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

scmcp_shared/server/util.py

@@ -3,7 +3,9 @@ import inspect
 from pathlib import Path
 import scanpy as sc
 from fastmcp import FastMCP , Context
+from fastmcp.exceptions import ToolError
 from ..schema.util import *
+from ..schema import AdataModel
 from ..util import filter_args, forward_request, get_ads, generate_msg,add_op_log
 
 
@@ -11,9 +13,12 @@ ul_mcp = FastMCP("SCMCP-Util-Server")
 
 
 @ul_mcp.tool()
-async def query_op_log(request: QueryOpLogModel = QueryOpLogModel()):
+async def query_op_log(
+    request: QueryOpLogModel = QueryOpLogModel(),
+    adinfo: AdataModel = AdataModel()
+):
     """Query the adata operation log"""
-    adata = get_ads().get_adata(request=request)
+    adata = get_ads().get_adata(adinfo=adinfo)
     op_dic = adata.uns["operation"]["op"]
     opids = adata.uns["operation"]["opid"][-n:]
     op_list = []
@@ -24,7 +29,8 @@ async def query_op_log(request: QueryOpLogModel = QueryOpLogModel()):
 
 @ul_mcp.tool()
 async def mark_var(
-    request: MarkVarModel = MarkVarModel() 
+    request: MarkVarModel = MarkVarModel(),
+    adinfo: AdataModel = AdataModel()
 ):
     """
     Determine if each gene meets specific conditions and store results in adata.var as boolean values.
@@ -32,10 +38,10 @@ async def mark_var(
     The tool should be called first when calculate quality control metrics for mitochondrion, ribosomal, harhemoglobin genes, or other qc_vars.
     """
     try:
-        result = await forward_request("ul_mark_var", request)
+        result = await forward_request("ul_mark_var", request, adinfo)
         if result is not None:
             return result
-        adata = get_ads().get_adata(request=request)
+        adata = get_ads().get_adata(adinfo=adinfo)
         var_name = request.var_name
         gene_class = request.gene_class
         pattern_type = request.pattern_type
@@ -64,120 +70,124 @@ async def mark_var(
     
         res = {var_name: adata.var[var_name].value_counts().to_dict(), "msg": f"add '{var_name}' column in adata.var"}
         func_kwargs = {"var_name": var_name, "gene_class": gene_class, "pattern_type": pattern_type, "patterns": patterns}
-        add_op_log(adata, "mark_var", func_kwargs)
+        add_op_log(adata, "mark_var", func_kwargs, adinfo)
         return res
-    except KeyError as e:
-        raise e
+    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)
 
 
 @ul_mcp.tool()
 async def list_var(
-    request: ListVarModel = ListVarModel() 
+    request: ListVarModel = ListVarModel(),
+    adinfo: AdataModel = AdataModel()
 ):
     """List key columns in adata.var. It should be called for checking when other tools need var key column names as input."""
     try:
-        result = await forward_request("ul_list_var", request)
+        result = await forward_request("ul_list_var", request, adinfo)
         if result is not None:
             return result
-        adata = get_ads().get_adata(request=request)
+        adata = get_ads().get_adata(adinfo=adinfo)
         columns = list(adata.var.columns)
-        add_op_log(adata, list_var, {})
+        add_op_log(adata, list_var, {}, adinfo)
         return columns
-    except KeyError as e:
-        raise e
+    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)
 
 @ul_mcp.tool()
 async def list_obs(
-    request: ListObsModel = ListObsModel() 
+    request: ListObsModel = ListObsModel(),
+    adinfo: AdataModel = AdataModel()
 ):
     """List key columns in adata.obs. It should be called before other tools need obs key column names input."""
     try:
-        result = await forward_request("ul_list_obs", request)
+        result = await forward_request("ul_list_obs", request, adinfo)
         if result is not None:
             return result    
-        adata = get_ads().get_adata(request=request)
+        adata = get_ads().get_adata(adinfo=adinfo)
         columns = list(adata.obs.columns)
-        add_op_log(adata, list_obs, {})
+        add_op_log(adata, list_obs, {}, adinfo)
         return columns
-    except KeyError as e:
-        raise e
+    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)
 
