tooluniverse 1.0.6__py3-none-any.whl → 1.0.7__py3-none-any.whl

tooluniverse/test/test_idmap_tools.py

@@ -1,61 +0,0 @@
-"""
-Concise Test Script - OpenTargets ID Mapping Tools
-Test three main ID mapping tools:
-1. Get disease IDs by name
-2. Get cross-reference IDs by EFO ID
-3. Bidirectional mapping between external IDs and diseases
-"""
-
-from tooluniverse import ToolUniverse
-
-
-def main():
-    # Initialize tools
-    print("🔧 Initializing ToolUniverse...")
-    tooluni = ToolUniverse()
-    tooluni.load_tools()
-    print("✅ Tools loaded successfully\n")
-
-    # Test cases
-    test_cases = [
-        {
-            "name": "OpenTargets_get_disease_ids_by_name",
-            "arguments": {"name": "neuroblastoma"},
-            "description": "Get disease IDs by name",
-        },
-        {
-            "name": "OpenTargets_get_disease_ids_by_efoId",
-            "arguments": {"efoId": "EFO_0000621"},
-            "description": "Get cross-references by EFO ID",
-        },
-        {
-            "name": "OpenTargets_map_any_disease_id_to_all_other_ids",
-            "arguments": {"inputId": "EFO_0000621"},
-            "description": "Map disease ID to all other IDs",
-        },
-    ]
-
-    # Run tests
-    print("🧪 Starting ID Mapping tools tests:\n")
-
-    for i, test in enumerate(test_cases, 1):
-        print(f"[{i}] {test['description']}")
-        print(f"    Tool: {test['name']}")
-        print(f"    Arguments: {test['arguments']}")
-
-        try:
-            result = tooluni.run(test)
-            if result:
-                print("    ✅ Success")
-                print(f"    📊 Result: {str(result)}")
-            else:
-                print("    ⚠️  No data returned")
-        except Exception as e:
-            print(f"    ❌ Failed: {str(e)}")
-        print()
-
-    print("🎉 Testing completed!")
-
-
-if __name__ == "__main__":
-    main()

tooluniverse/test/test_list_built_in_tools.py

@@ -1,33 +0,0 @@
-#!/usr/bin/env python3
-"""
-Basic test for list_built_in_tools including scan_all option.
-Run directly: python tests/test_list_built_in_tools.py
-"""
-
-from tooluniverse import ToolUniverse  # noqa: E402
-
-
-def main():
-    tu = ToolUniverse()
-
-    # Use predefined files (original behavior)
-    tool_names = tu.list_built_in_tools(mode="list_name", scan_all=False)
-    print(f"predefined tool names: {len(tool_names)}")
-
-    # Scan all JSON files
-    all_tool_names = tu.list_built_in_tools(mode="list_name", scan_all=True)
-    print(f"all tool names (scan_all): {len(all_tool_names)}")
-
-    # Get all tool specifications
-    all_tool_specs = tu.list_built_in_tools(mode="list_spec", scan_all=True)
-    print(f"all tool specs (scan_all): {len(all_tool_specs)}")
-
-    # Organize all tools by type
-    type_stats = tu.list_built_in_tools(mode="type", scan_all=True)
-    print(
-        f"type stats -> total_categories: {type_stats['total_categories']}, total_tools: {type_stats['total_tools']}"
-    )
-
-
-if __name__ == "__main__":
-    main()

tooluniverse/test/test_mcp_server.py

@@ -1,211 +0,0 @@
-#!/usr/bin/env python3
-"""
-Test script: Verify that the generated FastMCP server is working properly
-
-This script will start the MCP server and send some test requests
-"""
-
-import asyncio
-import aiohttp
-import sys
-import subprocess
-from pathlib import Path
-
-# Test MCP server URL
-MCP_SERVER_URL = "http://127.0.0.1:8000"
-
-
-async def test_mcp_server():
-    """Test basic functionality of MCP server"""
-
-    print("🚀 Starting FastMCP server test...")
