scmcp-shared 0.2.5__py3-none-any.whl → 0.3.5__py3-none-any.whl

scmcp_shared/server/tl.py

@@ -1,447 +1,398 @@
 from fastmcp import FastMCP, Context
 import os
+import inspect
+from fastmcp import FastMCP
 import scanpy as sc
 from fastmcp.exceptions import ToolError
 from ..schema.tl import *
-from ..schema import AdataModel
+from ..schema import AdataInfo
 from scmcp_shared.util import filter_args, add_op_log, forward_request, get_ads, generate_msg
-from scmcp_shared.logging_config import setup_logger
-logger = setup_logger()
-
-tl_mcp = FastMCP("ScanpyMCP-TL-Server")
-
-
-@tl_mcp.tool()
-async def tsne(
-    request: TSNEModel = TSNEModel(),
-    adinfo: AdataModel = AdataModel()
-):
-    """t-distributed stochastic neighborhood embedding (t-SNE) for visualization"""
-
-    try:
-        result = await forward_request("tl_tsne", request, adinfo)
-        if result is not None:
-            return result
-        func_kwargs = filter_args(request, sc.tl.tsne)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.tl.tsne(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.tsne, func_kwargs, adinfo)
-        return generate_msg(adinfo, adata, ads)
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-
-@tl_mcp.tool()
-async def umap(
-    request: UMAPModel = UMAPModel(),
-    adinfo: AdataModel = AdataModel()
-):
-    """Uniform Manifold Approximation and Projection (UMAP) for visualization"""
-
-    try:
-        result = await forward_request("tl_umap", request, adinfo)
-        if result is not None:
-            return result
-        func_kwargs = filter_args(request, sc.tl.umap)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.tl.umap(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.umap, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-@tl_mcp.tool()
-async def draw_graph(
-    request: DrawGraphModel = DrawGraphModel(),
-    adinfo: AdataModel = AdataModel()
-):
-    """Force-directed graph drawing"""
-
-    try:
-        result = await forward_request("tl_draw_graph", request, adinfo)
-        if result is not None:
-            return result    
-        func_kwargs = filter_args(request, sc.tl.draw_graph)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.tl.draw_graph(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.draw_graph, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-@tl_mcp.tool()
-async def diffmap(
-    request: DiffMapModel = DiffMapModel(),
-    adinfo: AdataModel = AdataModel()
-):
-    """Diffusion Maps for dimensionality reduction"""
-
-    try:
-        result = await forward_request("tl_diffmap", request, adinfo)
-        if result is not None:
-            return result    
-        func_kwargs = filter_args(request, sc.tl.diffmap)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.tl.diffmap(adata, **func_kwargs)
-        adata.obsm["X_diffmap"] = adata.obsm["X_diffmap"][:,1:]
-        add_op_log(adata, sc.tl.diffmap, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-@tl_mcp.tool()
-async def embedding_density(
-    request: EmbeddingDensityModel = EmbeddingDensityModel(),
-    adinfo: AdataModel = AdataModel()
-):
-    """Calculate the density of cells in an embedding"""
-
-    try:
-        result = await forward_request("tl_embedding_density", request, adinfo)
-        if result is not None:
-            return result        
-        func_kwargs = filter_args(request, sc.tl.embedding_density)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.tl.embedding_density(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.embedding_density, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-
-@tl_mcp.tool()
-async def leiden(
-    request: LeidenModel = LeidenModel(),
-    adinfo: AdataModel = AdataModel()
-):
-    """Leiden clustering algorithm for community detection"""
-
-    try:
-        result = await forward_request("tl_leiden", request, adinfo)
-        if result is not None:
-            return result            
-        func_kwargs = filter_args(request, sc.tl.leiden)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.tl.leiden(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.leiden, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-
-@tl_mcp.tool()
-async def louvain(
-    request: LouvainModel = LouvainModel(),
-    adinfo: AdataModel = AdataModel()
-):
-    """Louvain clustering algorithm for community detection"""
-
-    try:
-        result = await forward_request("tl_louvain", request, adinfo)
-        if result is not None:
-            return result          
-        func_kwargs = filter_args(request, sc.tl.louvain)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.tl.louvain(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.louvain, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-@tl_mcp.tool()
-async def dendrogram(
-    request: DendrogramModel,
-    adinfo: AdataModel = AdataModel()
-):
-    """Hierarchical clustering dendrogram"""
-
-    try:
-        result = await forward_request("tl_dendrogram", request, adinfo)
-        if result is not None:
-            return result        
-        func_kwargs = filter_args(request, sc.tl.dendrogram)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.tl.dendrogram(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.dendrogram, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-@tl_mcp.tool()
-async def dpt(
-    request: DPTModel = DPTModel(),
-    adinfo: AdataModel = AdataModel()
-):
-    """Diffusion Pseudotime (DPT) analysis"""
-
-    try:
-        result = await forward_request("tl_dpt", request, adinfo)
-        if result is not None:
-            return result          