 @ul_mcp.tool()
 async def check_var(
-    request: VarNamesModel = VarNamesModel() 
+    request: VarNamesModel = VarNamesModel(),
+    adinfo: AdataModel = AdataModel()
 ):
     """Check if genes/variables exist in adata.var_names. This tool should be called before gene expression visualizations or color by genes."""
     try:
-        result = await forward_request("ul_check_var", request)
+        result = await forward_request("ul_check_var", request, adinfo)
         if result is not None:
             return result     
-        adata = get_ads().get_adata(request=request)
+        adata = get_ads().get_adata(adinfo=adinfo)
         var_names = request.var_names
         result = {v: v in adata.var_names for v in var_names}
-        add_op_log(adata, check_var, {"var_names": var_names})
+        add_op_log(adata, check_var, {"var_names": var_names}, adinfo)
         return result
-    except KeyError as e:
-        raise e
+    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)
 
 @ul_mcp.tool()
 async def merge_adata(
-    request: ConcatAdataModel = ConcatAdataModel() 
+    request: ConcatBaseModel = ConcatBaseModel(),
+    adinfo: AdataModel = AdataModel()
 ):
     """Merge multiple adata objects."""
      
     try:
-        result = await forward_request("ul_merge_adata", request)
+        result = await forward_request("ul_merge_adata", 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 = {k: v for k, v in request.model_dump().items() if v is not None}
         merged_adata = adata.concat(list(ads.adata_dic[dtype].values()), **kwargs)
         ads.adata_dic[dtype] = {}
         ads.active_id = "merged_adata"
-        add_op_log(merged_adata, ad.concat, kwargs)
+        add_op_log(merged_adata, ad.concat, kwargs, adinfo)
         ads.adata_dic[ads.active_id] = merged_adata
         return {"status": "success", "message": "Successfully merged all AnnData objects"}
-    except KeyError as e:
-        raise e
+    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)
 
 
 @ul_mcp.tool()
 async def set_dpt_iroot(
     request: DPTIROOTModel,
-    
+    adinfo: AdataModel = AdataModel()
 ):
     """Set the iroot cell"""
     try:
-        result = await forward_request("ul_set_dpt_iroot", request)
+        result = await forward_request("ul_set_dpt_iroot", request, adinfo)
         if result is not None:
             return result     
-        adata = get_ads().get_adata(request=request)
+        adata = get_ads().get_adata(adinfo=adinfo)
         diffmap_key = request.diffmap_key
         dimension = request.dimension
         direction = request.direction
@@ -189,28 +199,29 @@ async def set_dpt_iroot(
             adata.uns["iroot"] = adata.obsm[diffmap_key][:, dimension].argmax()
         
         func_kwargs = {"diffmap_key": diffmap_key, "dimension": dimension, "direction": direction}
-        add_op_log(adata, "set_dpt_iroot", func_kwargs)
+        add_op_log(adata, "set_dpt_iroot", func_kwargs, adinfo)
         
         return {"status": "success", "message": f"Successfully set root cell for DPT using {direction} of dimension {dimension}"}
-    except KeyError as e:
-        raise e
+    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)
 
 @ul_mcp.tool()
 async def add_layer(
     request: AddLayerModel,
+    adinfo: AdataModel = AdataModel()
 ):
     """Add a layer to the AnnData object.
     """
     try:
-        result = await forward_request("ul_add_layer", request)
+        result = await forward_request("ul_add_layer", request, adinfo)
         if result is not None:
             return result         
-        adata = get_ads().get_adata(request=request)
+        adata = get_ads().get_adata(adinfo=adinfo)
         layer_name = request.layer_name
         
         # Check if layer already exists
@@ -220,19 +231,19 @@ async def add_layer(
         adata.layers[layer_name] = adata.X.copy()
 
         func_kwargs = {"layer_name": layer_name}
-        add_op_log(adata, "add_layer", func_kwargs)
+        add_op_log(adata, "add_layer", func_kwargs, adinfo)
         
         return {
             "status": "success", 
             "message": f"Successfully added layer '{layer_name}' to adata.layers"
         }
-    except KeyError as e:
-        raise e
+    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)
 
