MacOS(arm64)下Colab中Cytoscape Automation脚本连接失败求助

问题概述 #

• 在MacOS(arm64)设备上，Google Colab中的Cytoscape Automation脚本无法连接本地运行的Cytoscape；Windows 11上可正常运行的Overview-of-py4cytoscape.ipynb示例，在MacBook(ARM)上完全失效。
• 本地Cytoscape可正常启动，但调用p4c.cytoscape_version_info()函数时，Colab持续抛出RequestException: Cannot find local or remote Cytoscape错误。

环境信息 #

• Cytoscape版本：3.10.1
• Java版本：17.0.5 by Eclipse Adoptium
• Java Home：/Applications/Cytoscape_v3.10.1/.install4j/jre.bundle/Contents/Home
• 操作系统：Mac OS X 14.1.1 - aarch64

错误日志 #

RequestException                          Traceback (most recent call last)
<ipython-input-3-aac4e79c4feb> in <cell line: 1>()
----> 1 p4c.cytoscape_version_info()

9 frames
/usr/local/lib/python3.10/dist-packages/py4cytoscape/py4cytoscape_logger.py in wrapper_log(*args, **kwargs)
    131             return log_return(func, value)
    132         except Exception as e:
--> 133             log_exception(func, e)
    134         finally:
    135             log_finally()

/usr/local/lib/python3.10/dist-packages/py4cytoscape/py4cytoscape_logger.py in wrapper_log(*args, **kwargs)
    128         log_incoming(func, *args, **kwargs)
    129         try:
--> 130             value = func(*args, **kwargs) # Call function being logged
    131             return log_return(func, value)
    132         except Exception as e:

/usr/local/lib/python3.10/dist-packages/py4cytoscape/cytoscape_system.py in cytoscape_version_info(base_url)
     79         {'apiVersion': 'v1', 'cytoscapeVersion': '3.8.1', 'automationAPIVersion': '0.0.0', 'py4cytoscapeVersion': '0.0.2'}
     80     """
---> 81     versions = commands.cyrest_get('version', base_url=base_url)
     82     if len(versions) == 0:
     83         raise CyError('CyREST connection problem. py4cytoscape cannot continue!')

/usr/local/lib/python3.10/dist-packages/py4cytoscape/py4cytoscape_logger.py in wrapper_log(*args, **kwargs)
    131             return log_return(func, value)
    132         except Exception as e:
--> 133             log_exception(func, e)
    134         finally:
    135             log_finally()

/usr/local/lib/python3.10/dist-packages/py4cytoscape/py4cytoscape_logger.py in wrapper_log(*args, **kwargs)
    128         log_incoming(func, *args, **kwargs)
    129         try:
--> 130             value = func(*args, **kwargs) # Call function being logged
    131             return log_return(func, value)
    132         except Exception as e:

/usr/local/lib/python3.10/dist-packages/py4cytoscape/commands.py in cyrest_get(operation, parameters, base_url, require_json, raw_get)
    157                 return r.text
    158     except requests.exceptions.RequestException as e:
--> 159         _handle_error(e)
    160 
    161 

/usr/local/lib/python3.10/dist-packages/py4cytoscape/commands.py in cyrest_get(operation, parameters, base_url, require_json, raw_get)
    147     try:
    148         url = build_url(base_url, operation)
--> 149         r = _do_request('GET', url, params=parameters, base_url=base_url, raw_request=raw_get)
    150         r.raise_for_status()
    151         try:

/usr/local/lib/python3.10/dist-packages/py4cytoscape/commands.py in _do_request(method, url, base_url, raw_request, **kwargs)
    693 def _do_request(method, url, base_url=DEFAULT_BASE_URL, raw_request=False, **kwargs):
    694     # Determine whether actual call is local or remote
--> 695     requester, default_sandbox = _get_requester(base_url)
    696 
    697     if not raw_request:

/usr/local/lib/python3.10/dist-packages/py4cytoscape/commands.py in _get_requester(base_url)
    777 def _get_requester(base_url):
    778     # Figure out whether CyREST available only via Jupyter-Bridge and what the default sandbox should be
--> 779     environment = _find_execution_environment(base_url)
    780     if environment == ExecutionEnvironment.REMOTE_JUPYTER_BRIDGE:
    781         default_sandbox = set_default_sandbox(**sandbox_initializer(sandboxName=PREDEFINED_SANDBOX_NAME))

/usr/local/lib/python3.10/dist-packages/py4cytoscape/commands.py in _find_execution_environment(base_url)
    801     environment = check_execution_environment(base_url)
    802     if environment == ExecutionEnvironment.UNKNOWN:
--> 803         raise requests.exceptions.RequestException('Cannot find local or remote Cytoscape. Start Cytoscape and then proceed.')
    804     return environment

RequestException: Cannot find local or remote Cytoscape. Start Cytoscape and then proceed.

排查与解决方案 #

1. 确认CyREST服务端口可达 #

• 在本地浏览器访问http://localhost:1234/v1/version，检查是否能返回Cytoscape版本信息。若无法访问，说明CyREST服务未正常启动，重启Cytoscape后重试。
• 检查MacOS防火墙设置，确保允许Cytoscape接收本地连接，或临时关闭防火墙测试。

2. 强制指定本地连接地址 #

在Colab脚本中显式传入base_url参数，跳过环境自动检测逻辑：

import py4cytoscape as p4c
# 强制指向本地CyREST服务地址
p4c.cytoscape_version_info(base_url='http://localhost:1234/v1')

3. 修复ARM架构下的JAVA_HOME配置 #

尽管已配置JAVA_HOME，但ARM架构可能存在路径识别问题：

• 在终端执行echo $JAVA_HOME，确认输出为/Applications/Cytoscape_v3.10.1/.install4j/jre.bundle/Contents/Home。
• 若未正确设置，编辑~/.zshrc（或~/.bash_profile）添加：

export JAVA_HOME="/Applications/Cytoscape_v3.10.1/.install4j/jre.bundle/Contents/Home"
export PATH="$JAVA_HOME/bin:$PATH"

• 执行source ~/.zshrc使配置生效，重启Cytoscape。

4. 匹配py4cytoscape与Cytoscape版本 #

Colab默认安装的py4cytoscape版本可能与Cytoscape 3.10.1不兼容：

# 查看当前py4cytoscape版本
!pip show py4cytoscape
# 安装兼容版本（建议选择1.0.1及以上适配Cytoscape 3.10.x）
!pip install py4cytoscape==1.2.1

5. 云端到本地的端口映射 #

Colab运行在云端，需通过端口映射工具让云端脚本访问本地Cytoscape：

• 使用端口映射工具将本地1234端口映射到公网，修改Colab中的base_url为映射后的地址：

p4c.cytoscape_version_info(base_url='https://<映射公网ID>.ngrok.io/v1')

注意：需保持映射工具在终端持续运行，会话过期后需重新生成地址。

内容的提问来源于stack exchange，提问作者dtek