scmcp-shared 0.3.5__py3-none-any.whl → 0.3.7__py3-none-any.whl

scmcp_shared/server/util.py

@@ -4,8 +4,9 @@ from pathlib import Path
 import scanpy as sc
 from fastmcp import FastMCP , Context
 from fastmcp.exceptions import ToolError
+from fastmcp.tools.tool import Tool
 from ..schema.util import *
-from ..schema import AdataModel, AdataInfo
+from ..schema import AdataInfo
 from ..util import filter_args, forward_request, get_ads, generate_msg,add_op_log
 from .base import BaseMCP
 
@@ -24,7 +25,7 @@ class ScanpyUtilMCP(BaseMCP):
 
 
     def _tool_query_op_log(self):
-        def _query_op_log(request: QueryOpLogModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _query_op_log(request: QueryOpLogParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """Query the adata operation log"""
             adata = get_ads().get_adata(adinfo=adinfo)
             op_dic = adata.uns["operation"]["op"]
@@ -33,10 +34,10 @@ class ScanpyUtilMCP(BaseMCP):
             for opid in opids:
                 op_list.append(op_dic[opid])
             return op_list
-        return _query_op_log
+        return Tool.from_function(_query_op_log, name="query_op_log")
 
     def _tool_mark_var(self):
-        def _mark_var(request: MarkVarModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _mark_var(request: MarkVarParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """
             Determine if each gene meets specific conditions and store results in adata.var as boolean values.
             For example: mitochondrion genes startswith MT-.
@@ -84,10 +85,10 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _mark_var
+        return Tool.from_function(_mark_var, name="mark_var")
 
     def _tool_list_var(self):
-        def _list_var(request: ListVarModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _list_var(request: ListVarParams=ListVarParams(), adinfo: self.AdataInfo=self.AdataInfo()):
             """List key columns in adata.var. It should be called for checking when other tools need var key column names as input."""
             try:
                 result = forward_request("ul_list_var", request, adinfo)
@@ -95,7 +96,7 @@ class ScanpyUtilMCP(BaseMCP):
                     return result
                 adata = get_ads().get_adata(adinfo=adinfo)
                 columns = list(adata.var.columns)
-                add_op_log(adata, list_var, {}, adinfo)
+                add_op_log(adata, "list_var", {}, adinfo)
                 return columns
             except ToolError as e:
                 raise ToolError(e)
@@ -104,10 +105,10 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _list_var
+        return Tool.from_function(_list_var, name="list_var")
 
     def _tool_list_obs(self):
-        def _list_obs(request: ListObsModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _list_obs(request: ListObsParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """List key columns in adata.obs. It should be called before other tools need obs key column names input."""
             try:
                 result = forward_request("ul_list_obs", request, adinfo)
@@ -115,7 +116,7 @@ class ScanpyUtilMCP(BaseMCP):
                     return result    
                 adata = get_ads().get_adata(adinfo=adinfo)
                 columns = list(adata.obs.columns)
-                add_op_log(adata, list_obs, {}, adinfo)
+                add_op_log(adata, "list_obs", {}, adinfo)
                 return columns
             except ToolError as e:
                 raise ToolError(e)
@@ -124,10 +125,10 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _list_obs
+        return Tool.from_function(_list_obs, name="list_obs")
 
     def _tool_check_var(self):
-        def _check_var(request: VarNamesModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _check_var(request: VarNamesParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """Check if genes/variables exist in adata.var_names. This tool should be called before gene expression visualizations or color by genes."""
             try:
                 result = forward_request("ul_check_var", request, adinfo)
@@ -135,8 +136,12 @@ class ScanpyUtilMCP(BaseMCP):
                     return result     
                 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}, adinfo)
+                if adata.raw is not None:
+                    all_var_names = adata.raw.to_adata().var_names
+                else:
+                    all_var_names = adata.var_names
+                result = {v: v in all_var_names for v in var_names}
+                add_op_log(adata, "check_var", {"var_names": var_names}, adinfo)
                 return result
             except ToolError as e:
                 raise ToolError(e)
@@ -145,10 +150,10 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _check_var
+        return Tool.from_function(_check_var, name="check_var")
 
