scmcp-shared 0.2.0__py3-none-any.whl → 0.2.5__py3-none-any.whl

scmcp_shared/__init__.py

@@ -1,3 +1,3 @@
 
-__version__ = "0.2.0"
+__version__ = "0.2.5"
 

scmcp_shared/schema/__init__.py

@@ -1 +1,13 @@
-from .base import AdataModel
+from __future__ import annotations
+
+from pydantic import Field, BaseModel,ConfigDict
+
+
+class AdataModel(BaseModel):
+    """Input schema for the adata tool."""
+    sampleid: str | None = Field(default=None, description="adata sampleid")
+    adtype: str = Field(default="exp", description="The input adata.X data type for preprocess/analysis/plotting")
+
+    model_config = ConfigDict(
+        extra="ignore"
+    )

scmcp_shared/schema/io.py

@@ -1,13 +1,13 @@
 from pydantic import (
     Field,
     field_validator,
-    model_validator,
+    model_validator, BaseModel
 )
 from typing import Optional, Literal
-from .base import AdataModel
 
 
-class ReadModel(AdataModel):
+
+class ReadModel(BaseModel):
     """Input schema for the read tool."""
     filename: str = Field(
         ...,
@@ -86,7 +86,7 @@ class ReadModel(AdataModel):
         return v
 
 
-class WriteModel(AdataModel):
+class WriteModel(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

@@ -7,7 +7,6 @@ from pydantic import (
     model_validator,
     BaseModel
 )
-from .base import AdataModel
 
 # 创建 Mixin 类处理特定功能
 class LegendMixin:
@@ -73,7 +72,7 @@ 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(AdataModel, LegendMixin, ColorMappingMixin, FigureSizeMixin):
+class BaseVisualizationModel(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
 
@@ -632,7 +631,7 @@ class RankGenesGroupsModel(BaseVisualizationModel):
 
 
 # 重构 ClusterMapModel
-class ClusterMapModel(AdataModel):
+class ClusterMapModel(BaseModel):
     """Input schema for the clustermap plotting tool."""
 
     obs_keys: Optional[str] = Field(

scmcp_shared/schema/pp.py

@@ -3,15 +3,15 @@ from pydantic import (
     ValidationInfo,
     computed_field,
     field_validator,
-    model_validator,
+    model_validator,BaseModel
 )
-from .base import AdataModel
+
 from typing import Optional, Union, List, Dict, Any
 from typing import Literal
 import numpy as np
 
 
-class FilterCells(AdataModel):
+class FilterCells(BaseModel):
     """Input schema for the filter_cells preprocessing tool."""
     
     min_counts: Optional[int] = Field(
@@ -42,7 +42,7 @@ class FilterCells(AdataModel):
         return v
 
 
-class FilterGenes(AdataModel):
+class FilterGenes(BaseModel):
     """Input schema for the filter_genes preprocessing tool."""
     
     min_counts: Optional[int] = Field(
@@ -73,7 +73,7 @@ class FilterGenes(AdataModel):
         return v
 
 
-class SubsetCellModel(AdataModel):
+class SubsetCellModel(BaseModel):
     """Input schema for subsetting AnnData objects based on various criteria."""
     obs_key: Optional[str] = Field(
         default=None,
@@ -109,7 +109,7 @@ class SubsetCellModel(AdataModel):
     )
 
 
-class SubsetGeneModel(AdataModel):
+class SubsetGeneModel(BaseModel):
     """Input schema for subsetting AnnData objects based on various criteria."""
     min_counts: Optional[int] = Field(
         default=None,
@@ -145,7 +145,7 @@ class SubsetGeneModel(AdataModel):
     )
 
 
-class CalculateQCMetrics(AdataModel):
+class CalculateQCMetrics(BaseModel):
     """Input schema for the calculate_qc_metrics preprocessing tool."""
     
     expr_type: str = Field(
@@ -196,7 +196,7 @@ class CalculateQCMetrics(AdataModel):
     
 
 
-class Log1PModel(AdataModel):
+class Log1PModel(BaseModel):
     """Input schema for the log1p preprocessing tool."""
     
     base: Optional[Union[int, float]] = Field(
@@ -233,7 +233,7 @@ class Log1PModel(AdataModel):
 
 
 
-class HighlyVariableGenesModel(AdataModel):
+class HighlyVariableGenesModel(BaseModel):
     """Input schema for the highly_variable_genes preprocessing tool."""
     
