffusion map plotting tool."""
-    # 所有需要的字段已经在 BaseEmbeddingModel 中定义
+    # 所有需要的字段已经在 BaseEmbeddingParams 中定义
 
-class HighestExprGenesModel(BaseVisualizationModel):
+class HighestExprGenesParams(BaseVisualizationParams):
     """Input schema for the highest_expr_genes plotting tool."""
     
     n_top: int = Field(
@@ -803,7 +803,7 @@ class HighestExprGenesModel(BaseVisualizationModel):
         return v
 
 
-class HighlyVariableGenesModel(BaseVisualizationModel):
+class HighlyVariableGenesParams(BaseVisualizationParams):
     """Input schema for the highly_variable_genes plotting tool."""
     
     log: bool = Field(
@@ -816,7 +816,7 @@ class HighlyVariableGenesModel(BaseVisualizationModel):
         description="Whether to plot highly variable genes or all genes."
     )
 
-class PCAVarianceRatioModel(BaseVisualizationModel):
+class PCAVarianceRatioParams(BaseVisualizationParams):
     """Input schema for the pca_variance_ratio plotting tool."""
     
     n_pcs: int = Field(
@@ -839,7 +839,7 @@ class PCAVarianceRatioModel(BaseVisualizationModel):
 
 # ... existing code ...
 
-class RankGenesGroupsDotplotModel(BaseMatrixModel):
+class RankGenesGroupsDotplotParams(BaseMatrixParams):
     """Input schema for the rank_genes_groups_dotplot plotting tool."""
     
     groups: Optional[Union[str, List[str]]] = Field(
@@ -874,7 +874,7 @@ class RankGenesGroupsDotplotModel(BaseMatrixModel):
 
 
 
-class EmbeddingModel(BaseEmbeddingModel):
+class EmbeddingParams(BaseEmbeddingParams):
     """Input schema for the embedding plotting tool."""
     
     basis: str = Field(

scmcp_shared/schema/pp.py

@@ -73,7 +73,7 @@ class FilterGenes(BaseModel):
         return v
 
 
-class SubsetCellModel(BaseModel):
+class SubsetCellParams(BaseModel):
     """Input schema for subsetting AnnData objects based on various criteria."""
     obs_key: Optional[str] = Field(
         default=None,
@@ -109,7 +109,7 @@ class SubsetCellModel(BaseModel):
     )
 
 
-class SubsetGeneModel(BaseModel):
+class SubsetGeneParams(BaseModel):
     """Input schema for subsetting AnnData objects based on various criteria."""
     min_counts: Optional[int] = Field(
         default=None,
@@ -196,7 +196,7 @@ class CalculateQCMetrics(BaseModel):
     
 
 
-class Log1PModel(BaseModel):
+class Log1PParams(BaseModel):
     """Input schema for the log1p preprocessing tool."""
     
     base: Optional[Union[int, float]] = Field(
@@ -233,7 +233,7 @@ class Log1PModel(BaseModel):
 
 
 
-class HighlyVariableGenesModel(BaseModel):
+class HighlyVariableGenesParams(BaseModel):
     """Input schema for the highly_variable_genes preprocessing tool."""
     
     layer: Optional[str] = Field(
@@ -307,7 +307,7 @@ class HighlyVariableGenesModel(BaseModel):
         return v
 
 
-class RegressOutModel(BaseModel):
+class RegressOutParams(BaseModel):
     """Input schema for the regress_out preprocessing tool."""
     
     keys: Union[str, List[str]] = Field(
@@ -340,7 +340,7 @@ class RegressOutModel(BaseModel):
         raise ValueError("keys must be a string or list of strings")
 
 
-class ScaleModel(BaseModel):
+class ScaleParams(BaseModel):
     """Input schema for the scale preprocessing tool."""
     
     zero_center: bool = Field(
@@ -376,7 +376,7 @@ class ScaleModel(BaseModel):
         return v
 
 
-class CombatModel(BaseModel):
+class CombatParams(BaseModel):
     """Input schema for the combat batch effect correction tool."""
     
     key: str = Field(
@@ -405,7 +405,7 @@ class CombatModel(BaseModel):
         return v
 
