tooluniverse 1.0.3__py3-none-any.whl → 1.0.5__py3-none-any.whl
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- tooluniverse/__init__.py +17 -5
- tooluniverse/agentic_tool.py +268 -330
- tooluniverse/compose_scripts/output_summarizer.py +21 -15
- tooluniverse/data/agentic_tools.json +2 -2
- tooluniverse/data/odphp_tools.json +354 -0
- tooluniverse/data/output_summarization_tools.json +2 -2
- tooluniverse/default_config.py +1 -0
- tooluniverse/llm_clients.py +570 -0
- tooluniverse/mcp_tool_registry.py +3 -3
- tooluniverse/odphp_tool.py +226 -0
- tooluniverse/output_hook.py +92 -3
- tooluniverse/remote/boltz/boltz_mcp_server.py +2 -2
- tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py +2 -2
- tooluniverse/smcp.py +204 -112
- tooluniverse/smcp_server.py +23 -20
- tooluniverse/test/list_azure_openai_models.py +210 -0
- tooluniverse/test/test_agentic_tool_azure_models.py +91 -0
- tooluniverse/test/test_api_key_validation_min.py +64 -0
- tooluniverse/test/test_claude_sdk.py +86 -0
- tooluniverse/test/test_global_fallback.py +288 -0
- tooluniverse/test/test_hooks_direct.py +219 -0
- tooluniverse/test/test_odphp_tool.py +166 -0
- tooluniverse/test/test_openrouter_client.py +288 -0
- tooluniverse/test/test_stdio_hooks.py +285 -0
- tooluniverse/test/test_tool_finder.py +1 -1
- {tooluniverse-1.0.3.dist-info → tooluniverse-1.0.5.dist-info}/METADATA +101 -74
- {tooluniverse-1.0.3.dist-info → tooluniverse-1.0.5.dist-info}/RECORD +31 -19
- tooluniverse-1.0.5.dist-info/licenses/LICENSE +201 -0
- tooluniverse-1.0.3.dist-info/licenses/LICENSE +0 -21
- {tooluniverse-1.0.3.dist-info → tooluniverse-1.0.5.dist-info}/WHEEL +0 -0
- {tooluniverse-1.0.3.dist-info → tooluniverse-1.0.5.dist-info}/entry_points.txt +0 -0
- {tooluniverse-1.0.3.dist-info → tooluniverse-1.0.5.dist-info}/top_level.txt +0 -0
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#!/usr/bin/env python3
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"""
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测试 MCP stdio 模式下关闭和开启 hooks 的情况
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"""
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import subprocess
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import json
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import time
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import sys
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def run_stdio_test(hooks_enabled=False):
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"""运行 stdio 测试"""
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print(f"\n{'='*60}")
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print(f"测试模式: {'开启 hooks' if hooks_enabled else '关闭 hooks'}")
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print(f"{'='*60}")
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# 构建命令
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cmd = [
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sys.executable,
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"-c",
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f"""
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import sys
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sys.path.insert(0, 'src')
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from tooluniverse.smcp_server import run_stdio_server
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sys.argv = ['tooluniverse-stdio'] + (['--hooks'] if {hooks_enabled} else [])
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run_stdio_server()
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""",
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]
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print(f"启动命令: {' '.join(cmd[:3])} ...")
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# 启动服务器进程
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process = subprocess.Popen(
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cmd,
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stdin=subprocess.PIPE,
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stdout=subprocess.PIPE,
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stderr=subprocess.PIPE,
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text=True,
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bufsize=0,
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)
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try:
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# 等待服务器启动并读取启动日志
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time.sleep(3)
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# 读取并丢弃启动日志
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print("读取启动日志...")
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while True:
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line = process.stdout.readline()
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if not line:
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break
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print(f"启动日志: {line.strip()}")
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if "Starting ToolUniverse SMCP Server" in line:
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break
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# 发送初始化请求
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init_request = {
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"jsonrpc": "2.0",
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"id": 1,
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"method": "initialize",
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"params": {
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"protocolVersion": "2024-11-05",
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"capabilities": {},
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"clientInfo": {"name": "test-client", "version": "1.0.0"},
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},
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}
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print("发送初始化请求...")
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process.stdin.write(json.dumps(init_request) + "\n")
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process.stdin.flush()
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# 读取初始化响应
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init_response = process.stdout.readline()
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print(f"初始化响应: {init_response.strip()}")
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# 发送 tools/list 请求
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list_request = {"jsonrpc": "2.0", "id": 2, "method": "tools/list"}
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print("发送 tools/list 请求...")
