scmcp-shared 0.1.0__py3-none-any.whl

scmcp_shared/schema/util.py

@@ -0,0 +1,131 @@
+
+from pydantic import (
+    BaseModel,
+    Field,
+    ValidationInfo,
+    computed_field,
+    field_validator,
+    model_validator,
+)
+from typing import Optional, Union, List, Dict, Any, Callable, Collection, Literal
+
+
+
+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(
+        default=None,
+        description="Column name that will be added to adata.var, do not set if user does not ask"
+    )
+    pattern_type: Optional[Literal["startswith", "endswith", "contains"]] = Field(
+        default=None,
+        description="Pattern matching type (startswith/endswith/contains), it should be None when gene_class is not None"
+    )    
+    patterns: Optional[str] = Field(
+        default=None,
+        description="gene pattern to match, must be a string, it should be None when gene_class is not None"
+    )
+    
+    gene_class: Optional[Literal["mitochondrion", "ribosomal", "hemoglobin"]] = Field(
+        default=None,
+        description="Gene class type (Mitochondrion/Ribosomal/Hemoglobin)"
+    )
+
+
+class ListVarModel(BaseModel):
+    """ListVarModel"""    
+    pass
+
+class ListObsModel(BaseModel):
+    """ListObsModel"""    
+    pass    
+
+class VarNamesModel(BaseModel):
+    """ListObsModel"""    
+    var_names: List[str] = Field(
+            default=None,
+            description="gene names."
+        )
+
+
+class ConcatAdataModel(BaseModel):
+    """Model for concatenating AnnData objects"""
+    
+    axis: Literal['obs', 0, 'var', 1] = Field(
+        default='obs',
+        description="Which axis to concatenate along. 'obs' or 0 for observations, 'var' or 1 for variables."
+    )
+    join: Literal['inner', 'outer'] = Field(
+        default='inner',
+        description="How to align values when concatenating. If 'outer', the union of the other axis is taken. If 'inner', the intersection."
+    )
+    merge: Optional[Literal['same', 'unique', 'first', 'only']] = Field(
+        default=None,
+        description="How elements not aligned to the axis being concatenated along are selected."
+    )
+    uns_merge: Optional[Literal['same', 'unique', 'first', 'only']] = Field(
+        default=None,
+        description="How the elements of .uns are selected. Uses the same set of strategies as the merge argument, except applied recursively."
+    )
+    label: Optional[str] = Field(
+        default=None,
+        description="label different adata, Column in axis annotation (i.e. .obs or .var) to place batch information in. "
+    )
+    keys: Optional[List[str]] = Field(
+        default=None,
+        description="Names for each object being added. These values are used for column values for label or appended to the index if index_unique is not None."
+    )
+    index_unique: Optional[str] = Field(
+        default=None,
+        description="Whether to make the index unique by using the keys. If provided, this is the delimiter between '{orig_idx}{index_unique}{key}'."
+    )
+    fill_value: Optional[Any] = Field(
+        default=None,
+        description="When join='outer', this is the value that will be used to fill the introduced indices."
+    )
+    pairwise: bool = Field(
+        default=False,
+        description="Whether pairwise elements along the concatenated dimension should be included."
+    )
+
+
+class DPTIROOTModel(BaseModel):
+    """Input schema for setting the root cell for diffusion pseudotime."""
+    diffmap_key: str = Field(
+        default="X_diffmap",
+        description="Key for diffusion map coordinates stored in adata.obsm."
+    )
+    dimension: int = Field(
+        description="Dimension index to use for finding the root cell."
+    )
+    direction: Literal["min", "max"] = Field(
+        description="use the minimum or maximum value along the selected dimension to identify the root cell."
+    )
+
+
+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."
+    )
+    added_key: str = Field(
+        description="Key to add to adata.obs for cell type names."
+    )
+    mapping: Dict[str, str] = Field(
+        default=None,
+        description="Mapping Dictionary from cluster IDs to cell type names."
+    )
+    new_names: Optional[List[str]] = Field(
+        default=None,
+        description="a list of new cell type names."
+    )
+    
+
+
+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."
+    )
+ 