     def _tool_merge_adata(self):
-        def _merge_adata(request: ConcatBaseModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _merge_adata(request: ConcatBaseParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """Merge multiple adata objects."""
             try:
                 result = forward_request("ul_merge_adata", request, adinfo)
@@ -157,7 +162,7 @@ class ScanpyUtilMCP(BaseMCP):
                 ads = get_ads()
                 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)
+                merged_adata = adata.concat(ads.adata_dic, **kwargs)
                 ads.adata_dic[dtype] = {}
                 ads.active_id = "merged_adata"
                 add_op_log(merged_adata, ad.concat, kwargs, adinfo)
@@ -170,10 +175,10 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _merge_adata
+        return Tool.from_function(_merge_adata, name="merge_adata")
 
     def _tool_set_dpt_iroot(self):
-        def _set_dpt_iroot(request: DPTIROOTModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _set_dpt_iroot(request: DPTIROOTParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """Set the iroot cell"""
             try:
                 result = forward_request("ul_set_dpt_iroot", request, adinfo)
@@ -201,10 +206,10 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _set_dpt_iroot
+        return Tool.from_function(_set_dpt_iroot, name="set_dpt_iroot")
 
     def _tool_add_layer(self):
-        def _add_layer(request: AddLayerModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _add_layer(request: AddLayerParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """Add a layer to the AnnData object."""
             try:
                 result = forward_request("ul_add_layer", request, adinfo)
@@ -233,7 +238,7 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _add_layer
+        return Tool.from_function(_add_layer, name="add_layer")
 
     def _tool_check_samples(self):
         def _check_samples(request: None, adinfo: self.AdataInfo=self.AdataInfo()):
@@ -248,4 +253,4 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _check_samples
+        return Tool.from_function(_check_samples, name="check_samples")

scmcp_shared/util.py

@@ -104,6 +104,10 @@ def savefig(axes, func=None, **kwargs):
     args = []
     for k,v in kwargs.items():
         if isinstance(v, (tuple, list, set)):
+            v = v[:3]  ## show first 3 elements
+            args.append(f"{k}-{'-'.join([str(i) for i in v])}")
+        elif isinstance(v, dict):
+            v = list(v.keys())[:3]  ## show first 3 elements
             args.append(f"{k}-{'-'.join([str(i) for i in v])}")
         else:
             args.append(f"{k}-{v}")
@@ -209,7 +213,7 @@ def get_ads():
 
 
 def generate_msg(adinfo, adata, ads):
-    return {"sampleid": adinfo.sampleid or ads.active_id, "dtype": adinfo.adtype, "adata": adata}
+    return {"sampleid": adinfo.sampleid or ads.active_id, "adtype": adinfo.adtype, "adata": adata}
 
 
 def sc_like_plot(plot_func, adata, request, adinfo, **kwargs):
@@ -270,3 +274,9 @@ 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])
+
+
+def check_adata(adata, adinfo, ads):
+    sampleid = adinfo.sampleid or ads.active_id
+    if sampleid != adata.uns["scmcp_sampleid"]:
+        raise ValueError(f"sampleid mismatch: {sampleid} != {adata.uns['scmcp_sampleid']}")

{scmcp_shared-0.3.5.dist-info → scmcp_shared-0.3.7.dist-info}/METADATA

@@ -1,7 +1,10 @@
 Metadata-Version: 2.4
 Name: scmcp_shared
-Version: 0.3.5
+Version: 0.3.7
 Summary: A shared function libray for scmcphub
+Project-URL: Homepage, http://scmcphub.org/
+Project-URL: Repository, https://github.com/scmcphub/scmcp-shared
+Project-URL: Documentation, https://docs.scmcphub.org/
 Author-email: shuang <hsh-me@outlook.com>
 License: BSD 3-Clause License
         
