Older galaxy I'm keeping alive by drip feed, has problem restarting when I turn debug off.
I have an OLDER Galaxy install I was going to fade out. In meantime I saw that its debug flag should be turned off, so I did. But when it restarted it complained in the history tab with a server error. I put debug back into config and it runs fine. I haven't changed anything recently on it. Wondering if there is a simple remedy? Details below. Thanks, Damion ********************************************************* Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) And indeed, after the startup log message... serving on http://127.0.0.1:8080 There is an error that seems to be triggered when A GET /galaxy/history command is sent. ................ - - [15/Apr/2015:13:03:43 -0700] "GET /galaxy/history HTTP/1.1" 200 - "http://salk.bccdc.med.ubc.ca/galaxy/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2272.101 Safari/537.36" ................ - - [15/Apr/2015:13:03:43 -0700] "GET /galaxy/history HTTP/1.1" 500 - "http://salk.bccdc.med.ubc.ca/galaxy/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2272.101 Safari/537.36" Error - <type 'exceptions.TypeError'>: 'NoneType' object is not callable ................ - - [15/Apr/2015:13:03:43 -0700] "GET /galaxy/root/tool_menu HTTP/1.1" 200 - "http://salk.bccdc.med.ubc.ca/galaxy/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2272.101 Safari/537.36" URL: http://salk.bccdc.med.ubc.ca/galaxy/history File '/usr/lib/python2.6/site-packages/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/lib/python2.6/site-packages/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/lib/python2.6/site-packages/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', line 169 in __call__ return body( environ, start_response ) File '/usr/local/galaxy/production/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 759 in render template.render_context( context ) File '/usr/local/galaxy/production/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 319 in render_context **kwargs) File '/usr/local/galaxy/production/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/usr/local/galaxy/production/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/galaxy/production/galaxy-dist/database/compiled_templates/root/history.mako.py', line 61 in render_body __M_writer(u'\n\n') File '/usr/local/galaxy/production/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 756 in write response_write( d.encode( 'utf-8' ) ) TypeError: 'NoneType' object is not callable Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
Hi Damion, I'm suspicious of the compiled templates. Can you disable debug, then do something like "find /usr/local/galaxy/production/galaxy-dist -name '*.pyc' -delete", and then restart? -Dannon On Wed, Apr 15, 2015 at 4:16 PM, Dooley, Damion <Damion.Dooley@bccdc.ca> wrote:
I have an OLDER Galaxy install I was going to fade out. In meantime I saw that its debug flag should be turned off, so I did. But when it restarted it complained in the history tab with a server error. I put debug back into config and it runs fine. I haven't changed anything recently on it. Wondering if there is a simple remedy? Details below.
Thanks,
Damion
********************************************************* Server Error
An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)
And indeed, after the startup log message...
serving on http://127.0.0.1:8080
There is an error that seems to be triggered when A GET /galaxy/history command is sent.
................ - - [15/Apr/2015:13:03:43 -0700] "GET /galaxy/history HTTP/1.1" 200 - "http://salk.bccdc.med.ubc.ca/galaxy/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2272.101 Safari/537.36" ................ - - [15/Apr/2015:13:03:43 -0700] "GET /galaxy/history HTTP/1.1" 500 - "http://salk.bccdc.med.ubc.ca/galaxy/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2272.101 Safari/537.36" Error - <type 'exceptions.TypeError'>: 'NoneType' object is not callable ................ - - [15/Apr/2015:13:03:43 -0700] "GET /galaxy/root/tool_menu HTTP/1.1" 200 - " http://salk.bccdc.med.ubc.ca/galaxy/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/41.0.2272.101 Safari/537.36" URL: http://salk.bccdc.med.ubc.ca/galaxy/history File '/usr/lib/python2.6/site-packages/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/lib/python2.6/site-packages/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/lib/python2.6/site-packages/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', line 169 in __call__ return body( environ, start_response ) File '/usr/local/galaxy/production/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 759 in render template.render_context( context ) File '/usr/local/galaxy/production/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 319 in render_context **kwargs) File '/usr/local/galaxy/production/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/usr/local/galaxy/production/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/galaxy/production/galaxy-dist/database/compiled_templates/root/ history.mako.py', line 61 in render_body __M_writer(u'\n\n') File '/usr/local/galaxy/production/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 756 in write response_write( d.encode( 'utf-8' ) ) TypeError: 'NoneType' object is not callable
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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Darn, didn't change anything. I deleted them both as galaxy system account and as root, but still that error on restart. Thanks for this tip though. d. Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ________________________________________ From: Dannon Baker [dannon.baker@gmail.com] ... Hi Damion, I'm suspicious of the compiled templates. Can you disable debug, then do something like "find /usr/local/galaxy/production/galaxy-dist -name '*.pyc' -delete", and then restart? -Dannon
Hrmm, was worth a shot. And, I *think* the logic is such that this won't change anything, but you can also (safely) wipe out that whole compiled_templates directory and see if that does anything. When you say old, just how old (hg summary) *is* this install? That might give us a few tips. On Wed, Apr 15, 2015 at 5:24 PM, Dooley, Damion <Damion.Dooley@bccdc.ca> wrote:
Darn, didn't change anything. I deleted them both as galaxy system account and as root, but still that error on restart. Thanks for this tip though.
d.