scmcp_shared/server/__init__.py

@@ -0,0 +1 @@
+from .io import io_mcp

scmcp_shared/server/io.py

@@ -0,0 +1,80 @@
+import os
+import inspect
+from pathlib import Path
+import scanpy as sc
+from fastmcp import FastMCP , Context
+from ..schema.io import *
+from ..util import filter_args, forward_request
+
+
+io_mcp = FastMCP("SCMCP-IO-Server")
+
+
+@io_mcp.tool()
+async def read(
+    request: ReadModel, 
+    ctx: Context,
+    sampleid: str = Field(default=None, description="adata sampleid"),
+    dtype: str = Field(default="exp", description="adata.X data type")
+):
+    """
+    Read data from various file formats (h5ad, 10x, text files, etc.) or directory path.
+    """
+    try:
+        result = await forward_request("io_read", request, sampleid=sampleid, dtype=dtype)
+        if result is not None:
+            return result        
+        kwargs = request.model_dump()
+        ads = ctx.request_context.lifespan_context
+        if sampleid is not None:
+            ads.active_id = sampleid
+        else:
+            ads.active_id = f"adata{len(ads.adata_dic[dtype])}"
+
+        file = Path(kwargs.get("filename", None))
+        if file.is_dir():
+            kwargs["path"] = kwargs["filename"]
+            func_kwargs = filter_args(request, sc.read_10x_mtx)
+            adata = sc.read_10x_mtx(kwargs["path"], **func_kwargs)
+        elif file.is_file():
+            func_kwargs = filter_args(request, sc.read)
+            adata = sc.read(**func_kwargs)
+            if not kwargs.get("first_column_obs", True):
+                adata = adata.T
+        else:
+            raise FileNotFoundError(f"{kwargs['filename']} does not exist")
+        adata.layers["counts"] = adata.X
+        adata.var_names_make_unique()
+        adata.obs_names_make_unique()
+        ads.set_adata(adata, sampleid=sampleid, sdtype=dtype)
+        return {"sampleid": sampleid or ads.active_id, "dtype": dtype, "adata": adata}
+    except Exception as e:
+        if hasattr(e, '__context__') and e.__context__:
+            raise Exception(f"{str(e.__context__)}")
+        else:
+            raise e
+
+
+@io_mcp.tool()
+async def write(
+    request: WriteModel, 
+    ctx: Context,
+    sampleid: str = Field(default=None, description="adata sampleid"),
+    dtype: str = Field(default="exp", description="adata.X data type")
+):
+    """save adata into a file.
+    """
+    try:
+        result = await forward_request("io_write", request, sampleid=sampleid, dtype=dtype)
+        if result is not None:
+            return result
+        ads = ctx.request_context.lifespan_context
+        adata = ads.get_adata(sampleid=sampleid, dtype=dtype)
+        kwargs = request.model_dump()
+        sc.write(kwargs["filename"], adata)
+        return {"filename": kwargs["filename"], "msg": "success to save file"}
+    except Exception as e:
+        if hasattr(e, '__context__') and e.__context__:
+            raise Exception(f"{str(e.__context__)}")
+        else:
+            raise e    