     layer: Optional[str] = Field(
@@ -307,7 +307,7 @@ class HighlyVariableGenesModel(AdataModel):
         return v
 
 
-class RegressOutModel(AdataModel):
+class RegressOutModel(BaseModel):
     """Input schema for the regress_out preprocessing tool."""
     
     keys: Union[str, List[str]] = Field(
@@ -340,7 +340,7 @@ class RegressOutModel(AdataModel):
         raise ValueError("keys must be a string or list of strings")
 
 
-class ScaleModel(AdataModel):
+class ScaleModel(BaseModel):
     """Input schema for the scale preprocessing tool."""
     
     zero_center: bool = Field(
@@ -376,7 +376,7 @@ class ScaleModel(AdataModel):
         return v
 
 
-class CombatModel(AdataModel):
+class CombatModel(BaseModel):
     """Input schema for the combat batch effect correction tool."""
     
     key: str = Field(
@@ -405,7 +405,7 @@ class CombatModel(AdataModel):
         return v
 
 
-class ScrubletModel(AdataModel):
+class ScrubletModel(BaseModel):
     """Input schema for the scrublet doublet prediction tool."""
     
     adata_sim: Optional[str] = Field(
@@ -511,7 +511,7 @@ class ScrubletModel(AdataModel):
         return v.lower()
 
 
-class NeighborsModel(AdataModel):
+class NeighborsModel(BaseModel):
     """Input schema for the neighbors graph construction tool."""
     
     n_neighbors: int = Field(
@@ -589,7 +589,7 @@ class NeighborsModel(AdataModel):
         return v
 
 
-class NormalizeTotalModel(AdataModel):
+class NormalizeTotalModel(BaseModel):
     """Input schema for the normalize_total preprocessing tool."""
     
     target_sum: Optional[float] = Field(

scmcp_shared/schema/tl.py

@@ -1,9 +1,8 @@
-from pydantic import  Field, field_validator, ValidationInfo
+from pydantic import  Field, field_validator, ValidationInfo, BaseModel
 from typing import Optional, Union, List, Dict, Any, Tuple, Literal, Mapping
 
-from .base import AdataModel
 
-class TSNEModel(AdataModel):
+class TSNEModel(BaseModel):
     """Input schema for the t-SNE dimensionality reduction tool."""
     n_pcs: Optional[int] = Field(
         default=None,
@@ -60,7 +59,7 @@ class TSNEModel(AdataModel):
         return v.lower()
 
 
-class UMAPModel(AdataModel):
+class UMAPModel(BaseModel):
     """Input schema for the UMAP dimensionality reduction tool."""
     
     min_dist: Optional[float] = Field(
@@ -146,7 +145,7 @@ class UMAPModel(AdataModel):
         return v.lower()
 
 
-class DrawGraphModel(AdataModel):
+class DrawGraphModel(BaseModel):
     """Input schema for the force-directed graph drawing tool."""
     
     layout: str = Field(
@@ -200,7 +199,7 @@ class DrawGraphModel(AdataModel):
         return v
 
 
-class DiffMapModel(AdataModel):
+class DiffMapModel(BaseModel):
     """Input schema for the Diffusion Maps dimensionality reduction tool."""
     
     n_comps: int = Field(
@@ -230,7 +229,7 @@ class DiffMapModel(AdataModel):
         return v
 
 
-class EmbeddingDensityModel(AdataModel):
+class EmbeddingDensityModel(BaseModel):
     """Input schema for the embedding density calculation tool."""
     
     basis: str = Field(
@@ -258,7 +257,7 @@ class EmbeddingDensityModel(AdataModel):
         return v
 
 
-class LeidenModel(AdataModel):
+class LeidenModel(BaseModel):
     """Input schema for the Leiden clustering algorithm."""
     
     resolution: Optional[float] = Field(
@@ -330,7 +329,7 @@ class LeidenModel(AdataModel):
         return v
 
 
-class LouvainModel(AdataModel):
+class LouvainModel(BaseModel):
     """Input schema for the Louvain clustering algorithm."""
     
     resolution: Optional[float] = Field(
@@ -402,7 +401,7 @@ class LouvainModel(AdataModel):
         return v
 
 
-class DendrogramModel(AdataModel):
+class DendrogramModel(BaseModel):
     """Input schema for the hierarchical clustering dendrogram tool."""
     
     groupby: str = Field(
@@ -467,7 +466,7 @@ class DendrogramModel(AdataModel):
         return v
 