-        func_kwargs = filter_args(request, sc.tl.dpt)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.tl.dpt(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.dpt, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-
-@tl_mcp.tool()
-async def paga(
-    request: PAGAModel = PAGAModel(),
-    adinfo: AdataModel = AdataModel()
-):
-    """Partition-based graph abstraction"""
-
-    try:
-        result = await forward_request("tl_paga", request, adinfo)
-        if result is not None:
-            return result         
-        func_kwargs = filter_args(request, sc.tl.paga)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)    
-        sc.tl.paga(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.paga, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-
-@tl_mcp.tool()
-async def ingest(
-    request: IngestModel = IngestModel(),
-    adinfo: AdataModel = AdataModel()
-):
-    """Map labels and embeddings from reference data to new data"""
-
-    try:
-        result = await forward_request("tl_ingest", request, adinfo)
-        if result is not None:
-            return result       
-        func_kwargs = filter_args(request, sc.tl.ingest)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)    
-        sc.tl.ingest(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.ingest, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-@tl_mcp.tool()
-async def rank_genes_groups(
-    request: RankGenesGroupsModel,
-    adinfo: AdataModel = AdataModel()
-):
-    """Rank genes for characterizing groups, for differentially expressison analysis"""
-
-    try:
-        result = await forward_request("tl_rank_genes_groups", request, adinfo)
-        if result is not None:
-            return result         
-        func_kwargs = filter_args(request, sc.tl.rank_genes_groups)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.tl.rank_genes_groups(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.rank_genes_groups, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-
-@tl_mcp.tool()
-async def filter_rank_genes_groups(
-    request: FilterRankGenesGroupsModel = FilterRankGenesGroupsModel(),
-    adinfo: AdataModel = AdataModel()
-):
-    """Filter out genes based on fold change and fraction of genes"""
-
-    try:
-        result = await forward_request("tl_filter_rank_genes_groups", request, adinfo)
-        if result is not None:
-            return result          
-        func_kwargs = filter_args(request, sc.tl.filter_rank_genes_groups)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.tl.filter_rank_genes_groups(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.filter_rank_genes_groups, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-
-@tl_mcp.tool()
-async def marker_gene_overlap(
-    request: MarkerGeneOverlapModel = MarkerGeneOverlapModel(),
-    adinfo: AdataModel = AdataModel()
-):
-    """Calculate overlap between data-derived marker genes and reference markers"""
-
-    try:
-        result = await forward_request("tl_marker_gene_overlap", request, adinfo)
-        if result is not None:
-            return result         
-        func_kwargs = filter_args(request, sc.tl.marker_gene_overlap)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.tl.marker_gene_overlap(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.marker_gene_overlap, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-@tl_mcp.tool()
-async def score_genes(
-    request: ScoreGenesModel,
-    adinfo: AdataModel = AdataModel()
-):
-    """Score a set of genes based on their average expression"""
-    try:
-        result = await forward_request("tl_score_genes", request, adinfo)
-        if result is not None:
-            return result       
-        func_kwargs = filter_args(request, sc.tl.score_genes)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.tl.score_genes(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.score_genes, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-@tl_mcp.tool()
-async def score_genes_cell_cycle(
-    request: ScoreGenesCellCycleModel,
-    adinfo: AdataModel = AdataModel()
-):
-    """Score cell cycle genes and assign cell cycle phases"""
-
-    try:
-        result = await forward_request("tl_score_genes_cell_cycle", request, adinfo)
-        if result is not None:
-            return result       
-        func_kwargs = filter_args(request, sc.tl.score_genes_cell_cycle)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.tl.score_genes_cell_cycle(adata, **func_kwargs)
-        add_op_log(adata, sc.tl.score_genes_cell_cycle, func_kwargs, adinfo)
-        return [generate_msg(adinfo, adata, ads)]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
-
-
-@tl_mcp.tool()
-async def pca(
-    request: PCAModel = PCAModel(),
-    adinfo: AdataModel = AdataModel()
-):
-    """Principal component analysis"""
-
-    try:
-        result = await forward_request("tl_pca", request, adinfo)
-        if result is not None:
-            return result
-        func_kwargs = filter_args(request, sc.pp.pca)
-        ads = get_ads()
-        adata = ads.get_adata(adinfo=adinfo)
-        sc.pp.pca(adata, **func_kwargs)
-        add_op_log(adata, sc.pp.pca, func_kwargs, adinfo)
-        return [
-            generate_msg(adinfo, adata, ads)
-        ]
-    except ToolError as e:
-        raise ToolError(e)
-    except Exception as e:
-        if hasattr(e, '__context__') and e.__context__:
-            raise ToolError(e.__context__)
-        else:
-            raise ToolError(e)
+from .base import BaseMCP
+
+
+class ScanpyToolsMCP(BaseMCP):
+    def __init__(self, include_tools: list = None, exclude_tools: list = None, AdataInfo: AdataInfo = AdataInfo):
+        """
+        Initialize ScanpyMCP with optional tool filtering.
