Fix tool search to support substring matching in name and ID

mcp-server-galaxy-py/src/galaxy_mcp/server.py

@@ -342,10 +342,10 @@ def connect(url: str | None = None, api_key: str | None = None) -> dict[str, Any
 @mcp.tool()
 def search_tools_by_name(query: str) -> dict[str, Any]:
     """
-    Search Galaxy tools whose name contains the given query (substring match).
+    Search Galaxy tools whose name, ID, or description contains the given query (substring match).
 
     Args:
-        query: Search query (tool name to filter on)
+        query: Search query (tool name, ID, or description to filter on)
 
     Returns:
         List of tools matching the query
@@ -354,9 +354,21 @@ def search_tools_by_name(query: str) -> dict[str, Any]:
     gi: GalaxyInstance = state["gi"]
 
     try:
-        # The get_tools method is used with name filter parameter
-        tools = gi.tools.get_tools(name=query)
-        return {"tools": tools}
+        # Get all tools and filter client-side for substring matching
+        # The get_tools(name=query) parameter doesn't support substring matching
+        all_tools = gi.tools.get_tools()
+        query_lower = query.lower()
+
+        # Filter tools by substring match in name, ID, or description
+        matching_tools = [
+            tool
+            for tool in all_tools
+            if query_lower in tool.get("name", "").lower()
+            or query_lower in tool.get("id", "").lower()
+            or query_lower in tool.get("description", "").lower()
+        ]
+
+        return {"tools": matching_tools}
     except Exception as e:
         raise ValueError(format_error("Search tools", e, {"query": query})) from e
 

mcp-server-galaxy-py/tests/test_tool_operations.py

@@ -20,21 +20,29 @@ class TestToolOperations:
     def test_search_tools_fn(self, mock_galaxy_instance):
         """Test tool search functionality"""
         with patch.dict(galaxy_state, {"connected": True, "gi": mock_galaxy_instance}):
-            # Search should return dict with 'tools' key
+            # Mock get_tools to return all tools (no name parameter)
+            mock_galaxy_instance.tools.get_tools.return_value = [
+                {"id": "tool1", "name": "Test Tool 1", "description": "Aligns sequences"},
+                {"id": "tool2", "name": "Test Tool 2", "description": "Other tool"},
+            ]
+
+            # Search with empty query should return all tools
             result = search_tools_fn("")
             assert "tools" in result
             assert len(result["tools"]) == 2
             assert result["tools"][0]["id"] == "tool1"
 
-            # Search with query
-            mock_galaxy_instance.tools.get_tools.return_value = [
-                {"id": "tool1", "name": "Test Tool 1", "description": "Aligns sequences"}
-            ]
+            # Search with query should filter by name substring
+            result = search_tools_fn("tool 1")
+            assert "tools" in result
+            assert len(result["tools"]) == 1
+            assert result["tools"][0]["id"] == "tool1"
 
-            result = search_tools_fn("align")
+            # Search should also filter by ID substring
+            result = search_tools_fn("tool2")
             assert "tools" in result
             assert len(result["tools"]) == 1
-            assert "align" in result["tools"][0]["description"].lower()
+            assert result["tools"][0]["id"] == "tool2"
 
     def test_search_tools_with_results(self, mock_galaxy_instance):
         """Test search tools returns filtered results"""
@@ -45,26 +53,23 @@ def test_search_tools_with_results(self, mock_galaxy_instance):
         ]
 
         with patch.dict(galaxy_state, {"connected": True, "gi": mock_galaxy_instance}):
-            # Mock filtering behavior
-            def mock_get_tools(name=None):
-                if name and name.lower() == "align":
-                    return [
-                        t
-                        for t in all_tools
-                        if "align" in t["name"].lower() or "align" in t["description"].lower()
-                    ]
-                return all_tools
-
-            mock_galaxy_instance.tools.get_tools.side_effect = mock_get_tools
-
-            # Search for aligners
+            # Mock get_tools to return all tools
+            mock_galaxy_instance.tools.get_tools.return_value = all_tools
+
+            # Search for aligners by name substring
             result = search_tools_fn("align")
             assert "tools" in result
             aligners = result["tools"]
             assert len(aligners) == 2
             assert any("BWA" in t["name"] for t in aligners)
             assert any("HISAT2" in t["name"] for t in aligners)
 
+            # Search by ID substring
+            result = search_tools_fn("tool1")
+            assert "tools" in result
+            assert len(result["tools"]) == 1
+            assert result["tools"][0]["id"] == "tool1"
+
     def test_run_tool_fn(self, mock_galaxy_instance):
         """Test running a tool"""
         mock_galaxy_instance.tools.run_tool.return_value = {