scmcp_shared/util.py

@@ -0,0 +1,186 @@
+import inspect
+import os
+from pathlib import Path
+
+
+
+def get_env(key):
+    return os.environ.get(f"SCMCP_{key.upper()}")
+
+ 
+def filter_args(request, func):
+    # sometime,it is a bit redundant, but I think it adds robustness in case the function parameters change
+    kwargs = request.model_dump()
+    args = request.model_fields_set
+    parameters = inspect.signature(func).parameters
+    func_kwargs = {k: kwargs.get(k) for k in args if k in parameters}
+    return func_kwargs
+
+
+def add_op_log(adata, func, kwargs):
+    import hashlib
+    import json
+    
+    if "operation" not in adata.uns:
+        adata.uns["operation"] = {}
+        adata.uns["operation"]["op"] = {}
+        adata.uns["operation"]["opid"] = []
+    # Handle different function types to get the function name
+    if hasattr(func, "func") and hasattr(func.func, "__name__"):
+        # For partial functions, use the original function name
+        func_name = func.func.__name__
+    elif hasattr(func, "__name__"):
+        func_name = func.__name__
+    elif hasattr(func, "__class__"):
+        func_name = func.__class__.__name__
+    else:
+        func_name = str(func)
+    new_kwargs = {}
+    for k,v in kwargs.items():
+        if isinstance(v, tuple):
+            new_kwargs[k] = list(v)
+        else:
+            new_kwargs[k] = v
+    try:
+        kwargs_str = json.dumps(new_kwargs, sort_keys=True)
+    except:
+        kwargs_str = str(new_kwargs)
+    hash_input = f"{func_name}:{kwargs_str}"
+    hash_key = hashlib.md5(hash_input.encode()).hexdigest()
+    adata.uns["operation"]["op"][hash_key] = {func_name: new_kwargs}
+    adata.uns["operation"]["opid"].append(hash_key)
+    from .logging_config import setup_logger
+    logger = setup_logger(log_file=get_env("LOG_FILE"))
+    logger.info(f"{func}: {new_kwargs}")
+
+
+
+def savefig(fig, file):
+    try:
+        file_path = Path(file)
+        file_path.parent.mkdir(parents=True, exist_ok=True)
+        if hasattr(fig, 'figure'):  # if Axes
+            fig.figure.savefig(file_path)
+        elif hasattr(fig, 'save'):  # for plotnine.ggplot.ggplot
+            fig.save(file_path)
+        else:  # if Figure 
+            fig.savefig(file_path)
+        return file_path
+    except Exception as e:
+        raise e
+
+
+def set_fig_path(func, fig=None, **kwargs):
+    "maybe I need to save figure by myself, instead of using scanpy save function..."
+    fig_dir = Path(os.getcwd()) / "figures"
+
+    kwargs.pop("save", None)
+    kwargs.pop("show", None)
+    args = []
+    for k,v in kwargs.items():
+        if isinstance(v, (tuple, list, set)):
+            args.append(f"{k}-{'-'.join([str(i) for i in v])}")
+        else:
+            args.append(f"{k}-{v}")
+    args_str = "_".join(args)
+    if func == "rank_genes_groups_dotplot":
+        old_path = fig_dir / 'dotplot_.png'
+        fig_path = fig_dir / f"{func}_{args_str}.png"
+    elif func in ["scatter", "embedding"]:
+        if "basis" in kwargs and kwargs['basis'] is not None:
+            old_path = fig_dir / f"{kwargs['basis']}.png"
+            fig_path = fig_dir / f"{func}_{args_str}.png"
+        else:
+            old_path = fig_dir / f"{func}.png"
+            fig_path = fig_dir / f"{func}_{args_str}.png"
+    elif func == "highly_variable_genes":        
+        old_path = fig_dir / 'filter_genes_dispersion.png'
+        fig_path = fig_dir / f"{func}_{args_str}.png"
+    elif func == "scvelo_projection":
+        old_path = fig_dir / f"scvelo_{kwargs['kernel']}.png"
+        fig_path = fig_dir / f"{func}_{args_str}.png"
+    else:
+        if (fig_dir / f"{func}_.png").is_file():
+            old_path = fig_dir / f"{func}_.png"
+        else:
+            old_path = fig_dir / f"{func}.png"
+        fig_path = fig_dir / f"{func}_{args_str}.png"
+    try:
+        if fig is not None:
+            savefig(fig, fig_path)
+        else:
+            os.rename(old_path, fig_path)
+        return fig_path
+    except FileNotFoundError:
+        print(f"The file {old_path} does not exist")
+    except FileExistsError:
+        print(f"The file {fig_path} already exists")
+    except PermissionError:
+        print("You don't have permission to rename this file")
+    transport = get_env("TRANSPORT") 
+    if transport == "stdio":
+        return fig_path
+    else:
+        host = get_env("HOST")
+        port = get_env("PORT")
+        fig_path = f"http://{host}:{port}/figures/{Path(fig_path).name}"
+        return fig_path
+
+
+
+async def get_figure(request):
+    from starlette.responses import FileResponse, Response
+
+    figure_name = request.path_params["figure_name"]
+    figure_path = f"./figures/{figure_name}"
+    
+    # 检查文件是否存在
+    if not os.path.isfile(figure_path):
+        return Response(content={"error": "figure not found"}, media_type="application/json")
+    
+    return FileResponse(figure_path)
+
+
+async def forward_request(func, request, **kwargs):
+    from fastmcp import Client
+    forward_url = get_env("FORWARD")
+    request_kwargs = request.model_dump()
+    request_args = request.model_fields_set
+    func_kwargs = {"request": {k: request_kwargs.get(k) for k in request_args}}
+    func_kwargs.update({k:v for k,v in kwargs.items() if v is not None})
+    if not forward_url:
+        return None
+        
+    client = Client(forward_url)
+    async with client:
+        tools = await client.list_tools()
+        func = [t.name for t in tools if t.name.endswith(func)][0]
+        try:
+            result = await client.call_tool(func, func_kwargs)
+            return result
+        except Exception as e:
+            raise e
+
+def obsm2adata(adata, obsm_key):
+    from anndata import AnnData
+
+    if obsm_key not in adata.obsm_keys():
+        raise ValueError(f"key {obsm_key} not found in adata.obsm")
+    else:
+        return AnnData(adata.obsm[obsm_key], obs=adata.obs, obsm=adata.obsm)
+
+
+async def get_figure(request):
+    figure_name = request.path_params["figure_name"]
+    figure_path = f"./figures/{figure_name}"
+    
+    # 检查文件是否存在
+    if not os.path.isfile(figure_path):
+        return Response(content={"error": "figure not found"}, media_type="application/json")
+    
+    return FileResponse(figure_path)
+
+
+def add_figure_route(server):
+    from starlette.routing import Route
+    server._additional_http_routes = [Route("/figures/{figure_name}", endpoint=get_figure)]    