+        
+        Args:
+            include_tools (list, optional): List of tool names to include. If None, all tools are included.
+            exclude_tools (list, optional): List of tool names to exclude. If None, no tools are excluded.
+            AdataInfo: The AdataInfo class to use for type annotations.
+        """
+        super().__init__("ScanpyMCP-TL-Server", include_tools, exclude_tools, AdataInfo)
+
+    def _tool_tsne(self):
+        def _tsne(request: TSNEModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """t-distributed stochastic neighborhood embedding (t-SNE) for visualization"""
+            try:
+                result = forward_request("tl_tsne", request, adinfo)
+                if result is not None:
+                    return result
+                func_kwargs = filter_args(request, sc.tl.tsne)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.tsne(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.tsne, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _tsne
+
+    def _tool_umap(self):
+        def _umap(request: UMAPModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Uniform Manifold Approximation and Projection (UMAP) for visualization"""
+            try:
+                result = forward_request("tl_umap", request, adinfo)
+                if result is not None:
+                    return result
+                func_kwargs = filter_args(request, sc.tl.umap)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.umap(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.umap, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _umap
+
+    def _tool_draw_graph(self):
+        def _draw_graph(request: DrawGraphModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Force-directed graph drawing"""
+            try:
+                result = forward_request("tl_draw_graph", request, adinfo)
+                if result is not None:
+                    return result    
+                func_kwargs = filter_args(request, sc.tl.draw_graph)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.draw_graph(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.draw_graph, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _draw_graph
+
+    def _tool_diffmap(self):
+        def _diffmap(request: DiffMapModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Diffusion Maps for dimensionality reduction"""
+            try:
+                result = forward_request("tl_diffmap", request, adinfo)
+                if result is not None:
+                    return result    
+                func_kwargs = filter_args(request, sc.tl.diffmap)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.diffmap(adata, **func_kwargs)
+                adata.obsm["X_diffmap"] = adata.obsm["X_diffmap"][:,1:]
+                add_op_log(adata, sc.tl.diffmap, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _diffmap
+
+    def _tool_embedding_density(self):  
+        def _embedding_density(request: EmbeddingDensityModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Calculate the density of cells in an embedding"""
+            try:
+                result = forward_request("tl_embedding_density", request, adinfo)
+                if result is not None:
+                    return result        
+                func_kwargs = filter_args(request, sc.tl.embedding_density)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.embedding_density(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.embedding_density, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _embedding_density
+
+    def _tool_leiden(self):
+        def _leiden(request: LeidenModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Leiden clustering algorithm for community detection"""
+            try:
+                result = forward_request("tl_leiden", request, adinfo)
+                if result is not None:
+                    return result            
+                func_kwargs = filter_args(request, sc.tl.leiden)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.leiden(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.leiden, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _leiden
+
+    def _tool_louvain(self):
+        def _louvain(request: LouvainModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Louvain clustering algorithm for community detection"""
+            try:
+                result = forward_request("tl_louvain", request, adinfo)
+                if result is not None:
+                    return result          
+                func_kwargs = filter_args(request, sc.tl.louvain)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.louvain(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.louvain, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _louvain
+
+    def _tool_dendrogram(self):
+        def _dendrogram(request: DendrogramModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Hierarchical clustering dendrogram"""
+            try:
+                result = forward_request("tl_dendrogram", request, adinfo)
+                if result is not None:
+                    return result        
+                func_kwargs = filter_args(request, sc.tl.dendrogram)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.dendrogram(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.dendrogram, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _dendrogram
+
+    def _tool_dpt(self):
+        def _dpt(request: DPTModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Diffusion Pseudotime (DPT) analysis"""
+            try:
+                result = forward_request("tl_dpt", request, adinfo)
+                if result is not None:
+                    return result          
+                func_kwargs = filter_args(request, sc.tl.dpt)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.dpt(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.dpt, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _dpt