 
-class ScrubletModel(BaseModel):
+class ScrubletParams(BaseModel):
     """Input schema for the scrublet doublet prediction tool."""
     
     adata_sim: Optional[str] = Field(
@@ -511,7 +511,7 @@ class ScrubletModel(BaseModel):
         return v.lower()
 
 
-class NeighborsModel(BaseModel):
+class NeighborsParams(BaseModel):
     """Input schema for the neighbors graph construction tool."""
     
     n_neighbors: int = Field(
@@ -589,7 +589,7 @@ class NeighborsModel(BaseModel):
         return v
 
 
-class NormalizeTotalModel(BaseModel):
+class NormalizeTotalParams(BaseModel):
     """Input schema for the normalize_total preprocessing tool."""
     
     target_sum: Optional[float] = Field(

scmcp_shared/schema/tl.py

@@ -2,7 +2,7 @@ from pydantic import  Field, field_validator, ValidationInfo, BaseModel
 from typing import Optional, Union, List, Dict, Any, Tuple, Literal, Mapping
 
 
-class TSNEModel(BaseModel):
+class TSNEParams(BaseModel):
     """Input schema for the t-SNE dimensionality reduction tool."""
     n_pcs: Optional[int] = Field(
         default=None,
@@ -59,7 +59,7 @@ class TSNEModel(BaseModel):
         return v.lower()
 
 
-class UMAPModel(BaseModel):
+class UMAPParams(BaseModel):
     """Input schema for the UMAP dimensionality reduction tool."""
     
     min_dist: Optional[float] = Field(
@@ -145,7 +145,7 @@ class UMAPModel(BaseModel):
         return v.lower()
 
 
-class DrawGraphModel(BaseModel):
+class DrawGraphParams(BaseModel):
     """Input schema for the force-directed graph drawing tool."""
     
     layout: str = Field(
@@ -199,7 +199,7 @@ class DrawGraphModel(BaseModel):
         return v
 
 
-class DiffMapModel(BaseModel):
+class DiffMapParams(BaseModel):
     """Input schema for the Diffusion Maps dimensionality reduction tool."""
     
     n_comps: int = Field(
@@ -229,7 +229,7 @@ class DiffMapModel(BaseModel):
         return v
 
 
-class EmbeddingDensityModel(BaseModel):
+class EmbeddingDensityParams(BaseModel):
     """Input schema for the embedding density calculation tool."""
     
     basis: str = Field(
@@ -257,7 +257,7 @@ class EmbeddingDensityModel(BaseModel):
         return v
 
 
-class LeidenModel(BaseModel):
+class LeidenParams(BaseModel):
     """Input schema for the Leiden clustering algorithm."""
     
     resolution: Optional[float] = Field(
@@ -324,7 +324,7 @@ class LeidenModel(BaseModel):
         return v
 
 
-class LouvainModel(BaseModel):
+class LouvainParams(BaseModel):
     """Input schema for the Louvain clustering algorithm."""
     
     resolution: Optional[float] = Field(
@@ -396,7 +396,7 @@ class LouvainModel(BaseModel):
         return v
 
 
-class DendrogramModel(BaseModel):
+class DendrogramParams(BaseModel):
     """Input schema for the hierarchical clustering dendrogram tool."""
     
     groupby: str = Field(
@@ -461,7 +461,7 @@ class DendrogramModel(BaseModel):
         return v
 
 
-class DPTModel(BaseModel):
+class DPTParams(BaseModel):
     """Input schema for the Diffusion Pseudotime (DPT) tool."""
     
     n_dcs: int = Field(
@@ -510,7 +510,7 @@ class DPTModel(BaseModel):
             raise ValueError("min_group_size must be between 0 and 1")
         return v
 
-class PAGAModel(BaseModel):
+class PAGAParams(BaseModel):
     """Input schema for the Partition-based Graph Abstraction (PAGA) tool."""
     
     groups: Optional[str] = Field(
@@ -531,14 +531,14 @@ class PAGAModel(BaseModel):
     )
     
     @field_validator('model')
-    def validate_model(cls, v: str) -> str:
+    def validate_Params(cls, v: str) -> str:
         """Validate model version is supported"""
         if v not in ['v1.2', 'v1.0']:
             raise ValueError("model must be either 'v1.2' or 'v1.0'")
         return v
 
