scmcp-shared 0.2.1__py3-none-any.whl → 0.2.5__py3-none-any.whl

scmcp_shared/server/pp.py

@@ -5,6 +5,7 @@ import scanpy as sc
 from fastmcp import FastMCP , Context
 from fastmcp.exceptions import ToolError
 from ..schema.pp import *
+from ..schema import AdataModel
 from ..util import filter_args, add_op_log, forward_request, get_ads, generate_msg
 from ..logging_config import setup_logger
 logger = setup_logger()
@@ -15,21 +16,22 @@ pp_mcp = FastMCP("ScanpyMCP-PP-Server")
 
 @pp_mcp.tool()
 async def subset_cells(
-    request: SubsetCellModel = SubsetCellModel() 
+    request: SubsetCellModel = SubsetCellModel(),
+    adinfo: AdataModel = AdataModel()
 ):
     """filter or subset cells based on total genes expressed counts and numbers. or values in adata.obs[obs_key]"""
 
     try:
-        result = await forward_request("subset_cells", request)
+        result = await forward_request("subset_cells", request, adinfo)
         if result is not None:
             return result
 
         ads = get_ads()
-        adata = ads.get_adata(request=request).copy()
+        adata = ads.get_adata(adinfo=adinfo).copy()
         func_kwargs = filter_args(request, sc.pp.filter_cells)
         if func_kwargs:
             sc.pp.filter_cells(adata, **func_kwargs)
-            add_op_log(adata, sc.pp.filter_cells, func_kwargs)
+            add_op_log(adata, sc.pp.filter_cells, func_kwargs, adinfo)
         # Subset based on obs (cells) criteria
         if request.obs_key is not None:
             if request.obs_key not in adata.obs.columns:
@@ -46,11 +48,11 @@ async def subset_cells(
                 {
                 "obs_key": request.obs_key, "obs_value": request.obs_value, 
                 "obs_min": request.obs_min, "obs_max": request.obs_max
-                }
+                }, adinfo
             )
-        ads.set_adata(adata, request=request)
+        ads.set_adata(adata, adinfo=adinfo)
         return [
-            generate_msg(request, adata, ads)
+            generate_msg(adinfo, adata, ads)
         ]
     except ToolError as e:
         raise ToolError(e)
@@ -63,19 +65,20 @@ async def subset_cells(
 
 @pp_mcp.tool()
 async def subset_genes(
-    request: SubsetGeneModel = SubsetGeneModel() 
+    request: SubsetGeneModel = SubsetGeneModel(),
+    adinfo: AdataModel = AdataModel()
 ):
     """filter or subset genes based on number of cells or counts, or values in adata.var[var_key] or subset highly variable genes""" 
     try:
-        result = await forward_request("pp_subset_genes", request)
+        result = await forward_request("pp_subset_genes", request, adinfo)
         if result is not None:
             return result
         func_kwargs = filter_args(request, sc.pp.filter_genes)
         ads = get_ads()
-        adata = ads.get_adata(request=request).copy()
+        adata = ads.get_adata(adinfo=adinfo).copy()
         if func_kwargs:
             sc.pp.filter_genes(adata, **func_kwargs)
-            add_op_log(adata, sc.pp.filter_genes, func_kwargs)
+            add_op_log(adata, sc.pp.filter_genes, func_kwargs, adinfo)
         if request.var_key is not None:
             if request.var_key not in adata.var.columns:
                 raise ValueError(f"Key '{request.var_key}' not found in adata.var")
@@ -91,11 +94,11 @@ async def subset_genes(
                 {
                 "var_key": request.var_key, "var_value": request.var_value, 
                 "var_min": request.var_min, "var_max": request.var_max, "hpv":  request.highly_variable
-                }
+                }, adinfo
             )
-        ads.set_adata(adata, request=request)
+        ads.set_adata(adata, adinfo=adinfo)
         return [
-            generate_msg(request, adata, ads)
+            generate_msg(adinfo, adata, ads)
         ]
     except ToolError as e:
         raise ToolError(e)
@@ -107,26 +110,27 @@ async def subset_genes(
 
 @pp_mcp.tool()
 async def calculate_qc_metrics(
-    request: CalculateQCMetrics = CalculateQCMetrics() 
+    request: CalculateQCMetrics = CalculateQCMetrics(),
+    adinfo: AdataModel = AdataModel()
 ):
     """Calculate quality control metrics(common metrics: total counts, gene number, percentage of counts in ribosomal and mitochondrial) for AnnData."""
 