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ________________________________________ From: Dannon Baker [dannon.baker@gmail.com] ... Hi Damion,
I'm suspicious of the compiled templates. Can you disable debug, then do something like "find /usr/local/galaxy/production/galaxy-dist -name '*.pyc' -delete", and then restart?
-Dannon
Hi Damion, Another thing to try, is to set up and use a virutalenv, as the last time this error was reported (2012), it was suggested that a local site-packages version of Paste, instead of Galaxy’s provided egg, was to blame. Thanks for using Galaxy, Dan On Apr 15, 2015, at 5:36 PM, Dannon Baker <dannon.baker@gmail.com> wrote:
Hrmm, was worth a shot. And, I *think* the logic is such that this won't change anything, but you can also (safely) wipe out that whole compiled_templates directory and see if that does anything.
When you say old, just how old (hg summary) *is* this install? That might give us a few tips.
On Wed, Apr 15, 2015 at 5:24 PM, Dooley, Damion <Damion.Dooley@bccdc.ca> wrote: Darn, didn't change anything. I deleted them both as galaxy system account and as root, but still that error on restart. Thanks for this tip though.
d.
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ________________________________________ From: Dannon Baker [dannon.baker@gmail.com] ... Hi Damion,
I'm suspicious of the compiled templates. Can you disable debug, then do something like "find /usr/local/galaxy/production/galaxy-dist -name '*.pyc' -delete", and then restart?
-Dannon
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Ok, Daniel I don't really know egg vs site-packages install or how to change that; I tried upgrading our python 2.6 Paste to 1.7.5 but that didn't effect a change. Dannon I tried toasting compiled_templates directory, to no avail. The site was last upgraded in 2012. I'm afraid to mess with it :{ I could settle for leaving debugging on, but disable anonymous access. Would that still leave site vulnerable? hg summary parent: 7148:17d57db9a7c0 Fix for history_contents API file display. branch: default commit: 9 modified, 166 unknown (new branch head) update: 6506 new changesets (update) Thanks, d. ________________________________________ From: Dannon Baker [dannon.baker@gmail.com] Sent: Wednesday, April 15, 2015 2:36 PM ... Hrmm, was worth a shot. And, I *think* the logic is such that this won't change anything, but you can also (safely) wipe out that whole compiled_templates directory and see if that does anything. When you say old, just how old (hg summary) *is* this install? That might give us a few tips.
Ok, yeah, that's pretty old :) I'd second the virtualenv suggestion, then, as a next easy thing to try. It's really easy to set up, and to test it you'd basically have to do this: (sudo) pip install virtualenv cd <galaxy_directory> virtualenv .venv source .venv/bin/activate sh run.sh (in this now-activated virtualenv, start galaxy) And see if that fixes the problem. Let us know how that goes and if there's anything else we can help. That said, it's a *really* good idea to probably go ahead and update this Galaxy as soon as possible for security (and other) fixes. You can always back up the db, back up the galaxy directory with the exact state of the code, and try an upgrade to see what happens, reverting both should things go awry. -Dannon On Wed, Apr 15, 2015 at 6:45 PM Dooley, Damion <Damion.Dooley@bccdc.ca> wrote:
Ok, Daniel I don't really know egg vs site-packages install or how to change that; I tried upgrading our python 2.6 Paste to 1.7.5 but that didn't effect a change. Dannon I tried toasting compiled_templates directory, to no avail.
The site was last upgraded in 2012. I'm afraid to mess with it :{
I could settle for leaving debugging on, but disable anonymous access. Would that still leave site vulnerable?
hg summary parent: 7148:17d57db9a7c0 Fix for history_contents API file display. branch: default commit: 9 modified, 166 unknown (new branch head) update: 6506 new changesets (update)
Thanks,
d.
________________________________________ From: Dannon Baker [dannon.baker@gmail.com] Sent: Wednesday, April 15, 2015 2:36 PM ... Hrmm, was worth a shot. And, I *think* the logic is such that this won't change anything, but you can also (safely) wipe out that whole compiled_templates directory and see if that does anything.
When you say old, just how old (hg summary) *is* this install? That might give us a few tips.
participants (3)
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Daniel Blankenberg -
Dannon Baker -
Dooley, Damion