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

scmcp_shared/util.py

@@ -1,8 +1,11 @@
 import inspect
 import os
+from enum import Enum
 from pathlib import Path
 from fastmcp.server.dependencies import get_context
-
+from fastmcp.exceptions import ToolError
+import asyncio
+import nest_asyncio
 
 
 def get_env(key):
@@ -19,7 +22,7 @@ def filter_args(request, func, **extra_kwargs):
     return func_kwargs
 
 
-def add_op_log(adata, func, kwargs):
+def add_op_log(adata, func, kwargs, adinfo):
     import hashlib
     import json
     
@@ -37,7 +40,7 @@ def add_op_log(adata, func, kwargs):
         func_name = func.__class__.__name__
     else:
         func_name = str(func)
-    new_kwargs = {}
+    new_kwargs = {**adinfo.model_dump()}
     for k,v in kwargs.items():
         if isinstance(v, tuple):
             new_kwargs[k] = list(v)
@@ -50,6 +53,7 @@ def add_op_log(adata, func, 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"] = list(adata.uns["operation"]["opid"])
     adata.uns["operation"]["opid"].append(hash_key)
     from .logging_config import setup_logger
     logger = setup_logger(log_file=get_env("LOG_FILE"))
@@ -57,7 +61,7 @@ def add_op_log(adata, func, kwargs):
 
 
 
-def savefig(axes, file):
+def save_fig_path(axes, file):
     from matplotlib.axes import Axes
 
     try:
@@ -83,7 +87,7 @@ def savefig(axes, file):
         raise e
 
 
-def set_fig_path(axes, func=None, **kwargs):
+def savefig(axes, func=None, **kwargs):
     if hasattr(func, "func") and hasattr(func.func, "__name__"):
         # For partial functions, use the original function name
         func_name = func.func.__name__
@@ -103,12 +107,12 @@ def set_fig_path(axes, func=None, **kwargs):
             args.append(f"{k}-{'-'.join([str(i) for i in v])}")
         else:
             args.append(f"{k}-{v}")
-    args_str = "_".join(args)
+    args_str = "_".join(args).replace(" ", "")
     fig_path = fig_dir / f"{func_name}_{args_str}.png"
     try:
-        savefig(axes, fig_path)
+        save_fig_path(axes, fig_path)
     except PermissionError:
-        raise PermissionError("You don't have permission to rename this file")
+        raise PermissionError("You don't have permission to save figure")
     except Exception as e:
         raise e
     transport = get_env("TRANSPORT") 
@@ -134,13 +138,20 @@ async def get_figure(request):
     return FileResponse(figure_path)
 
 
-async def forward_request(func, request, **kwargs):
+def add_figure_route(server):
+    from starlette.routing import Route
+    server._additional_http_routes = [Route("/figures/{figure_name}", endpoint=get_figure)]
+
+
+async def async_forward_request(func, request, adinfo, **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})
+    func_kwargs = {
+        "request": {k: request_kwargs.get(k) for k in request_args},
+        "adinfo": adinfo.model_dump()
+    }
     if not forward_url:
         return None
         
@@ -151,31 +162,44 @@ async def forward_request(func, request, **kwargs):
         try:
             result = await client.call_tool(func, func_kwargs)
             return result
+        except ToolError as e:
+            raise ToolError(e)
         except Exception as e:
+            if hasattr(e, '__context__') and e.__context__:
+                raise Exception(f"{str(e.__context__)}")
+            else:
+                raise e
+
+
+
+def forward_request(func, request, adinfo, **kwargs):
+    """Synchronous wrapper for forward_request"""
+    try:
+        # Apply nest_asyncio to allow nested event loops
+        nest_asyncio.apply()
+        loop = asyncio.get_event_loop()
+        if loop.is_running():
+            # If we're in a running event loop, use create_task
+            async def _run():
+                return await async_forward_request(func, request, adinfo, **kwargs)
+            return loop.run_until_complete(_run())
+        else:
+            # If no event loop is running, use asyncio.run()
+            return asyncio.run(async_forward_request(func, request, adinfo, **kwargs))
+    except Exception as e:
+        if hasattr(e, '__context__') and e.__context__:
+            raise Exception(f"{str(e.__context__)}")
+        else:
             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}"
-    
-    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)]
+        return AnnData(adata.obsm[obsm_key], obs=adata.obs, obsm=adata.obsm, uns=adata.uns)
 
 
 def get_ads():
@@ -184,26 +208,69 @@ def get_ads():
     return ads
 
 
-def generate_msg(request, adata, ads):
-    kwargs = request.model_dump()
-    sampleid = kwargs.get("sampleid")
-    dtype = kwargs.get("dtype", "exp")
-    return {"sampleid": sampleid or ads.active_id, "dtype": dtype, "adata": adata}
+def generate_msg(adinfo, adata, ads):
+    return {"sampleid": adinfo.sampleid or ads.active_id, "dtype": adinfo.adtype, "adata": adata}
 