     try:
-        result = await forward_request("pp_calculate_qc_metrics", request)
+        result = await forward_request("pp_calculate_qc_metrics", request, adinfo)
         if result is not None:
             return result
         logger.info(f"calculate_qc_metrics {request.model_dump()}")
         func_kwargs = filter_args(request, sc.pp.calculate_qc_metrics)
         ads = get_ads()
-        adata = ads.get_adata(request=request)
+        adata = ads.get_adata(adinfo=adinfo)
         func_kwargs["inplace"] = True
         try:
             sc.pp.calculate_qc_metrics(adata, **func_kwargs)
-            add_op_log(adata, sc.pp.calculate_qc_metrics, func_kwargs)
+            add_op_log(adata, sc.pp.calculate_qc_metrics, func_kwargs, adinfo)
         except KeyError as e:
             raise KeyError(f"Cound find {e} in adata.var")
         return [
-            generate_msg(request, adata, ads)
+            generate_msg(adinfo, adata, ads)
         ]
     except ToolError as e:
         raise ToolError(e)
@@ -139,26 +143,27 @@ async def calculate_qc_metrics(
 
 @pp_mcp.tool()
 async def log1p(
-    request: Log1PModel = Log1PModel() 
+    request: Log1PModel = Log1PModel(),
+    adinfo: AdataModel = AdataModel()
 ):
     """Logarithmize the data matrix"""
 
     try:
-        result = await forward_request("pp_log1p", request)
+        result = await forward_request("pp_log1p", request, adinfo)
         if result is not None:
             return result
         func_kwargs = filter_args(request, sc.pp.log1p)
         ads = get_ads()
-        adata = ads.get_adata(request=request).copy()
+        adata = ads.get_adata(adinfo=adinfo).copy()
         try:
             sc.pp.log1p(adata, **func_kwargs)
             adata.raw = adata.copy()
-            add_op_log(adata, sc.pp.log1p, func_kwargs)
+            add_op_log(adata, sc.pp.log1p, func_kwargs, adinfo)
         except Exception as e:
             raise e
-        ads.set_adata(adata, request=request)
+        ads.set_adata(adata, adinfo=adinfo)
         return [
-            generate_msg(request, adata, ads)
+                generate_msg(adinfo, adata, ads)
         ]
     except ToolError as e:
         raise ToolError(e)
@@ -171,22 +176,23 @@ async def log1p(
 
 @pp_mcp.tool()
 async def normalize_total(
-    request: NormalizeTotalModel = NormalizeTotalModel() 
+    request: NormalizeTotalModel = NormalizeTotalModel(),
+    adinfo: AdataModel = AdataModel()
 ):
     """Normalize counts per cell to the same total count"""
 
     try:
-        result = await forward_request("pp_normalize_total", request)
+        result = await forward_request("pp_normalize_total", request, adinfo)
         if result is not None:
             return result
         func_kwargs = filter_args(request, sc.pp.normalize_total)
         ads = get_ads()
-        adata = ads.get_adata(request=request).copy()
+        adata = ads.get_adata(adinfo=adinfo).copy()
         sc.pp.normalize_total(adata, **func_kwargs)
-        add_op_log(adata, sc.pp.normalize_total, func_kwargs)
-        ads.set_adata(adata, request=request)
+        add_op_log(adata, sc.pp.normalize_total, func_kwargs, adinfo)
+        ads.set_adata(adata, adinfo=adinfo)
         return [
-            generate_msg(request, adata, ads)
+            generate_msg(adinfo, adata, ads)
         ]
     except ToolError as e:
         raise ToolError(e)
@@ -200,25 +206,26 @@ async def normalize_total(
 
 @pp_mcp.tool()
 async def highly_variable_genes(
-    request: HighlyVariableGenesModel = HighlyVariableGenesModel() 
+    request: HighlyVariableGenesModel = HighlyVariableGenesModel(),
+    adinfo: AdataModel = AdataModel()
 ):
     """Annotate highly variable genes"""
 
     try:
-        result = await forward_request("pp_highly_variable_genes", request)
+        result = await forward_request("pp_highly_variable_genes", request, adinfo)
         if result is not None:
             return result
         try:  
             func_kwargs = filter_args(request, sc.pp.highly_variable_genes)
             ads = get_ads()
-            adata = ads.get_adata(request=request)
+            adata = ads.get_adata(adinfo=adinfo)
             sc.pp.highly_variable_genes(adata, **func_kwargs)
-            add_op_log(adata, sc.pp.highly_variable_genes, func_kwargs)
+            add_op_log(adata, sc.pp.highly_variable_genes, func_kwargs, adinfo)
         except Exception as e:
             logger.error(f"Error in pp_highly_variable_genes: {str(e)}")
             raise e
         return [
-            generate_msg(request, adata, ads)
+            generate_msg(adinfo, adata, ads)
         ]
     except ToolError as e:
         raise ToolError(e)
@@ -232,22 +239,22 @@ async def highly_variable_genes(
 @pp_mcp.tool()
 async def regress_out(
     request: RegressOutModel,
-    
+    adinfo: AdataModel = AdataModel()
 ):
     """Regress out (mostly) unwanted sources of variation."""
 