-
-    # Wait for server to start
-    print("⏳ Waiting for server to start...")
-    await asyncio.sleep(3)
-
-    async with aiohttp.ClientSession() as session:
-        # Test 1: Get tool list
-        print("\n📋 Test 1: Get available tool list")
-        tools_request = {
-            "jsonrpc": "2.0",
-            "id": "test-1",
-            "method": "tools/list",
-            "params": {},
-        }
-
-        try:
-            async with session.post(
-                f"{MCP_SERVER_URL}/mcp/",
-                json=tools_request,
-                headers={"Content-Type": "application/json"},
-            ) as response:
-                if response.status == 200:
-                    result = await response.json()
-                    tools = result.get("result", {}).get("tools", [])
-                    print(
-                        f"✅ Successfully retrieved tool list, {len(tools)} tools in total"
-                    )
-
-                    # Show first few tools
-                    for _i, tool in enumerate(tools[:3]):
-                        print(
-                            f"   - {tool.get('name', 'unknown')}: {tool.get('description', 'no description')[:80]}..."
-                        )
-
-                    if len(tools) > 3:
-                        print(f"   ... and {len(tools) - 3} more tools")
-
-                else:
-                    print(f"❌ Failed to get tool list, status code: {response.status}")
-                    print(f"Response: {await response.text()}")
-                    return False
-
-        except Exception as e:
-            print(f"❌ Failed to connect to server: {e}")
-            return False
-
-        # Test 2: Call a simple tool
-        print("\n🔧 Test 2: Call a tool function")
-        tool_request = {
-            "jsonrpc": "2.0",
-            "id": "test-2",
-            "method": "tools/call",
-            "params": {
-                "name": "get_phenotype_by_HPO_ID",
-                "arguments": {"id": "HP:0000001"},  # Test HPO ID
-            },
-        }
-
-        try:
-            async with session.post(
-                f"{MCP_SERVER_URL}/mcp/",
-                json=tool_request,
-                headers={"Content-Type": "application/json"},
-            ) as response:
-                if response.status == 200:
-                    result = await response.json()
-                    if "error" in result:
-                        print(f"⚠️  Tool execution returned error: {result['error']}")
-                    else:
-                        print("✅ Tool call successful")
-                        print(
-                            f"   Return result type: {type(result.get('result', {}))}"
-                        )
-                else:
-                    print(f"❌ Tool call failed, status code: {response.status}")
-                    print(f"Response: {await response.text()}")
-
-        except Exception as e:
-            print(f"❌ Tool call exception: {e}")
-
-        # Test 3: Call FDA tool
-        print("\n💊 Test 3: Call FDA drug query tool")
-        fda_request = {
-            "jsonrpc": "2.0",
-            "id": "test-3",
-            "method": "tools/call",
-            "params": {
-                "name": "FDA_get_active_ingredient_info_by_drug_name",
-                "arguments": {"drug_name": "aspirin", "limit": 5, "skip": 0},
-            },
-        }
-
-        try:
-            async with session.post(
-                f"{MCP_SERVER_URL}/mcp/",
-                json=fda_request,
-                headers={"Content-Type": "application/json"},
-            ) as response:
-                if response.status == 200:
-                    result = await response.json()
-                    if "error" in result:
-                        print(
-                            f"⚠️  FDA tool execution returned error: {result['error']}"
-                        )
-                    else:
-                        print("✅ FDA tool call successful")
-                        print(
-                            f"   Return result type: {type(result.get('result', {}))}"
-                        )
-                else:
-                    print(f"❌ FDA tool call failed, status code: {response.status}")
-
-        except Exception as e:
-            print(f"❌ FDA tool call exception: {e}")
-
-    print("\n🎉 Test completed!")
-    return True
-
-
-def start_mcp_server():
-    """Start MCP server"""
-    print("🚀 Starting MCP server...")
