scmcp-shared 0.2.0__py3-none-any.whl → 0.3.0__py3-none-any.whl

scmcp_shared/__init__.py

@@ -1,3 +1,3 @@
 
-__version__ = "0.2.0"
+__version__ = "0.3.0"
 

scmcp_shared/cli.py

@@ -0,0 +1,96 @@
+import typer
+from typing import Optional, Union, Type
+from enum import Enum
+from .util import add_figure_route, set_env,setup_mcp
+
+
+class TransportEnum(str, Enum):
+    STDIO = "stdio"
+    SSE = "sse"
+    SHTTP = "shttp"
+
+    @property
+    def transport_value(self) -> str:
+        """Get the actual transport value to use."""
+        if self == TransportEnum.SHTTP:
+            return "streamable-http"
+        return self.value
+
+
+class ModuleEnum(str, Enum):
+    """Base class for module types."""
+    ALL = "all"
+
+
+
+class MCPCLI:
+    """Base class for CLI applications with support for dynamic modules and parameters."""
+    
+    def __init__(self, name: str, help_text: str, manager=None, modules=ModuleEnum):
+        self.name = name
+        self.modules = modules
+        self.manager = manager
+        self.app = typer.Typer(
+            name=name,
+            help=help_text,
+            add_completion=False,
+            no_args_is_help=True,
+        )
+        self._setup_commands()
+    
+    def _setup_commands(self):
+        """Setup the main commands for the CLI."""
+        self.app.command(name="run", help="Start the server with the specified configuration")(self.run_command())
+        self.app.callback()(self._callback)
+
+    def run_command(self):
+        def _run_command(
+            log_file: Optional[str] = typer.Option(None, "--log-file", help="log file path, use stdout if None"),
+            transport: TransportEnum = typer.Option(TransportEnum.STDIO, "-t", "--transport", help="specify transport type", 
+                                        case_sensitive=False),
+            port: int = typer.Option(8000, "-p", "--port", help="transport port"),
+            host: str = typer.Option("127.0.0.1", "--host", help="transport host"),
+            forward: str = typer.Option(None, "-f", "--forward", help="forward request to another server"),
+            module: list[self.modules] = typer.Option(
+                [self.modules.ALL], 
+                "-m", 
+                "--module", 
+                help="specify module to run"
+            ),
+        ):
+            """Start the server with the specified configuration."""
+            if "all" in module:
+                modules = None
+            elif isinstance(module, list) and bool(module):
+                modules = [m.value for m in module]
+            self.mcp =  self.manager(self.name, include_modules=modules).mcp
+
+            self.run_mcp(log_file, forward, transport, host, port)
+        return _run_command
+        
+
+    def _callback(self):
+        """Liana MCP CLI root command."""
+        pass
+
+    def run_mcp(self, log_file, forward, transport, host, port):
+        set_env(log_file, forward, transport, host, port)
+        from .logging_config import setup_logger
+        setup_logger(log_file)
+        if transport == "stdio":
+            self.mcp.run()
+        elif transport in ["sse", "shttp"]:
+            add_figure_route(self.mcp)
+            transport = transport.transport_value
+            self.mcp.run(
+                transport=transport,
+                host=host, 
+                port=port, 
+                log_level="info"
+            )
+ 
+    def run_cli(self, mcp=None, module_dic=None):
+        """Run the CLI application."""
+        self.mcp = mcp
+        self.module_dic = module_dic
+        self.app()

scmcp_shared/schema/__init__.py

@@ -1 +1,22 @@
-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"
+    )
+
+class AdataInfo(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(
         ...,
@@ -22,10 +22,6 @@ class ReadModel(AdataModel):
         default=None,
         description="Name of sheet/table in hdf5 or Excel file."
     )
-    ext: str = Field(
-        default=None,
-        description="Extension that indicates the file type. If None, uses extension of filename."
-    )
     delimiter: str = Field(
         default=None,
         description="Delimiter that separates data within text file. If None, will split at arbitrary number of white spaces, which is different from enforcing splitting at any single white space."
@@ -86,7 +82,7 @@ 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(
@@ -301,11 +300,6 @@ class LeidenModel(AdataModel):
         description="Which package's implementation to use."
     )
     