 
-class IngestModel(BaseModel):
+class IngestParams(BaseModel):
     """Input schema for the ingest tool that maps labels and embeddings from reference data to new data."""
     
     obs: Optional[Union[str, List[str]]] = Field(
@@ -587,7 +587,7 @@ class IngestModel(BaseModel):
         return v.lower()
 
 
-class RankGenesGroupsModel(BaseModel):
+class RankGenesGroupsParams(BaseModel):
     """Input schema for the rank_genes_groups tool."""
     
     groupby: str = Field(
@@ -669,7 +669,7 @@ class RankGenesGroupsModel(BaseModel):
         return v
 
 
-class FilterRankGenesGroupsModel(BaseModel):
+class FilterRankGenesGroupsParams(BaseModel):
     """Input schema for filtering ranked genes groups."""
     
     key: Optional[str] = Field(
@@ -732,7 +732,7 @@ class FilterRankGenesGroupsModel(BaseModel):
         return v
 
 
-class MarkerGeneOverlapModel(BaseModel):
+class MarkerGeneOverlapParams(BaseModel):
     """Input schema for the marker gene overlap tool."""
     
     key: str = Field(
@@ -803,7 +803,7 @@ class MarkerGeneOverlapModel(BaseModel):
         return v
 
 
-class ScoreGenesModel(BaseModel):
+class ScoreGenesParams(BaseModel):
     """Input schema for the score_genes tool that calculates gene scores based on average expression."""
     
     ctrl_size: int = Field(
@@ -846,7 +846,7 @@ class ScoreGenesModel(BaseModel):
         return v
 
 
-class ScoreGenesCellCycleModel(BaseModel):
+class ScoreGenesCellCycleParams(BaseModel):
     """Input schema for the score_genes_cell_cycle tool that scores cell cycle genes."""
     
     s_genes: List[str] = Field(
@@ -896,7 +896,7 @@ class ScoreGenesCellCycleModel(BaseModel):
 
 
 
-class PCAModel(BaseModel):
+class PCAParams(BaseModel):
     """Input schema for the PCA preprocessing tool."""
     
     n_comps: Optional[int] = Field(

scmcp_shared/schema/util.py

@@ -10,7 +10,7 @@ from typing import Optional, Union, List, Dict, Any, Callable, Collection, Liter
 
 
 
-class MarkVarModel(BaseModel):
+class MarkVarParams(BaseModel):
     """Determine or mark if each gene meets specific conditions and store results in adata.var as boolean values"""
     
     var_name: str = Field(
@@ -32,15 +32,15 @@ class MarkVarModel(BaseModel):
     )
 
 
-class ListVarModel(BaseModel):
+class ListVarParams(BaseModel):
     """ListVarModel"""    
     pass
 
-class ListObsModel(BaseModel):
+class ListObsParams(BaseModel):
     """ListObsModel"""    
     pass    
 
-class VarNamesModel(BaseModel):
+class VarNamesParams(BaseModel):
     """ListObsModel"""    
     var_names: List[str] = Field(
             default=None,
@@ -48,7 +48,7 @@ class VarNamesModel(BaseModel):
         )
 
 
-class ConcatBaseModel(BaseModel):
+class ConcatBaseParams(BaseModel):
     """Model for concatenating AnnData objects"""
     
     axis: Literal['obs', 0, 'var', 1] = Field(
@@ -89,7 +89,7 @@ class ConcatBaseModel(BaseModel):
     )
 
 
-class DPTIROOTModel(BaseModel):
+class DPTIROOTParams(BaseModel):
     """Input schema for setting the root cell for diffusion pseudotime."""
     diffmap_key: str = Field(
         default="X_diffmap",
@@ -103,7 +103,7 @@ class DPTIROOTModel(BaseModel):
     )
 
 
-class CelltypeMapCellTypeModel(BaseModel):
+class CelltypeMapCellTypeParams(BaseModel):
     """Input schema for mapping cluster IDs to cell type names."""
     cluster_key: str = Field(
         description="Key in adata.obs containing cluster IDs."
@@ -122,14 +122,14 @@ class CelltypeMapCellTypeModel(BaseModel):
     
 
 