+
+    def _tool_paga(self):
+        def _paga(request: PAGAModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Partition-based graph abstraction"""
+            try:
+                result = forward_request("tl_paga", request, adinfo)
+                if result is not None:
+                    return result         
+                func_kwargs = filter_args(request, sc.tl.paga)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)    
+                sc.tl.paga(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.paga, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _paga
+
+    def _tool_ingest(self):
+        def _ingest(request: IngestModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Map labels and embeddings from reference data to new data"""
+            try:
+                result = forward_request("tl_ingest", request, adinfo)
+                if result is not None:
+                    return result       
+                func_kwargs = filter_args(request, sc.tl.ingest)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)    
+                sc.tl.ingest(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.ingest, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _ingest
+
+    def _tool_rank_genes_groups(self):
+        def _rank_genes_groups(request: RankGenesGroupsModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Rank genes for characterizing groups, for differentially expressison analysis"""
+            try:
+                result = forward_request("tl_rank_genes_groups", request, adinfo)
+                if result is not None:
+                    return result         
+                func_kwargs = filter_args(request, sc.tl.rank_genes_groups)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.rank_genes_groups(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.rank_genes_groups, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _rank_genes_groups
+
+    def _tool_filter_rank_genes_groups(self):
+        def _filter_rank_genes_groups(request: FilterRankGenesGroupsModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Filter out genes based on fold change and fraction of genes"""
+            try:
+                result = forward_request("tl_filter_rank_genes_groups", request, adinfo)
+                if result is not None:
+                    return result          
+                func_kwargs = filter_args(request, sc.tl.filter_rank_genes_groups)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.filter_rank_genes_groups(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.filter_rank_genes_groups, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _filter_rank_genes_groups
+
+    def _tool_marker_gene_overlap(self):
+        def _marker_gene_overlap(request: MarkerGeneOverlapModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Calculate overlap between data-derived marker genes and reference markers"""
+            try:
+                result = forward_request("tl_marker_gene_overlap", request, adinfo)
+                if result is not None:
+                    return result         
+                func_kwargs = filter_args(request, sc.tl.marker_gene_overlap)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.marker_gene_overlap(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.marker_gene_overlap, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _marker_gene_overlap
+
+    def _tool_score_genes(self):
+        def _score_genes(request: ScoreGenesModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Score a set of genes based on their average expression"""
+            try:
+                result = forward_request("tl_score_genes", request, adinfo)
+                if result is not None:
+                    return result       
+                func_kwargs = filter_args(request, sc.tl.score_genes)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.score_genes(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.score_genes, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _score_genes
+
+    def _tool_score_genes_cell_cycle(self):
+        def _score_genes_cell_cycle(request: ScoreGenesCellCycleModel, adinfo: self.AdataInfo=self.AdataInfo()):
+            """Score cell cycle genes and assign cell cycle phases"""
+            try:
+                result = forward_request("tl_score_genes_cell_cycle", request, adinfo)
+                if result is not None:
+                    return result       
+                func_kwargs = filter_args(request, sc.tl.score_genes_cell_cycle)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.score_genes_cell_cycle(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.score_genes_cell_cycle, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _score_genes_cell_cycle
+
+    def _tool_pca(self):
+        def _pca(request: PCAModel=PCAModel(), adinfo: self.AdataInfo=self.AdataInfo()):
+            """Compute PCA (Principal Component Analysis)."""
+            try:
+                result = forward_request("tl_pca", request, adinfo)
+                if result is not None:
+                    return result
+                func_kwargs = filter_args(request, sc.tl.pca)
+                ads = get_ads()
+                adata = ads.get_adata(adinfo=adinfo)
+                sc.tl.pca(adata, **func_kwargs)
+                add_op_log(adata, sc.tl.pca, func_kwargs, adinfo)
+                return [generate_msg(adinfo, adata, ads)]
+            except ToolError as e:
+                raise ToolError(e)
+            except Exception as e:
+                if hasattr(e, '__context__') and e.__context__:
+                    raise ToolError(e.__context__)
+                else:
+                    raise ToolError(e)
+        return _pca