@@ -32,8 +35,11 @@ License: BSD 3-Clause License
         OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
         OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 License-File: LICENSE
+Keywords: AI,agent,bioinformatics,llm,mcp,model context protocol,scRNA-seq,single cell
 Requires-Python: >=3.10
-Requires-Dist: fastmcp>=2.3.4
+Requires-Dist: fastmcp>=2.7.0
+Requires-Dist: igraph
+Requires-Dist: leidenalg
 Requires-Dist: mcp>=1.8.0
 Requires-Dist: nest-asyncio
 Requires-Dist: scanpy

scmcp_shared-0.3.7.dist-info/RECORD

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+scmcp_shared/cli.py,sha256=KYHp5_VE2JVVT4Su57ELzQa1lI2P8Gw0b4ruBP_Dtxk,4396
+scmcp_shared/logging_config.py,sha256=eCuLuyxMmbj8A1E0VqYWoKA5JPTSbo6cmjS4LOyd0RQ,872
+scmcp_shared/util.py,sha256=8_c6WPNpYNoxKpq6tQCC4elCQkWyk3rH-hTe1sqff4A,9535
+scmcp_shared/schema/__init__.py,sha256=Kwkc7kPLjExOlxt1sWEy_5qa96MvOS8sNCMlZa6yRg8,737
+scmcp_shared/schema/io.py,sha256=-wgL2NQBXwAcojid8rF2Y46GsKL7H6JiheKE6frMotw,4638
+scmcp_shared/schema/pl.py,sha256=7AFXgqb2GAlmeXS6m3IdJgThLz6-FTDBmrJqoAi8j98,29612
+scmcp_shared/schema/pp.py,sha256=WtaugFLP9vfusBZQCXGAYPmYu-5yWHC2wJTSZutS1XM,21674
+scmcp_shared/schema/tl.py,sha256=FEZpr218eaQ8rUp5EJzbjyw1ejqCX4Shsf9CumaKs8A,34425
+scmcp_shared/schema/util.py,sha256=fMZxTNf9Bv_xDzrW7YK08q0tCoC3L7ofqPY0K2ykG8k,4824
+scmcp_shared/server/__init__.py,sha256=4KE2Y_gDenF0ZyTGicQW0fTgJfMIQYZfpRP4hQ4rFYs,416
+scmcp_shared/server/base.py,sha256=o6NSi39I6xe7p-00-7FMR3gYwRCsM8D2WQhwWvlJcrU,6400
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+scmcp_shared/server/tl.py,sha256=LeKcR6F4PNRHZomlD3-igrF44YBQW6Kg7h75psGl9c0,19112
+scmcp_shared/server/util.py,sha256=b6gG1dfXe5GdhM4yUtpxBqx1gMRyQVu3dytmzJeD9zs,12590
+scmcp_shared-0.3.7.dist-info/METADATA,sha256=vK9jmNEbuZCt-DhGbLMyGhFd6_HXZpkxAy2a1XgvH58,2402
+scmcp_shared-0.3.7.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+scmcp_shared-0.3.7.dist-info/licenses/LICENSE,sha256=YNr1hpea195yq-wGtB8j-2dGtt7A5G00WENmxa7JGco,1495
+scmcp_shared-0.3.7.dist-info/RECORD,,

scmcp_shared-0.3.5.dist-info/RECORD

@@ -1,21 +0,0 @@
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-scmcp_shared/cli.py,sha256=KYHp5_VE2JVVT4Su57ELzQa1lI2P8Gw0b4ruBP_Dtxk,4396
-scmcp_shared/logging_config.py,sha256=eCuLuyxMmbj8A1E0VqYWoKA5JPTSbo6cmjS4LOyd0RQ,872
-scmcp_shared/util.py,sha256=bJmbgYjhY44flRo51XDiH-5w7OztG34XxGL6JSGG9fo,9101
-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=DaZUce33OW67h-caK9BW4sD9zhlehmj3mCq1P-3vllM,34407
-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=nneWj9SHNcZulhn3WRQrsoecHNsG2apDctB8H5OtQNI,18331
-scmcp_shared/server/util.py,sha256=L51fFL7Nb84JCQrFYyZIGsfmNFlA9uGzTV93hvc9mfI,12025
-scmcp_shared-0.3.5.dist-info/METADATA,sha256=SPZehu8YN559S-rEBcNViW5vf1h0TUjlzXhIAVxuQ3w,2103
-scmcp_shared-0.3.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-scmcp_shared-0.3.5.dist-info/licenses/LICENSE,sha256=YNr1hpea195yq-wGtB8j-2dGtt7A5G00WENmxa7JGco,1495
-scmcp_shared-0.3.5.dist-info/RECORD,,