-
-    # Modify the generated file, add correct startup code
-    server_file = Path(__file__).parent / "mcp_server_test.py"
-
-    server_code = """#!/usr/bin/env python3
-# Import generated MCP wrapper
-import sys
-import os
-sys.path.append(os.path.dirname(__file__))
-
-# Read generated code and execute
-with open("mcp_wrappers_generated.txt", "r") as f:
-    generated_code = f.read()
-
-# Execute generated code
-exec(generated_code)
-
-# Start server
-if __name__ == "__main__":
-    print("🚀 Starting ToolUniverse MCP server...")
-    print(f"Server address: http://127.0.0.1:8000")
-    print("Press Ctrl+C to stop server")
-    run_server()
-"""
-
-    with open(server_file, "w") as f:
-        f.write(server_code)
-
-    # Start server process
-    return subprocess.Popen(
-        [sys.executable, str(server_file)],
-        stdout=subprocess.PIPE,
-        stderr=subprocess.PIPE,
-    )
-
-
-async def main():
-    """Main function"""
-    print("🧪 FastMCP Server Test Tool")
-    print("=" * 50)
-
-    # Start server
-    server_process = start_mcp_server()
-
-    try:
-        # Run tests
-        success = await test_mcp_server()
-
-        if success:
-            print("\n✅ All tests passed! MCP server is working properly.")
-        else:
-            print("\n❌ Some tests failed, please check server configuration.")
-
-    except KeyboardInterrupt:
-        print("\n⏹️  Test interrupted by user")
-    finally:
-        # Cleanup: terminate server process
-        print("\n🧹 Cleanup: closing server...")
-        server_process.terminate()
-        try:
-            server_process.wait(timeout=5)
-        except subprocess.TimeoutExpired:
-            server_process.kill()
-        print("✅ Server closed")
-
-
-if __name__ == "__main__":
-    asyncio.run(main())

tooluniverse/test/test_mcp_tool.py

@@ -1,247 +0,0 @@
-#!/usr/bin/env python3
-"""
-Test file for MCP Tools in ToolUniverse
-
-This file tests the MCP (Model Context Protocol) integration functionality,
-including MCPClientTool and MCPAutoLoaderTool.
-
-Usage:
-    python test_mcp_tool.py
-"""
-
-from tooluniverse import ToolUniverse
-from typing import Any, Dict, List
-import time
-import json
-
-# Step 1: Initialize tool universe
-print("🔧 Initializing ToolUniverse...")
-tooluni = ToolUniverse()
-tooluni.load_tools()
-
-print("✅ ToolUniverse initialized successfully")
-print(f"📊 Total tools loaded: {len(tooluni.all_tool_dict)}")
-
-# Step 2: Check if MCP tools are available
-mcp_tools = [
-    name for name in list(tooluni.all_tool_dict.keys()) if "mcp" in name.lower()
-]
-print(f"🔍 Found {len(mcp_tools)} MCP-related tools: {mcp_tools}")
-
-# Step 3: Define test queries for MCP tools
-test_queries: List[Dict[str, Any]] = [
-    # Test mock MCP tools (these should work without requiring external servers)
-    # {
-    #     "name": "mcp_mock_calculator",
-    #     "arguments": {
-    #         "operation": "add",
-    #         "a": 10,
-    #         "b": 5
-    #     }
-    # },
-    # {
-    #     "name": "mcp_mock_greeter",
-    #     "arguments": {
-    #         "name": "ToolUniverse User"
-    #     }
-    # },
-    # Test auto-discovered MCP tools from server 1
-    # {
-    #     "name": "mcp_s1_calculate",
-    #     "arguments": {
-    #         "expression": "2 + 3 * 4"
-    #     }
-    # },
-    # {
-    #     "name": "mcp_s1_get_weather",
-    #     "arguments": {
-    #         "city": "New York",