     try:
-        result = await forward_request("pp_regress_out", request)
+        result = await forward_request("pp_regress_out", request, adinfo)
         if result is not None:
             return result        
         func_kwargs = filter_args(request, sc.pp.regress_out)
         ads = get_ads()
-        adata = ads.get_adata(request=request).copy()
+        adata = ads.get_adata(adinfo=adinfo).copy()
         sc.pp.regress_out(adata, **func_kwargs)
-        add_op_log(adata, sc.pp.regress_out, func_kwargs)
-        ads.set_adata(adata, request=request)
+        add_op_log(adata, sc.pp.regress_out, func_kwargs, adinfo)
+        ads.set_adata(adata, adinfo=adinfo)
         return [
-            generate_msg(request, adata, ads)
+            generate_msg(adinfo, adata, ads)
         ]
     except ToolError as e:
         raise ToolError(e)
@@ -259,24 +266,25 @@ async def regress_out(
 
 @pp_mcp.tool()
 async def scale(
-    request: ScaleModel = ScaleModel() 
+    request: ScaleModel = ScaleModel(),
+    adinfo: AdataModel = AdataModel()
 ):
     """Scale data to unit variance and zero mean"""
 
     try:
-        result = await forward_request("pp_scale", request)
+        result = await forward_request("pp_scale", request, adinfo)
         if result is not None:
             return result     
         func_kwargs = filter_args(request, sc.pp.scale)
         ads = get_ads()
-        adata = ads.get_adata(request=request).copy()
+        adata = ads.get_adata(adinfo=adinfo).copy()
 
         sc.pp.scale(adata, **func_kwargs)
-        add_op_log(adata, sc.pp.scale, func_kwargs)
+        add_op_log(adata, sc.pp.scale, func_kwargs, adinfo)
  
-        ads.set_adata(adata, request=request)
+        ads.set_adata(adata, adinfo=adinfo)
         return [
-            generate_msg(request, adata, ads)
+            generate_msg(adinfo, adata, ads)
         ]
     except ToolError as e:
         raise ToolError(e)
@@ -288,24 +296,25 @@ async def scale(
 
 @pp_mcp.tool()
 async def combat(
-    request: CombatModel = CombatModel() 
+    request: CombatModel = CombatModel(),
+    adinfo: AdataModel = AdataModel()
 ):
     """ComBat function for batch effect correction"""
 
     try:
-        result = await forward_request("pp_combat", request)
+        result = await forward_request("pp_combat", request, adinfo)
         if result is not None:
             return result        
         func_kwargs = filter_args(request, sc.pp.combat)
         ads = get_ads()
-        adata = ads.get_adata(request=request).copy()
+        adata = ads.get_adata(adinfo=adinfo).copy()
 
         sc.pp.combat(adata, **func_kwargs)
-        add_op_log(adata, sc.pp.combat, func_kwargs)
+        add_op_log(adata, sc.pp.combat, func_kwargs, adinfo)
 
-        ads.set_adata(adata, request=request)
+        ads.set_adata(adata, adinfo=adinfo)
         return [
-            generate_msg(request, adata, ads)
+            generate_msg(adinfo, adata, ads)
         ]
     except ToolError as e:
         raise ToolError(e)
@@ -317,21 +326,22 @@ async def combat(
 
 @pp_mcp.tool()
 async def scrublet(
-    request: ScrubletModel = ScrubletModel() 
+    request: ScrubletModel = ScrubletModel(),
+    adinfo: AdataModel = AdataModel()
 ):
     """Predict doublets using Scrublet"""
 
     try:
-        result = await forward_request("pp_scrublet", request)
+        result = await forward_request("pp_scrublet", request, adinfo)
         if result is not None:
             return result          
         func_kwargs = filter_args(request, sc.pp.scrublet)
         ads = get_ads()
-        adata = ads.get_adata(request=request)
+        adata = ads.get_adata(adinfo=adinfo)
         sc.pp.scrublet(adata, **func_kwargs)
-        add_op_log(adata, sc.pp.scrublet, func_kwargs)
+        add_op_log(adata, sc.pp.scrublet, func_kwargs, adinfo)
         return [
-            generate_msg(request, adata, ads)
+            generate_msg(adinfo, adata, ads)
         ]
     except ToolError as e:
         raise ToolError(e)
@@ -343,21 +353,22 @@ async def scrublet(
 
 @pp_mcp.tool()
 async def neighbors(
-    request: NeighborsModel = NeighborsModel() 
+    request: NeighborsModel = NeighborsModel(),
+    adinfo: AdataModel = AdataModel()
 ):
     """Compute nearest neighbors distance matrix and neighborhood graph"""
 
     try:
-        result = await forward_request("pp_neighbors", request)
+        result = await forward_request("pp_neighbors", request, adinfo)
         if result is not None:
             return result
         func_kwargs = filter_args(request, sc.pp.neighbors)
         ads = get_ads()
-        adata = ads.get_adata(request=request)
+        adata = ads.get_adata(adinfo=adinfo)
         sc.pp.neighbors(adata, **func_kwargs)
-        add_op_log(adata, sc.pp.neighbors, func_kwargs)
+        add_op_log(adata, sc.pp.neighbors, func_kwargs, adinfo)
         return [
-            generate_msg(request, adata, ads)
+            generate_msg(adinfo, adata, ads)
         ]
     except ToolError as e:
         raise ToolError(e)