scmcp_shared-0.1.0.dist-info/METADATA

@@ -0,0 +1,44 @@
+Metadata-Version: 2.4
+Name: scmcp_shared
+Version: 0.1.0
+Summary: A shared function libray for scmcphub
+Author-email: shuang <hsh-me@outlook.com>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2025, scmcphub
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: fastmcp>=2.3.0
+Requires-Dist: mcp>=1.8.0
+Requires-Dist: pydantic
+Requires-Dist: scanpy
+Description-Content-Type: text/markdown
+
+# scmcp-shared
+
+Shared functions for scmcphub

scmcp_shared-0.1.0.dist-info/RECORD

@@ -0,0 +1,15 @@
+scmcp_shared/__init__.py,sha256=2Ff5FiaFaDmrGrcJagyK7JKuraTfI0CnRahAnXLS53w,24
+scmcp_shared/logging_config.py,sha256=eCuLuyxMmbj8A1E0VqYWoKA5JPTSbo6cmjS4LOyd0RQ,872
+scmcp_shared/util.py,sha256=jY-HbMzpqKQpzm0UhiyrUwtjtx31_KKUmewlyZYpfZA,6300
+scmcp_shared/schema/__init__.py,sha256=uEIJaRLssrbI9KYOH3RxtMRU63Bes9SkLBskxNBt0hA,18
+scmcp_shared/schema/io.py,sha256=V6Bv6No_FH0Ps2E6VkkHBu7z2EQku9XcG4iWkxMPjiU,4965
+scmcp_shared/schema/pl.py,sha256=yP9XnotdEvY6iPKfvz0otfJFyDJh7FkaIJx7FG4Em44,29548
+scmcp_shared/schema/pp.py,sha256=aAHECfM1LSCRDZkgtPpoMxLXurEyVdG_9dyhj0HSOlw,23507
+scmcp_shared/schema/tl.py,sha256=VNoNBf7hFF_4SG31vNYX52i0M38Bj6ryBJpCJYtedVw,32848
+scmcp_shared/schema/util.py,sha256=rMb29eCu2hVhkggYeOPA2b72Aa8VPDq58nd2Rz8OmoI,4652
+scmcp_shared/server/__init__.py,sha256=V4eLId2ZvwoPTE_53uimF02hLnY8X9iXlA4ri-WfvjM,22
+scmcp_shared/server/io.py,sha256=AQ90QtQdfv2IFo_IPU6dmfk1redF3HPt30DHHv5_3qo,2815
+scmcp_shared-0.1.0.dist-info/METADATA,sha256=VpPvS7tbQQJLtsCNbCJfIAi-iiDf2mm9VCBdqaelcbg,2099
+scmcp_shared-0.1.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+scmcp_shared-0.1.0.dist-info/licenses/LICENSE,sha256=YNr1hpea195yq-wGtB8j-2dGtt7A5G00WENmxa7JGco,1495
+scmcp_shared-0.1.0.dist-info/RECORD,,

scmcp_shared-0.1.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.27.0
+Root-Is-Purelib: true
+Tag: py3-none-any

scmcp_shared-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, scmcphub
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.