-    #         "units": "celsius"
-    #     }
-    # },
-    # Test MCP client tool (if available)
-    # {
-    #     "name": "mcp_client_example",
-    #     "arguments": {
-    #         "operation": "list_tools"
-    #     }
-    # },
-    # Test MCPAutoLoaderTool - Discover tools (will show connection errors if servers not running)
-    # {
-    #     "name": "mcp_auto_loader_server1",
-    #     "arguments": {
-    #         "operation": "discover"
-    #     }
-    # },
-    # {
-    #     "name": "mcp_mock_greeter",
-    #     "arguments": {
-    #         "name": "ToolUniverse User"
-    #     }
-    # },
-    # # Test MCP client tool (if available)
-    # {
-    #     "name": "mcp_client_example",
-    #     "arguments": {
-    #         "operation": "list_tools"
-    #     }
-    # },
-    # # Test MCPAutoLoaderTool - Discover tools (will show connection errors if servers not running)
-    # {
-    #     "name": "mcp_auto_loader_server1",
-    #     "arguments": {
-    #         "operation": "discover"
-    #     }
-    # },
-    # Test MCP client with simple operations
-    # {
-    #     "name": "mcp_client_example",
-    #     "arguments": {
-    #         "operation": "call_tool",
-    #         "tool_name": "get_weather",
-    #         "tool_arguments": {
-    #             "city": "New York",
-    #             "units": "celsius"
-    #         }
-    #     }
-    # },
-    # # Test calculator operation
-    # {
-    #     "name": "mcp_client_example",
-    #     "arguments": {
-    #         "operation": "call_tool",
-    #         "tool_name": "calculate",
-    #         "tool_arguments": {
-    #             "expression": "10 * 5 + 2"
-    #         }
-    #     }
-    # },
-    # # Test Official SDK server (if running)
-    # {
-    #     "name": "mcp_auto_loader_official_sdk",
-    #     "arguments": {
-    #         "operation": "discover"
-    #     }
-    # },
-    # # Test file listing operation
-    # {
-    #     "name": "mcp_client_example",
-    #     "arguments": {
-    #         "operation": "call_tool",
-    #         "tool_name": "list_files",
-    #         "tool_arguments": {
-    #             "directory": ".",
-    #             "pattern": "*.py"
-    #         }
-    #     }
-    # }
-    # Test US Patent and Trademark Office (USPTO) tools (if uspto_downloader_MCP.py is running)
-    {
-        "name": "mcp_download_abst",
-        "arguments": {"query": {"applicationNumberText": "19053071"}},
-    },
-    {
-        "name": "mcp_download_claims",
-        "arguments": {"query": {"applicationNumberText": "19053071"}},
-    },
-    # {
-    #     "name": "mcp_download_full_text",
-    #     "arguments": {
-    #         "query": {"applicationNumberText": "19053071"}
-    #     }
-    # },
-    {
-        "name": "mcp_download_full_text",
-        "arguments": {
-            "query": {
-                "applicationNumberText": "18837017"
-            }  # This one should not have a full text document
-        },
-    },
-    # # Test Boltz2 tool (if boltz_mcp_server.py is running)
-    # {
-    #     "name": "mcp_run_boltz2",
-    #     "arguments": {
-    #         "query": {
