New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[BUG][17.09] Ignore OSError when chmod'ing integrated_tool_panel_conf.xml #5071

Merged
merged 1 commit into from Nov 24, 2017

Conversation

Projects
None yet
5 participants
@mvdbeek
Member

mvdbeek commented Nov 24, 2017

This fixes the first error in #5031:

Exception in thread ToolConfWatcher.thread:
Traceback (most recent call last):
  File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
  File "/usr/lib/python2.7/threading.py", line 763, in run
    self.__target(*self.__args, **self.__kwargs)
  File "lib/galaxy/tools/toolbox/watcher.py", line 138, in check
    self.reload_callback()
  File "lib/galaxy/webapps/galaxy/config_watchers.py", line 24, in <lambda>
    self.tool_config_watcher = get_tool_conf_watcher(reload_callback=lambda: reload_toolbox(self.app), tool_cache=self.app.tool_cache)
  File "lib/galaxy/queue_worker.py", line 92, in reload_toolbox
    _get_new_toolbox(app)
  File "lib/galaxy/queue_worker.py", line 111, in _get_new_toolbox
    new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app)
  File "lib/galaxy/tools/__init__.py", line 226, in __init__
    app=app,
  File "lib/galaxy/tools/toolbox/base.py", line 1061, in __init__
    super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app)
  File "lib/galaxy/tools/toolbox/base.py", line 87, in __init__
    self._save_integrated_tool_panel()
  File "lib/galaxy/tools/toolbox/integrated_panel.py", line 46, in _save_integrated_tool_panel
    self._write_integrated_tool_panel_config_file()
  File "lib/galaxy/tools/toolbox/integrated_panel.py", line 106, in _write_integrated_tool_panel_config_file
    os.chmod(self._integrated_tool_panel_config, 0o644)
OSError: [Errno 2] No such file or directory: '/data/users/mvandenb/gx/config/integrated_tool_panel.xml'

That actually also happens sometime when starting up many handlers at the same time.

Ignore OSError when chmod'ing integrated_tool_panel_conf.xml
This fixes the first error in #5031:
```
Exception in thread ToolConfWatcher.thread:
Traceback (most recent call last):
  File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner
    self.run()
  File "/usr/lib/python2.7/threading.py", line 763, in run
    self.__target(*self.__args, **self.__kwargs)
  File "lib/galaxy/tools/toolbox/watcher.py", line 138, in check
    self.reload_callback()
  File "lib/galaxy/webapps/galaxy/config_watchers.py", line 24, in <lambda>
    self.tool_config_watcher = get_tool_conf_watcher(reload_callback=lambda: reload_toolbox(self.app), tool_cache=self.app.tool_cache)
  File "lib/galaxy/queue_worker.py", line 92, in reload_toolbox
    _get_new_toolbox(app)
  File "lib/galaxy/queue_worker.py", line 111, in _get_new_toolbox
    new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app)
  File "lib/galaxy/tools/__init__.py", line 226, in __init__
    app=app,
  File "lib/galaxy/tools/toolbox/base.py", line 1061, in __init__
    super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app)
  File "lib/galaxy/tools/toolbox/base.py", line 87, in __init__
    self._save_integrated_tool_panel()
  File "lib/galaxy/tools/toolbox/integrated_panel.py", line 46, in _save_integrated_tool_panel
    self._write_integrated_tool_panel_config_file()
  File "lib/galaxy/tools/toolbox/integrated_panel.py", line 106, in _write_integrated_tool_panel_config_file
    os.chmod(self._integrated_tool_panel_config, 0o644)
OSError: [Errno 2] No such file or directory: '/data/users/mvandenb/gx/config/integrated_tool_panel.xml'
```

@jmchilton jmchilton merged commit a71d5aa into galaxyproject:release_17.09 Nov 24, 2017

7 checks passed

api test Build finished. 293 tests run, 4 skipped, 0 failed.
Details
continuous-integration/travis-ci/pr The Travis CI build passed
Details
framework test Build finished. 162 tests run, 0 skipped, 0 failed.
Details
integration test Build finished. 46 tests run, 0 skipped, 0 failed.
Details
lgtm analysis: JavaScript No alert changes
Details
selenium test Build finished. No test results found.
Details
toolshed test Build finished. 579 tests run, 0 skipped, 0 failed.
Details
@galaxybot

This comment has been minimized.

galaxybot commented Nov 24, 2017

This PR was merged without a milestone attached.

@bgruening bgruening added this to the 17.09 milestone Nov 24, 2017

@nsoranzo nsoranzo modified the milestones: 17.09, 18.01 Nov 24, 2017

@mvdbeek mvdbeek deleted the mvdbeek:installation_fixes branch Jun 12, 2018

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment