scmcp-shared 0.1.0__py3-none-any.whl → 0.2.1__py3-none-any.whl

scmcp_shared/util.py

@@ -1,19 +1,21 @@
 import inspect
 import os
 from pathlib import Path
-
+from fastmcp.server.dependencies import get_context
+from fastmcp.exceptions import ToolError
 
 
 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
+def filter_args(request, func, **extra_kwargs):
     kwargs = request.model_dump()
     args = request.model_fields_set
     parameters = inspect.signature(func).parameters
+    extra_kwargs = {k: extra_kwargs[k] for k in extra_kwargs if k in parameters}
     func_kwargs = {k: kwargs.get(k) for k in args if k in parameters}
+    func_kwargs.update(extra_kwargs)
     return func_kwargs
 
 
@@ -48,6 +50,7 @@ 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"))
@@ -55,25 +58,44 @@ def add_op_log(adata, func, kwargs):
 
 
 
-def savefig(fig, file):
+def savefig(axes, file):
+    from matplotlib.axes import Axes
+
     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)
+        if isinstance(axes, list):
+            if isinstance(axes[0], Axes):
+                axes[0].figure.savefig(file_path)
+        elif isinstance(axes, dict):
+            ax = list(axes.values())[0]
+            if isinstance(ax, Axes):
+                ax.figure.savefig(file_path)
+        elif isinstance(axes, Axes):
+            axes.figure.savefig(file_path)
+        elif hasattr(axes, 'savefig'):  # if Figure 
+            axes.savefig(file_path)
+        elif hasattr(axes, 'save'):  # for plotnine.ggplot.ggplot
+            axes.save(file_path)
+        else:
+            raise ValueError(f"axes must be a Axes or plotnine object, but got {type(axes)}")
         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"
+def set_fig_path(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__
+    elif hasattr(func, "__name__"):
+        func_name = func.__name__
+    elif hasattr(func, "__class__"):
+        func_name = func.__class__.__name__
+    else:
+        func_name = str(func)
 
+    fig_dir = Path(os.getcwd()) / "figures"
     kwargs.pop("save", None)
     kwargs.pop("show", None)
     args = []
@@ -83,40 +105,13 @@ def set_fig_path(func, fig=None, **kwargs):
         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"
+    fig_path = fig_dir / f"{func_name}_{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")
+        savefig(axes, fig_path)
     except PermissionError:
-        print("You don't have permission to rename this file")
+        raise PermissionError("You don't have permission to rename this file")
+    except Exception as e:
+        raise e
     transport = get_env("TRANSPORT") 
     if transport == "stdio":
         return fig_path
@@ -134,7 +129,6 @@ 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")
     
@@ -158,8 +152,14 @@ 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:
-            raise 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
@@ -174,7 +174,6 @@ 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")
     
@@ -183,4 +182,35 @@ async def get_figure(request):
 
 def add_figure_route(server):
     from starlette.routing import Route
-    server._additional_http_routes = [Route("/figures/{figure_name}", endpoint=get_figure)]    
+    server._additional_http_routes = [Route("/figures/{figure_name}", endpoint=get_figure)]
+
+
+def get_ads():
+    ctx = get_context()
+    ads = ctx.request_context.lifespan_context
+    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 sc_like_plot(plot_func, adata, request, **kwargs):
+    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)
+    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

{scmcp_shared-0.1.0.dist-info → scmcp_shared-0.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scmcp_shared
-Version: 0.1.0
+Version: 0.2.1
 Summary: A shared function libray for scmcphub
 Author-email: shuang <hsh-me@outlook.com>
 License: BSD 3-Clause License
@@ -33,7 +33,7 @@ License: BSD 3-Clause License
         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: fastmcp>=2.3.4
 Requires-Dist: mcp>=1.8.0
 Requires-Dist: pydantic
 Requires-Dist: scanpy

scmcp_shared-0.2.1.dist-info/RECORD

@@ -0,0 +1,20 @@
+scmcp_shared/__init__.py,sha256=_oNJ0-RgmWF_9YXGOzXxULVblXWDY-ijzApYQs3nBNU,24
+scmcp_shared/logging_config.py,sha256=eCuLuyxMmbj8A1E0VqYWoKA5JPTSbo6cmjS4LOyd0RQ,872
+scmcp_shared/util.py,sha256=yQpVLqzvDNMRGF9sywh0l5M0XH_u3gbi8MC8aQHj-CQ,7130
+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=zT9HBVMhIznm7im22ixGtlqFQSUyiengjgSk2Hi6WYI,2568
+scmcp_shared/server/pl.py,sha256=TbgfOPxh0b01Er7qVN0QrPd54HF2Dcf7LBgGG7DtNaA,11414
+scmcp_shared/server/pp.py,sha256=iVCHhQJKNPAboJmb1vvjbFfLOH8yibFRm8mCk2-JhHs,12382
+scmcp_shared/server/tl.py,sha256=fFTfE0_kXQ6e21pj-sS8vwkyCp8pqe2Mhe1avA9wjZ8,14024
+scmcp_shared/server/util.py,sha256=LSdsBpk_deQZPT33nedyvILdHKcPFaHsr8s-oREh9Sc,9175
+scmcp_shared-0.2.1.dist-info/METADATA,sha256=u91DFN3s3GzOmnB8MrZWSSnlRf9zbRFpGRogLzM-G7o,2099
+scmcp_shared-0.2.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+scmcp_shared-0.2.1.dist-info/licenses/LICENSE,sha256=YNr1hpea195yq-wGtB8j-2dGtt7A5G00WENmxa7JGco,1495
+scmcp_shared-0.2.1.dist-info/RECORD,,

scmcp_shared-0.1.0.dist-info/RECORD

@@ -1,15 +0,0 @@
-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,,