Main Atlassian MCP server lifespan shutting down unexpectedly

[chenhchenh]

Hi,

I am ran into issues that mcp-atlassian server shutdown when I run the command (uvx mcp-atlassian in python. But no issue when I run cvx mcp-atlassian command in terminal. Can anyone assist? Thanks,

INFO - mcp-atlassian.utils.environment - Using Jira Cloud Basic Authentication (API Token)
INFO - mcp-atlassian.server.main - Jira configuration loaded and authentication is configured.
INFO - mcp-atlassian.server.main - Confluence configuration loaded and authentication is configured.
INFO - mcp-atlassian.server.main - Read-only mode: DISABLED
INFO - mcp-atlassian.server.main - Enabled tools filter: All tools enabled
INFO - mcp.server.lowlevel.server - Processing request of type ListToolsRequest
INFO - mcp.server.lowlevel.server - Processing request of type ListToolsRequest
/Documents/Tools/CrewAI Demo/JIRA_Generate_Test/.venv/lib/python3.12/site-packages/pydantic/fields.py:1089: PydanticDeprecatedSince20: Using extra keyword arguments on Field is deprecated and will be removed. Use json_schema_extra instead. (Extra keys: 'items', 'anyOf', 'enum', 'properties'). Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.11/migration/
warn(
Available MCP Tools: ['jira_get_user_profile', 'jira_get_issue', 'jira_search', 'jira_search_fields', 'jira_get_project_issues', 'jira_get_transitions', 'jira_get_worklog', 'jira_download_attachments', 'jira_get_agile_boards', 'jira_get_board_issues', 'jira_get_sprints_from_board', 'jira_get_sprint_issues', 'jira_get_link_types', 'jira_create_issue', 'jira_batch_create_issues', 'jira_batch_get_changelogs', 'jira_update_issue', 'jira_delete_issue', 'jira_add_comment', 'jira_add_worklog', 'jira_link_to_epic', 'jira_create_issue_link', 'jira_create_remote_issue_link', 'jira_remove_issue_link', 'jira_transition_issue', 'jira_create_sprint', 'jira_update_sprint', 'jira_get_project_versions', 'jira_get_all_projects', 'jira_create_version', 'jira_batch_create_versions', 'confluence_search', 'confluence_get_page', 'confluence_get_page_children', 'confluence_get_comments', 'confluence_get_labels', 'confluence_add_label', 'confluence_create_page', 'confluence_update_page', 'confluence_delete_page', 'confluence_add_comment', 'confluence_search_user']
INFO - mcp-atlassian.server.main - Main Atlassian MCP server lifespan shutting down...
INFO - mcp-atlassian.server.main - Main Atlassian MCP server lifespan shutdown complete.
INFO - mcp-atlassian.utils.lifecycle - Server stopped, flushing output streams...

[guhuajun]

Hmm, which version is stable? Just switched several times in past a few hours.

core@flatcar61 ~ $ kubectl logs mcp-mcp-atlassian-77cc489945-rhwlv
INFO - mcp-atlassian.server.main - Added /healthz endpoint for Kubernetes probes
INFO - mcp-atlassian - Starting server with STDIO transport.
INFO - mcp-atlassian.server.main - Main Atlassian MCP server lifespan starting...
INFO - mcp-atlassian.utils.environment - Using Confluence Server/Data Center authentication (PAT or Basic Auth)
INFO - mcp-atlassian.utils.environment - Jira is not configured or required environment variables are missing.
INFO - mcp-atlassian.server.main - Confluence configuration loaded and authentication is configured.
INFO - mcp-atlassian.server.main - Read-only mode: DISABLED
INFO - mcp-atlassian.server.main - Enabled tools filter: All tools enabled
INFO - mcp-atlassian.server.main - Main Atlassian MCP server lifespan shutting down...
INFO - mcp-atlassian.server.main - Main Atlassian MCP server lifespan shutdown complete.
--- Logging error ---
Traceback (most recent call last):
  File "/usr/local/lib/python3.10/logging/__init__.py", line 1103, in emit
    stream.write(msg + self.terminator)
ValueError: I/O operation on closed file.
Call stack:
  File "/app/.venv/bin/mcp-atlassian", line 10, in <module>
    sys.exit(main())
  File "/app/.venv/lib/python3.10/site-packages/click/core.py", line 1161, in __call__
    return self.main(*args, **kwargs)
  File "/app/.venv/lib/python3.10/site-packages/click/core.py", line 1082, in main
    rv = self.invoke(ctx)
  File "/app/.venv/lib/python3.10/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/app/.venv/lib/python3.10/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
  File "/app/.venv/lib/python3.10/site-packages/mcp_atlassian/__init__.py", line 357, in main
    ensure_clean_exit()
  File "/app/.venv/lib/python3.10/site-packages/mcp_atlassian/utils/lifecycle.py", line 138, in ensure_clean_exit
    logger.info("Server stopped, flushing output streams...")
Message: 'Server stopped, flushing output streams...'
Arguments: ()
Traceback (most recent call last):
  File "/app/.venv/bin/mcp-atlassian", line 10, in <module>
    sys.exit(main())
  File "/app/.venv/lib/python3.10/site-packages/click/core.py", line 1161, in __call__
    return self.main(*args, **kwargs)
  File "/app/.venv/lib/python3.10/site-packages/click/core.py", line 1082, in main
    rv = self.invoke(ctx)
  File "/app/.venv/lib/python3.10/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/app/.venv/lib/python3.10/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
  File "/app/.venv/lib/python3.10/site-packages/mcp_atlassian/__init__.py", line 357, in main
    ensure_clean_exit()
  File "/app/.venv/lib/python3.10/site-packages/mcp_atlassian/utils/lifecycle.py", line 140, in ensure_clean_exit
    sys.stdout.flush()
ValueError: I/O operation on closed file.

[guhuajun]

Now, it's working. I switched to SSE.