 @ul_mcp.tool()
 async def check_samples():
@@ -241,10 +252,10 @@ async def check_samples():
     try:
         ads = get_ads()
         return {"sampleid": [list(ads.adata_dic[dk].keys()) for dk in ads.adata_dic.keys()]}
-    except KeyError as e:
-        raise e
+    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)

scmcp_shared/util.py

@@ -2,7 +2,7 @@ import inspect
 import os
 from pathlib import Path
 from fastmcp.server.dependencies import get_context
-
+from fastmcp.exceptions import ToolError
 
 
 def get_env(key):
@@ -19,7 +19,7 @@ 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 +37,7 @@ 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 +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"))
@@ -103,7 +104,7 @@ 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)
@@ -134,13 +135,22 @@ 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 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()
+    }
+    print(func_kwargs)
+    # func_kwargs.update({k:v for k,v in kwargs.items() if v is not None})
     if not forward_url:
         return None
         
@@ -151,8 +161,14 @@ 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
@@ -163,39 +179,25 @@ def obsm2adata(adata, obsm_key):
         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)]
-
-
 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 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, adinfo, **kwargs):
+    from matplotlib import pyplot as plt
 
-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)
+    if axes is None:
+        axes = plt.gca()
     fig_path = set_fig_path(axes, plot_func, **func_kwargs)
-    add_op_log(adata, plot_func, func_kwargs)
+    add_op_log(adata, plot_func, func_kwargs, adinfo)
     return fig_path
 
 

{scmcp_shared-0.2.0.dist-info → scmcp_shared-0.2.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scmcp_shared
-Version: 0.2.0
+Version: 0.2.5
 Summary: A shared function libray for scmcphub
 Author-email: shuang <hsh-me@outlook.com>
 License: BSD 3-Clause License

scmcp_shared-0.2.5.dist-info/RECORD

@@ -0,0 +1,19 @@
+scmcp_shared/__init__.py,sha256=9WXFueskl8xksdIA9MJUyauJD-k4jXiK79wuJfC3MuI,24
+scmcp_shared/logging_config.py,sha256=eCuLuyxMmbj8A1E0VqYWoKA5JPTSbo6cmjS4LOyd0RQ,872
+scmcp_shared/util.py,sha256=pQFqFVf8leGqKK38RgXzgtEvXWi8dZBjTuJB0rKTOnw,6957
+scmcp_shared/schema/__init__.py,sha256=iwFLgyjBFYDS2OMCXhv54Jb3LUQr2EH5POqaqN5gBX0,412
+scmcp_shared/schema/io.py,sha256=jpWcw4nUKsCRkG9ybOHLb2kS4wyN16Rj1AuzR-8Sm6U,4893
+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=9mYTwdk3XSJ2A_TdqS_974VSS7Nl4NKyewVN1bwnJBg,34450
+scmcp_shared/schema/util.py,sha256=x_2GPsmliHabi9V5C6YEv_M8ZHJsinDZJ6ePWrLPmcI,4815
+scmcp_shared/server/__init__.py,sha256=zLV89TwMICoaAIqx65_Vbh1RP72Z0EgSvqBMFZhYBpc,1790
+scmcp_shared/server/io.py,sha256=0XzQoxipwK4ml2gmPfrZqMYyy37kqyUyr8hSCnjzyVE,2631
+scmcp_shared/server/pl.py,sha256=9DGF7PM-rB1CDMdv_vHiSZmI-ggMWcRKEZwB1GVenxI,12426
+scmcp_shared/server/pp.py,sha256=6p6jGTunU858uuGoXHodiWTdHRufKs9-_WlWtS82esQ,12976
+scmcp_shared/server/tl.py,sha256=OAF-dFQ5Lhw8RrAUir860IWgbPcaeAyQbFdKcP_tlQ4,14912
+scmcp_shared/server/util.py,sha256=MXDpJA1Zn2eFE_LpW5t4eVUdGr6dUOXIM8KoyfweJUA,9607
+scmcp_shared-0.2.5.dist-info/METADATA,sha256=dTs0LfEmYxRWQpv9rkvfnkeqzCRTGrHfzhZZCYBLdeE,2099
+scmcp_shared-0.2.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+scmcp_shared-0.2.5.dist-info/licenses/LICENSE,sha256=YNr1hpea195yq-wGtB8j-2dGtt7A5G00WENmxa7JGco,1495
+scmcp_shared-0.2.5.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,,