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process.stdin.write(json.dumps(list_request) + "\n")
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process.stdin.flush()
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# 读取 tools/list 响应
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list_response = process.stdout.readline()
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print(f"tools/list 响应长度: {len(list_response)} 字符")
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# 发送测试工具调用请求
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test_request = {
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"jsonrpc": "2.0",
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"id": 3,
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"method": "tools/call",
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"params": {
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"name": "OpenTargets_get_target_gene_ontology_by_ensemblID",
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"arguments": {"ensemblId": "ENSG00000012048"},
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},
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}
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print("发送测试工具调用请求...")
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process.stdin.write(json.dumps(test_request) + "\n")
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process.stdin.flush()
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# 读取工具调用响应（可能需要等待更长时间）
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print("等待工具调用响应...")
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start_time = time.time()
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# 读取多行响应，直到找到 JSON 响应
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tool_response = ""
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timeout = 30 # 30秒超时
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while time.time() - start_time < timeout:
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line = process.stdout.readline()
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if not line:
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time.sleep(0.1)
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continue
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tool_response += line
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print(f"收到响应行: {repr(line)}")
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# 检查是否是 JSON 响应
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try:
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json.loads(line.strip())
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break
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except json.JSONDecodeError:
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continue
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end_time = time.time()
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response_time = end_time - start_time
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response_length = len(tool_response)
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print(f"工具调用响应时间: {response_time:.2f} 秒")
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print(f"工具调用响应长度: {response_length} 字符")
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print(f"原始响应内容: {repr(tool_response)}")
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# 尝试解析 JSON 响应
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json_response = None
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for line in tool_response.split("\n"):
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if line.strip().startswith('{"jsonrpc"'):
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try:
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json_response = json.loads(line.strip())
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break
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except json.JSONDecodeError:
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continue
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if json_response:
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print("✅ 成功解析 JSON 响应")
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print(f"响应 ID: {json_response.get('id')}")
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if "result" in json_response:
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print("✅ 工具调用成功")
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elif "error" in json_response:
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print(f"❌ 工具调用失败: {json_response['error']}")
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else:
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print("⚠️ 未找到有效的 JSON 响应")
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# 继续等待实际的工具调用响应
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print("等待工具调用完成...")
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time.sleep(5) # 等待工具执行完成
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# 读取工具调用的实际响应
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actual_response = ""
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while True:
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line = process.stdout.readline()
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if not line:
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break
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actual_response += line
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print(f"工具响应行: {repr(line)}")
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# 检查是否是 JSON 响应
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try:
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json.loads(line.strip())
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break
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except json.JSONDecodeError:
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continue
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if actual_response:
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print(f"工具调用实际响应长度: {len(actual_response)} 字符")
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# 尝试解析工具调用响应
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tool_json_response = None
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for line in actual_response.split("\n"):
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if line.strip().startswith('{"jsonrpc"'):
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try:
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tool_json_response = json.loads(line.strip())
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break
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except json.JSONDecodeError:
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continue
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if tool_json_response and "result" in tool_json_response:
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result_content = tool_json_response["result"]
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if "content" in result_content:
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content_text = str(result_content["content"])
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content_length = len(content_text)
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print(f"工具响应内容长度: {content_length} 字符")
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# 检查是否是摘要
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if "summary" in content_text.lower() or "摘要" in content_text:
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print("✅ 检测到摘要内容")
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else:
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print("📄 原始内容（未摘要）")
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else:
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print("⚠️ 工具响应中没有 content 字段")
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else:
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print("⚠️ 无法解析工具调用响应")
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return {
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"hooks_enabled": hooks_enabled,
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"response_time": response_time,
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"response_length": response_length,
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"success": True,
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}
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except Exception as e:
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print(f"❌ 测试失败: {e}")