 
-class DPTModel(AdataModel):
+class DPTModel(BaseModel):
     """Input schema for the Diffusion Pseudotime (DPT) tool."""
     
     n_dcs: int = Field(
@@ -516,7 +515,7 @@ class DPTModel(AdataModel):
             raise ValueError("min_group_size must be between 0 and 1")
         return v
 
-class PAGAModel(AdataModel):
+class PAGAModel(BaseModel):
     """Input schema for the Partition-based Graph Abstraction (PAGA) tool."""
     
     groups: Optional[str] = Field(
@@ -544,7 +543,7 @@ class PAGAModel(AdataModel):
         return v
 
 
-class IngestModel(AdataModel):
+class IngestModel(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(
@@ -593,7 +592,7 @@ class IngestModel(AdataModel):
         return v.lower()
 
 
-class RankGenesGroupsModel(AdataModel):
+class RankGenesGroupsModel(BaseModel):
     """Input schema for the rank_genes_groups tool."""
     
     groupby: str = Field(
@@ -675,7 +674,7 @@ class RankGenesGroupsModel(AdataModel):
         return v
 
 
-class FilterRankGenesGroupsModel(AdataModel):
+class FilterRankGenesGroupsModel(BaseModel):
     """Input schema for filtering ranked genes groups."""
     
     key: Optional[str] = Field(
@@ -738,7 +737,7 @@ class FilterRankGenesGroupsModel(AdataModel):
         return v
 
 
-class MarkerGeneOverlapModel(AdataModel):
+class MarkerGeneOverlapModel(BaseModel):
     """Input schema for the marker gene overlap tool."""
     
     key: str = Field(
@@ -809,7 +808,7 @@ class MarkerGeneOverlapModel(AdataModel):
         return v
 
 
-class ScoreGenesModel(AdataModel):
+class ScoreGenesModel(BaseModel):
     """Input schema for the score_genes tool that calculates gene scores based on average expression."""
     
     ctrl_size: int = Field(
@@ -852,7 +851,7 @@ class ScoreGenesModel(AdataModel):
         return v
 
 
-class ScoreGenesCellCycleModel(AdataModel):
+class ScoreGenesCellCycleModel(BaseModel):
     """Input schema for the score_genes_cell_cycle tool that scores cell cycle genes."""
     
     s_genes: List[str] = Field(
@@ -902,7 +901,7 @@ class ScoreGenesCellCycleModel(AdataModel):
 
 
 
-class PCAModel(AdataModel):
+class PCAModel(BaseModel):
     """Input schema for the PCA preprocessing tool."""
     
     n_comps: Optional[int] = Field(

scmcp_shared/schema/util.py

@@ -4,13 +4,13 @@ from pydantic import (
     ValidationInfo,
     computed_field,
     field_validator,
-    model_validator,
+    model_validator,BaseModel
 )
 from typing import Optional, Union, List, Dict, Any, Callable, Collection, Literal
-from .base import AdataModel
 
 
-class MarkVarModel(AdataModel):
+
+class MarkVarModel(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(AdataModel):
     )
 
 
-class ListVarModel(AdataModel):
+class ListVarModel(BaseModel):
     """ListVarModel"""    
     pass
 
-class ListObsModel(AdataModel):
+class ListObsModel(BaseModel):
     """ListObsModel"""    
     pass    
 
-class VarNamesModel(AdataModel):
+class VarNamesModel(BaseModel):
     """ListObsModel"""    
     var_names: List[str] = Field(
             default=None,
@@ -48,7 +48,7 @@ class VarNamesModel(AdataModel):
         )
 
 
-class ConcatAdataModel(AdataModel):
+class ConcatBaseModel(BaseModel):
     """Model for concatenating AnnData objects"""
     
     axis: Literal['obs', 0, 'var', 1] = Field(
@@ -89,7 +89,7 @@ class ConcatAdataModel(AdataModel):
     )
 
 
-class DPTIROOTModel(AdataModel):
+class DPTIROOTModel(BaseModel):
     """Input schema for setting the root cell for diffusion pseudotime."""
     diffmap_key: str = Field(
         default="X_diffmap",
@@ -103,7 +103,7 @@ class DPTIROOTModel(AdataModel):
     )
 
 
-class CelltypeMapCellTypeModel(AdataModel):
+class CelltypeMapCellTypeModel(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(AdataModel):
     
 
 