 
-def sc_like_plot(plot_func, adata, request, **kwargs):
+def sc_like_plot(plot_func, adata, request, adinfo, **kwargs):
+    from matplotlib import pyplot as plt
+
     func_kwargs = filter_args(request, plot_func, show=False, save=False)
     axes = plot_func(adata, **func_kwargs)
-    fig_path = set_fig_path(axes, plot_func, **func_kwargs)
-    add_op_log(adata, plot_func, func_kwargs)
+    if axes is None:
+        axes = plt.gca()
+    fig_path = savefig(axes, plot_func, **func_kwargs)
+    add_op_log(adata, plot_func, func_kwargs, adinfo)
     return fig_path
 
 
-async def filter_tools(mcp, include_tools=None, exclude_tools=None):
-    tools = await mcp.get_tools()
-    for tool in tools:
-        if exclude_tools and tool in exclude_tools:
-            mcp.remove_tool(tool)
-        if include_tools and tool not in include_tools:
-            mcp.remove_tool(tool)
-    return mcp
+def filter_tools(mcp, include_tools=None, exclude_tools=None):
+    import asyncio
+    import copy
+    mcp = copy.deepcopy(mcp)
+    async def _filter_tools(mcp, include_tools=None, exclude_tools=None):
+        tools = await mcp.get_tools()
+        for tool in tools:
+            if exclude_tools and tool in exclude_tools:
+                mcp.remove_tool(tool)
+            if include_tools and tool not in include_tools:
+                mcp.remove_tool(tool)
+        return mcp
+    return asyncio.run(_filter_tools(mcp, include_tools, exclude_tools))
+
+
+ 
+def set_env(log_file, forward, transport, host, port):
+    if log_file is not None:
+        os.environ['SCMCP_LOG_FILE'] = log_file
+    if forward is not None:
+        os.environ['SCMCP_FORWARD'] = forward           
+    os.environ['SCMCP_TRANSPORT'] = transport
+    os.environ['SCMCP_HOST'] = host
+    os.environ['SCMCP_PORT'] = str(port)
+
+
+
+def setup_mcp(mcp, sub_mcp_dic, modules=None):
+    import asyncio
+    if modules is None or modules == "all":
+        modules = sub_mcp_dic.keys()
+    for module in modules:
+        asyncio.run(mcp.import_server(module, sub_mcp_dic[module]))
+    return mcp
+
+def _update_args(mcp, func, args_dic : dict):
+    defs = mcp._tool_manager._tools[func].parameters['$defs']
+    model_names = list(defs.keys())
+    args_model = model_names[0] if  model_names[0] != "AdataModel" else model_names[1]
+    for args, property_dic in args_dic.items():
+        for pk, v in property_dic.items():
+            for model in model_names:
+                if args in mcp._tool_manager._tools[func].parameters['$defs'][model]["properties"]:
+                    mcp._tool_manager._tools[func].parameters['$defs'][model]["properties"][args][pk] = v
+
+
+def update_mcp_args(mcp, tool_args : dict):
+    tools = mcp._tool_manager._tools.keys()
+    for tool in tool_args: 
+        _update_args(mcp, tool, tool_args[tool])

{scmcp_shared-0.2.0.dist-info → scmcp_shared-0.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scmcp_shared
-Version: 0.2.0
+Version: 0.3.0
 Summary: A shared function libray for scmcphub
 Author-email: shuang <hsh-me@outlook.com>
 License: BSD 3-Clause License

scmcp_shared-0.3.0.dist-info/RECORD

@@ -0,0 +1,21 @@
+scmcp_shared/__init__.py,sha256=nSn3YFzkE-BAmUSmif33CxdohNxkgmLE9cYFNbjEu_E,24
+scmcp_shared/cli.py,sha256=NU31Vv-xev8yGtl1KHZhVswJNbK18x2AVzhhH9MR03M,3325
+scmcp_shared/logging_config.py,sha256=eCuLuyxMmbj8A1E0VqYWoKA5JPTSbo6cmjS4LOyd0RQ,872
+scmcp_shared/util.py,sha256=vxmR6_iOBa5jaBNBWl3QBysJ14kXRrqrENDRl3_TChQ,9339
+scmcp_shared/schema/__init__.py,sha256=Kwkc7kPLjExOlxt1sWEy_5qa96MvOS8sNCMlZa6yRg8,737
+scmcp_shared/schema/io.py,sha256=ZKJpKkKazDE3_ZX3GtMIT08kSaiNmy0qVaxivhN7Dx4,4744
+scmcp_shared/schema/pl.py,sha256=rzE09wHMY3JR56HZc-QfIUUM0fGXRKd-7Dh3CrQrFB0,29547
+scmcp_shared/schema/pp.py,sha256=48F6oKf-I8IZuNQDfq_Lpp3fLLKA4PruqRje_ZrtTyw,21664
+scmcp_shared/schema/tl.py,sha256=0HlZ_WQkgnc93LfIYapRCijWBBaFAdM5SV3Ioht_1wI,34281
+scmcp_shared/schema/util.py,sha256=x_2GPsmliHabi9V5C6YEv_M8ZHJsinDZJ6ePWrLPmcI,4815
+scmcp_shared/server/__init__.py,sha256=4KE2Y_gDenF0ZyTGicQW0fTgJfMIQYZfpRP4hQ4rFYs,416
+scmcp_shared/server/base.py,sha256=kaOfi4yHLWr_AdBdpKzDrJiwRmbHF2jbsfI5g2qqgRA,6576
+scmcp_shared/server/io.py,sha256=yrQXdkAsPvk_62xQk5-SRmc5-jAvI-d3sE0QqHDXfMM,3424
+scmcp_shared/server/pl.py,sha256=HdhjrZfEx-IzCkZ03IGCW-mjUItfNvKdSOFbJ2_-2XQ,14854
+scmcp_shared/server/pp.py,sha256=neyRV3yEZ2a08eO-COI-t-PFFvntRzNmu19SQ77do_4,15406
+scmcp_shared/server/tl.py,sha256=2vfl5FrWQgQlPTB4-QLFMuMrtCux6ppmFttKOrryhF0,18320
+scmcp_shared/server/util.py,sha256=L51fFL7Nb84JCQrFYyZIGsfmNFlA9uGzTV93hvc9mfI,12025
+scmcp_shared-0.3.0.dist-info/METADATA,sha256=M8NokyJHPjAVnN-JYmprlFhAfDq_XvAAU1l-kiH8LOA,2099
+scmcp_shared-0.3.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+scmcp_shared-0.3.0.dist-info/licenses/LICENSE,sha256=YNr1hpea195yq-wGtB8j-2dGtt7A5G00WENmxa7JGco,1495
+scmcp_shared-0.3.0.dist-info/RECORD,,