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return {
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"hooks_enabled": hooks_enabled,
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"response_time": None,
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"response_length": None,
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"success": False,
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"error": str(e),
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}
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finally:
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# 清理进程
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try:
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process.terminate()
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process.wait(timeout=5)
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except Exception:
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process.kill()
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def main():
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"""主函数"""
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print("MCP stdio 模式 hooks 测试")
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print("测试工具: OpenTargets_get_target_gene_ontology_by_ensemblID")
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print("测试参数: ensemblId=ENSG00000012048")
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# 测试关闭 hooks
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result_no_hooks = run_stdio_test(hooks_enabled=False)
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# 测试开启 hooks
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result_with_hooks = run_stdio_test(hooks_enabled=True)
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# 对比结果
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print(f"\n{'='*60}")
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print("测试结果对比")
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print(f"{'='*60}")
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print("关闭 hooks:")
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if result_no_hooks["success"]:
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print(
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f" ✅ 成功 - 响应时间: {result_no_hooks['response_time']:.2f}s, 长度: {result_no_hooks['response_length']} 字符"
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)
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else:
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print(f" ❌ 失败 - {result_no_hooks.get('error', '未知错误')}")
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print("开启 hooks:")
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if result_with_hooks["success"]:
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print(
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f" ✅ 成功 - 响应时间: {result_with_hooks['response_time']:.2f}s, 长度: {result_with_hooks['response_length']} 字符"
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)
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else:
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print(f" ❌ 失败 - {result_with_hooks.get('error', '未知错误')}")
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# 性能对比
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if result_no_hooks["success"] and result_with_hooks["success"]:
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time_diff = (
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result_with_hooks["response_time"] - result_no_hooks["response_time"]
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)
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length_diff = (
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result_with_hooks["response_length"] - result_no_hooks["response_length"]
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)
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print("\n性能对比:")
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print(
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f" 时间差异: {time_diff:+.2f}s ({'hooks 更慢' if time_diff > 0 else 'hooks 更快'})"
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)
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print(
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f" 长度差异: {length_diff:+d} 字符 ({'hooks 更长' if length_diff > 0 else 'hooks 更短'})"
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)
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if abs(time_diff) < 1.0:
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print(" ✅ 时间差异在可接受范围内")
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else:
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print(" ⚠️ 时间差异较大，需要进一步优化")
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# <img src="docs/_static/logo.png" alt="ToolUniverse Logo" height="28" style="vertical-align: middle; margin-right: 8px;" /> ToolUniverse: Democratizing AI scientists
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[(Also in Bilibili)](https://www.bilibili.com/video/BV1GynhzjEos/?share_source=copy_web&vd_source=b398f13447281e748f5c41057a2c6858)
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- [**Easy to Load & Find & Call Tool**](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/index.html) (*[WebService](https://aiscientist.tools/), [PythonAPI](https://zitniklab.hms.harvard.edu/ToolUniverse/api/modules.html), [MCP](https://zitniklab.hms.harvard.edu/ToolUniverse/guide/mcp_support.html)*): Maps natural-language descriptions to tool specifications and executes tools with structured results
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→ **Complete Quick Start Tutorial**: [Quick Start Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/quickstart.html) [Getting Started Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/getting_started.html)
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**Hypercholesterolemia Drug Discovery** [[Tutorial]](https://zitniklab.hms.harvard.edu/
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**Hypercholesterolemia Drug Discovery** [[Tutorial]](https://zitniklab.hms.harvard.edu/ToolUniverse/tutorials/tooluniverse_case_study.html) [[Code]](https://colab.research.google.com/drive/1UwJ6RwyUoqI5risKQ365EeFdDQWOeOCv?usp=sharing)
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- **Contribute**: See our [Contributing Tutorial](https://zitniklab.hms.harvard.edu/
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- **Contribute**: See our [Contributing Tutorial](https://zitniklab.hms.harvard.edu/ToolUniverse/expand_tooluniverse/comprehensive_tool_guide.html)
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→ **Browse All Documentation**: [ToolUniverse Documentation](https://zitniklab.hms.harvard.edu/
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→ **Browse All Documentation**: [ToolUniverse Documentation](https://zitniklab.hms.harvard.edu/ToolUniverse/)
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### Citation
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```
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@
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@article{gao2025democratizingaiscientistsusing,
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title={Democratizing AI scientists using ToolUniverse},
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author={Shanghua Gao and Richard Zhu and Pengwei Sui and Zhenglun Kong and Sufian Aldogom and Yepeng Huang and Ayush Noori and Reza Shamji and Krishna Parvataneni and Theodoros Tsiligkaridis and Marinka Zitnik},
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eprint={2509.23426},
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archivePrefix={arXiv},
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primaryClass={cs.AI},
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url={https://arxiv.org/abs/2509.23426},
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}
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@article{gao2025txagent,
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title={TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools},
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author={Shanghua Gao and Richard Zhu and Zhenglun Kong and Ayush Noori and Xiaorui Su and Curtis Ginder and Theodoros Tsiligkaridis and Marinka Zitnik},
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### Acknowledgments
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*Democratizing AI agents for science with ToolUniverse.*
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