-    #             "protein_sequence": "MLSRLFRMHGLFVASHPWEVIVGTVTLTICMMSMNMFTGNNKICGWNYECPKFEEDVLSSDIIILTITRCIAILYIYFQFQNLRQLGSKYILGIAGLFTIFSSFVFSTVVIHFLDKELTGLNEALPFFLLLIDLSRASTLAKFALSSNSQDEVRENIARGMAILGPTFTLDALVECLVIGVGTMSGVRQLEIMCCFGCMSVLANYFVFMTFFPACVSLVLELSRESREGRPIWQLSHFARVLEEEENKPNPVTQRVKMIMSLGLVLVHAHSRWIADPSPQNSTADTSKVSLGLDENVSKRIEPSVSLWQFYLSKMISMDIEQVITLSLALLLAVKYIFFEQTETESTLSLKNPITSPVVTQKKVPDNCCRREPMLVRNNQKCDSVEEETGINRERKVEVIKPLVAETDTPNRATFVVGNSSLLDTSSVLVTQEPEIELPREPRPNEECLQILGNAEKGAKFLSDAEIIQLVNAKHIPAYKLETLMETHERGVSIRRQLLSKKLSEPSSLQYLPYRDYNYSLVMGACCENVIGYMPIPVGVAGPLCLDEKEFQVPMATTEGCLVASTNRGCRAIGLGGGASSRVLADGMTRGPVVRLPRACDSAEVKAWLETSEGFAVIKEAFDSTSRFARLQKLHTSIAGRNLYIRFQSRSGDAMGMNMISKGTEKALSKLHEYFPEMQILAVSGNYCTDKKPAAINWIEGRGKSVVCEAVIPAKVVREVLKTTTEAMIEVNINKNLVGSAMAGSIGGYNAHAANIVTAIYIACGQDAAQNVGSSNCITLMEASGPTNEDLYISCTMPSIEIGTVGGGTNLLPQQACLQMLGVQGACKDNPGENARQLARIVCGTVMAGELSLMAALAAGHLVKSHMIHNRSKINLQDLQGACTKKTA",
-    #             "ligands": [
-    #                 {"id": "L1", "smiles": "CC[C@H](C)C(=O)O[C@H]1C[C@@H](C=C2[C@H]1[C@H]([C@H](C=C2)C)CC[C@H](C[C@H](CC(=O)O)O)O)O"},
-    #             ],
-    #             "use_potentials": True,
-    #             "diffusion_samples": 1,
-    #             "return_structure": False
-    #         }
-    #     }
-    # }
-]
-
-# Step 4: Run test queries with error handling
-print(f"\n🧪 Running {len(test_queries)} MCP tool tests...")
-print("=" * 60)
-
-successful_tests = 0
-failed_tests = 0
-
-for idx, query in enumerate(test_queries):
-    print(f"\n[Test {idx+1}/{len(test_queries)}] {query['name']}")
-    print(f"Operation: {query['arguments'].get('operation', 'N/A')}")
-
-    if "tool_name" in query["arguments"]:
-        print(f"Tool: {query['arguments']['tool_name']}")
-
-    try:
-        # Add timeout to prevent hanging
-        start_time = time.time()
-        result = tooluni.run(query)
-        execution_time = time.time() - start_time
-
-        print(f"✅ Success in {execution_time:.2f}s")
-
-        # Format output nicely
-        if isinstance(result, dict):
-            if "error" in result:
-                print(f"⚠️  Tool returned error: {result['error']}")
-            else:
-                # Show a snippet of the result
-                result_str = json.dumps(result, indent=2)
-                print(f"📊 Result: {result_str}")
-        else:
-            result_str = str(result)
-            print(f"📊 Result: {result_str}")
-
-        if "error" not in result:
-            successful_tests += 1
-        else:
-            failed_tests += 1
-            print(f"❌ Test failed with error: {result['error']}")
-
-    except Exception as e:
-        print(f"❌ Failed: {str(e)}")
-        failed_tests += 1
-
-    # Small delay between tests
-    time.sleep(0.5)
-
-# Step 5: Test Summary
-print("\n" + "=" * 60)
-print("🎯 MCP Tool Test Summary")
-print("=" * 60)
-print(f"✅ Successful tests: {successful_tests}")
-print(f"❌ Failed tests: {failed_tests}")
-print(
-    f"📊 Success rate: {(successful_tests/(successful_tests + failed_tests)*100):.1f}%"
-)
-
-# if failed_tests > 0:
-#     print("\n💡 Tips for failed tests:")
-#     print("- Make sure MCP servers are running (e.g., python fastmcp_official_example.py)")
-#     print("- Check server URLs and ports in mcp_client_tools.json")
-#     print("- Verify network connectivity to MCP servers")
-#     print("- Some tools may require specific arguments or server capabilities")
-
-# print("\n🔧 Available MCP tools in ToolUniverse:")
-# for tool_name in mcp_tools:
-#     tool_config = tooluni.all_tool_dict.get(tool_name, {})
-#     print(f"  - {tool_name}: {tool_config.get('description', 'No description')}")
-
-print("\n✨ MCP integration test completed!")