scmcp_shared/schema/base.py

@@ -1,11 +0,0 @@
-from pydantic import Field, BaseModel,ConfigDict
-
-
-class AdataModel(BaseModel):
-    """Input schema for the adata tool."""
-    sampleid: str = Field(default=None, description="adata sampleid")
-    adtype: str = Field(default="exp", description="adata.X data type")
-
-    model_config = ConfigDict(
-        extra="ignore"
-    )

scmcp_shared-0.2.0.dist-info/RECORD

@@ -1,20 +0,0 @@
-scmcp_shared/__init__.py,sha256=ZJMoFGVU2-tXepjhh5Fhy8ZyNHtOIGZWbJygHmqwmCA,24
-scmcp_shared/logging_config.py,sha256=eCuLuyxMmbj8A1E0VqYWoKA5JPTSbo6cmjS4LOyd0RQ,872
-scmcp_shared/util.py,sha256=Ul88pY0aHFN42tiWwexO5LfQJgNslyOD4Jb9HTMy3uI,6814
-scmcp_shared/schema/__init__.py,sha256=fwMJT4mQ3rvRJpSz9ruwwZU1GbXsUYPVQRpP56Az_JM,28
-scmcp_shared/schema/base.py,sha256=hWh0534xon4gyIxwXUBVR067uFiW73nZccSs6DkcwYc,326
-scmcp_shared/schema/io.py,sha256=yxa0BGQXuHCUvv6ZGQApPqMOlyJuC-eQNk7jlRGsMJ8,4913
-scmcp_shared/schema/pl.py,sha256=I9SCJgjmfB0VTNio4uNnP26ajWCnsHPsDoO-yMuzYVo,29578
-scmcp_shared/schema/pp.py,sha256=Uhe28zD71UDZbziesH6bgQXIRXQz_HHrr8-Hb4RQsKI,21696
-scmcp_shared/schema/tl.py,sha256=QV0dP-5ZtEKUDmSV9m5ryx7uQub4rw4in7PYsxId5nU,34485
-scmcp_shared/schema/util.py,sha256=R0MThHKKGYGGJu-hMc-i7fomW-6ugaoQqPi_hbKrB5A,4844
-scmcp_shared/server/__init__.py,sha256=vGYGUpLt8XHRbJI84Ox6WnK4ntzsbTal99Uu14nav60,1796
-scmcp_shared/server/io.py,sha256=agioBQeTREqOX8qJsP2aOTkaU3dT04uvObWhUSfOPTg,2422
-scmcp_shared/server/pl.py,sha256=0KIB9n-h5L3F4TOO_ezPAEX7TVCVBOsiZd6bqD5WbGQ,11126
-scmcp_shared/server/pp.py,sha256=iS-GrU2-Fyw0phLI4A44g2Y3LpFfYF7AWU5ueyzLFxY,12116
-scmcp_shared/server/tl.py,sha256=k8GCTmrFh63jI5REO4-BmfCgyvcGgNpvtsxrn_0K67k,13228
-scmcp_shared/server/util.py,sha256=eBkwWUSrndTb6RHujgXGZYU1aitJEocEuV6U5IOLsws,9030
-scmcp_shared-0.2.0.dist-info/METADATA,sha256=Ayh--1Js_wfAHx1Wep-tw0fxihV9ikUYRWttSwAZL88,2099
-scmcp_shared-0.2.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-scmcp_shared-0.2.0.dist-info/licenses/LICENSE,sha256=YNr1hpea195yq-wGtB8j-2dGtt7A5G00WENmxa7JGco,1495
-scmcp_shared-0.2.0.dist-info/RECORD,,