-class AddLayerModel(AdataModel):
+class AddLayerModel(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(AdataModel):
+class QueryOpLogModel(BaseModel):
     """QueryOpLogModel"""    
     n: int = Field(
         default=10,

scmcp_shared/server/__init__.py

@@ -23,9 +23,9 @@ class AdataState:
         self.cr_kernel = {}
         self.cr_estimator = {}
         
-    def get_adata(self, sampleid=None, adtype="exp", request=None):
-        if request is not None:
-            kwargs = request.model_dump()
+    def get_adata(self, sampleid=None, adtype="exp", adinfo=None):
+        if adinfo is not None:
+            kwargs = adinfo.model_dump()
             sampleid = kwargs.get("sampleid", None)
             adtype = kwargs.get("adtype", "exp")
         try:
@@ -38,9 +38,9 @@ class AdataState:
         except Exception as e:
             raise Exception(f"fuck {e} {type(e)}")
     
-    def set_adata(self, adata, sampleid=None, sdtype="exp", request=None):
-        if request is not None:
-            kwargs = request.model_dump()
+    def set_adata(self, adata, sampleid=None, sdtype="exp", adinfo=None):
+        if adinfo is not None:
+            kwargs = adinfo.model_dump()
             sampleid = kwargs.get("sampleid", None)
             sdtype = kwargs.get("adtype", "exp")
         sampleid = sampleid or self.active_id

scmcp_shared/server/io.py

@@ -3,6 +3,8 @@ import inspect
 from pathlib import Path
 import scanpy as sc
 from fastmcp import FastMCP , Context
+from fastmcp.exceptions import ToolError
+from ..schema import AdataModel
 from ..schema.io import *
 from ..util import filter_args, forward_request, get_ads, generate_msg
 
@@ -11,12 +13,15 @@ io_mcp = FastMCP("SCMCP-IO-Server")
 
 
 @io_mcp.tool()
-async def read(request: ReadModel):
+async def read(
+    request: ReadModel, 
+    adinfo: AdataModel = AdataModel()
+):
     """
     Read data from 10X directory or various file formats (h5ad, 10x, text files, etc.).
     """
     try:
-        result = await forward_request("io_read", request)
+        result = await forward_request("io_read", request, adinfo)
         if result is not None:
             return result        
         kwargs = request.model_dump()
@@ -34,41 +39,46 @@ async def read(request: ReadModel):
         else:
             raise FileNotFoundError(f"{kwargs['filename']} does not exist")
 
-        sampleid = kwargs.get("sampleid", None)
-        adtype = kwargs.get("adtype", "exp")
         ads = get_ads()
-        if sampleid is not None:
-            ads.active_id = sampleid
+        if adinfo.sampleid is not None:
+            ads.active_id = adinfo.sampleid
         else:
-            ads.active_id = f"adata{len(ads.adata_dic[adtype])}"
+            ads.active_id = f"adata{len(ads.adata_dic[adinfo.adtype])}"
             
         adata.layers["counts"] = adata.X
         adata.var_names_make_unique()
         adata.obs_names_make_unique()
-        ads.set_adata(adata, request=request)
-        return generate_msg(request, adata, ads)
+        ads.set_adata(adata, adinfo=adinfo)
+        return generate_msg(adinfo, adata, ads)
+    except ToolError as e:
+        raise ToolError(e)
     except Exception as e:
         if hasattr(e, '__context__') and e.__context__:
-            raise Exception(f"{str(e.__context__)}")
+            raise ToolError(e.__context__)
         else:
-            raise e
+            raise ToolError(e)
 
 
 @io_mcp.tool()
-async def write(request: WriteModel):
+async def write(
+    request: WriteModel, 
+    adinfo: AdataModel = AdataModel()
+):
     """save adata into a file.
     """
     try:
-        result = await forward_request("io_write", request)
+        result = await forward_request("io_write", request, adinfo)
         if result is not None:
             return result
         ads = get_ads()
-        adata = ads.get_adata(request=request)
+        adata = ads.get_adata(adinfo=adinfo)
         kwargs = request.model_dump()
         sc.write(kwargs["filename"], adata)
         return {"filename": kwargs["filename"], "msg": "success to save file"}
+    except ToolError as e:
+        raise ToolError(e)
     except Exception as e:
         if hasattr(e, '__context__') and e.__context__:
-            raise Exception(f"{str(e.__context__)}")
+            raise ToolError(e.__context__)
         else:
-            raise e    
+            raise ToolError(e)