-class AddLayerModel(BaseModel):
+class AddLayerParams(BaseModel):
     """Input schema for adding a layer to AnnData object."""
     layer_name: str = Field(
         description="Name of the layer to add to adata.layers."
     )
  
 
-class QueryOpLogModel(BaseModel):
+class QueryOpLogParams(BaseModel):
     """QueryOpLogModel"""    
     n: int = Field(
         default=10,

scmcp_shared/server/base.py

@@ -33,25 +33,20 @@ class BaseMCP:
         methods = inspect.getmembers(self, predicate=inspect.ismethod)
         
         # Filter methods that start with _tool_
-        tool_methods = {
-            name[6:]: method  # Remove '_tool_' prefix
-            for name, method in methods
-            if name.startswith('_tool_')
-        }
+        tool_methods = [tl_method() for name, tl_method in methods if name.startswith('_tool_')]
         
         # Filter tools based on include/exclude lists
         if self.include_tools is not None:
-            tool_methods = {k: v for k, v in tool_methods.items() if k in self.include_tools}
+            tool_methods = [tl for tl in tool_methods if tl.name in self.include_tools]
         
         if self.exclude_tools is not None:
-            tool_methods = {k: v for k, v in tool_methods.items() if k not in self.exclude_tools}
+            tool_methods = [tl for tl in tool_methods if tl.name not in self.exclude_tools]
 
         # Register filtered tools
-        for tool_name, tool_method in tool_methods.items():
+        for tool in tool_methods:
             # Get the function returned by the tool method
-            tool_func = tool_method()
-            if tool_func is not None:
-                self.mcp.add_tool(tool_func, name=tool_name)
+            if tool is not None:
+                self.mcp.add_tool(tool)
 
 
 class AdataState:

scmcp_shared/server/io.py

@@ -3,6 +3,7 @@ import inspect
 from pathlib import Path
 import scanpy as sc
 from fastmcp import FastMCP, Context
+from fastmcp.tools.tool import Tool
 from fastmcp.exceptions import ToolError
 from ..schema import AdataInfo
 from ..schema.io import *
@@ -16,7 +17,7 @@ class ScanpyIOMCP(BaseMCP):
         super().__init__("SCMCP-IO-Server", include_tools, exclude_tools, AdataInfo)
 
     def _tool_read(self):
-        def _read(request: ReadModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _read(request: ReadParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """
             Read data from 10X directory or various file formats (h5ad, 10x, text files, etc.).
             """
@@ -33,7 +34,7 @@ class ScanpyIOMCP(BaseMCP):
                 elif file.is_file():
                     func_kwargs = filter_args(request, sc.read)
                     adata = sc.read(**func_kwargs)
-                    if not kwargs.get("first_column_obs", True):
+                    if not kwargs.get("transpose", True):
                         adata = adata.T
                 else:
                     raise FileNotFoundError(f"{kwargs['filename']} does not exist")
@@ -47,8 +48,18 @@ class ScanpyIOMCP(BaseMCP):
                 adata.layers["counts"] = adata.X
                 adata.var_names_make_unique()
                 adata.obs_names_make_unique()
+                adata.obs["scmcp_sampleid"] = adinfo.sampleid or ads.active_id
                 ads.set_adata(adata, adinfo=adinfo)
-                return generate_msg(adinfo, adata, ads)
+                return [
+                    {
+                        "sampleid": adinfo.sampleid or ads.active_id, 
+                        "adtype": adinfo.adtype, 
+                        "adata": adata,
+                        "adata.obs_names[:10]": adata.obs_names[:10],
+                        "adata.var_names[:10]": adata.var_names[:10],
+                        "notice": "check obs_names and var_names. transpose the data if needed"
+                    }
+                    ]
             except ToolError as e:
                 raise ToolError(e)
             except Exception as e:
@@ -56,10 +67,10 @@ class ScanpyIOMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _read
+        return Tool.from_function(_read, name="read")
 
     def _tool_write(self):
-        def _write(request: WriteModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _write(request: WriteParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """save adata into a file."""
             try:
                 res = forward_request("io_write", request, adinfo)
@@ -77,7 +88,7 @@ class ScanpyIOMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _write
+        return Tool.from_function(_write, name="write")
 
 
 # Create an instance of the class