-    clustering_args: Optional[Dict[str, Any]] = Field(
-        default=None,
-        description="Any further arguments to pass to the clustering algorithm."
-    )
-    
     @field_validator('resolution')
     def validate_resolution(cls, v: float) -> float:
         """Validate resolution is positive"""
@@ -330,7 +324,7 @@ class LeidenModel(AdataModel):
         return v
 
 
-class LouvainModel(AdataModel):
+class LouvainModel(BaseModel):
     """Input schema for the Louvain clustering algorithm."""
     
     resolution: Optional[float] = Field(
@@ -402,7 +396,7 @@ class LouvainModel(AdataModel):
         return v
 
 
-class DendrogramModel(AdataModel):
+class DendrogramModel(BaseModel):
     """Input schema for the hierarchical clustering dendrogram tool."""
     
     groupby: str = Field(
@@ -467,7 +461,7 @@ 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 +510,7 @@ 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 +538,7 @@ 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 +587,7 @@ 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 +669,7 @@ class RankGenesGroupsModel(AdataModel):
         return v
 
 
-class FilterRankGenesGroupsModel(AdataModel):
+class FilterRankGenesGroupsModel(BaseModel):
     """Input schema for filtering ranked genes groups."""
     
     key: Optional[str] = Field(
@@ -738,7 +732,7 @@ class FilterRankGenesGroupsModel(AdataModel):
         return v
 
 
-class MarkerGeneOverlapModel(AdataModel):
+class MarkerGeneOverlapModel(BaseModel):
     """Input schema for the marker gene overlap tool."""
     
     key: str = Field(
@@ -809,7 +803,7 @@ 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 +846,7 @@ 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 +896,7 @@ 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

@@ -1,51 +1,13 @@
 from __future__ import annotations
 
-from collections.abc import Iterable
-from typing import Any
-
-from .io import io_mcp
-from .util import ul_mcp
-from .pl import pl_mcp
-from .pp import pp_mcp
-from .tl import tl_mcp
-
-
-
-class AdataState:
-    def __init__(self, add_adtypes=None):
-        self.adata_dic = {"exp": {}, "activity": {}, "cnv": {}, "splicing": {}}
-        if isinstance(add_adtypes, str):
-            self.adata_dic[add_adtypes] = {}
-        elif isinstance(add_adtypes, Iterable):
-            self.adata_dic.update({adtype: {} for adtype in add_adtypes})
-        self.active_id = None
-        self.metadatWa = {}
-        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()
-            sampleid = kwargs.get("sampleid", None)
-            adtype = kwargs.get("adtype", "exp")
-        try:
-            if self.active_id is None:
-                return None
-            sampleid = sampleid or self.active_id
-            return self.adata_dic[adtype][sampleid]
-        except KeyError as e:
-            raise KeyError(f"Key {e} not found in adata_dic[{adtype}].Please check the sampleid or adtype.")
-        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()
-            sampleid = kwargs.get("sampleid", None)
-            sdtype = kwargs.get("adtype", "exp")
-        sampleid = sampleid or self.active_id
-        if sdtype not in self.adata_dic:
-            self.adata_dic[sdtype] = {}
-        self.adata_dic[sdtype][sampleid] = adata
-                          
-
+from collections.abc import Iterable, AsyncIterator
+from typing import Any, Dict, List, Optional
+from contextlib import asynccontextmanager
+import asyncio
+
+from .base import BaseMCP,AdataState,BaseMCPManager
+from .io import ScanpyIOMCP, io_mcp
+from .util import ScanpyUtilMCP
+from .pl import ScanpyPlottingMCP
+from .pp import ScanpyPreprocessingMCP
+from .tl import ScanpyToolsMCP