Re: [galaxy-dev] Error editing users associated with a quota

2013-11-12 Thread Peter Cock 
On Mon, Nov 11, 2013 at 6:55 PM, John Chilton chil...@msi.umn.edu wrote:
 Hey Peter,

   Does your universe_wsgi.ini have enable_quotas = True set?

 -John

No,

$ grep enable_quotas universe_wsgi.ini
(nothing)

I had suspected the quotas might not be working...

If the default is not to enable quotas, then the Manage quotas
entry of the Admin page ought perhaps to be disabled?

Peter
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Re: [galaxy-dev] Error editing users associated with a quota

2013-11-12 Thread John Chilton 
On Tue, Nov 12, 2013 at 3:32 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
 On Mon, Nov 11, 2013 at 6:55 PM, John Chilton chil...@msi.umn.edu wrote:
 Hey Peter,

   Does your universe_wsgi.ini have enable_quotas = True set?

 -John

 No,

 $ grep enable_quotas universe_wsgi.ini
 (nothing)

 I had suspected the quotas might not be working...

 If the default is not to enable quotas, then the Manage quotas
 entry of the Admin page ought perhaps to be disabled?

I was going to make you Trello card for this entirely logical request
and then I decided in the time it would take the Trello interface to
load I could do a pull request instead.

https://bitbucket.org/galaxy/galaxy-central/pull-request/258/only-show-manage-quotas-if-quotas-are/diff


 Peter
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Re: [galaxy-dev] Error editing users associated with a quota

2013-11-12 Thread Peter Cock 
On Tue, Nov 12, 2013 at 3:12 PM, John Chilton chil...@msi.umn.edu wrote:
 On Tue, Nov 12, 2013 at 3:32 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
 On Mon, Nov 11, 2013 at 6:55 PM, John Chilton chil...@msi.umn.edu wrote:
 Hey Peter,

   Does your universe_wsgi.ini have enable_quotas = True set?

 -John

 No,

 $ grep enable_quotas universe_wsgi.ini
 (nothing)

 I had suspected the quotas might not be working...

 If the default is not to enable quotas, then the Manage quotas
 entry of the Admin page ought perhaps to be disabled?

 I was going to make you Trello card for this entirely logical request
 and then I decided in the time it would take the Trello interface to
 load I could do a pull request instead.

 https://bitbucket.org/galaxy/galaxy-central/pull-request/258/only-show-manage-quotas-if-quotas-are/diff


Thanks - at some point I will need to set enable_quotas = True,
and retest to see if the original bug persists.

Peter
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[galaxy-dev] Error editing users associated with a quota

2013-11-11 Thread Peter Cock 
Hi all,

I'm trying to remove a user from our default quota (while they
run a large analysis), but am getting an error:

Internal Server Error
Galaxy was unable to successfully complete your request
An error occurred.
This may be an intermittent problem due to load or other unpredictable
factors, reloading the page may address the problem.
The error has been logged to our team.

Has anyone else seen this?

Thanks,

Peter


$ hg branch
stable
[galaxy@ppserver galaxy-dist]$ hg head | more
changeset:   11219:5c789ab4144a
branch:  stable
tag: tip
user:Nate Coraor n...@bx.psu.edu
date:Mon Nov 04 15:04:42 2013 -0500
summary: Added tag release_2013.11.04 for changeset 26f58e05aa10

changeset:   11216:c458a0fe1ba8
parent:  11213:6d633418ecfa
parent:  11215:f79149dd3d35
user:Nate Coraor n...@bx.psu.edu
date:Mon Nov 04 14:56:57 2013 -0500
summary: Merge security fix for filtering tools from stable/next-stable.

From the pasteur.log file,

xxx.xxx.xxx.xxx - - [11/Nov/2013:12:04:45 +0100] POST
/galaxy/admin/manage_users_and_groups_for_quota?id=7a72206f0ccffc2e
HTTP/1.1 500 -
http://xxx/galaxy/admin/manage_users_and_groups_for_quota?webapp=galaxyid=7a72206f0ccffc2e;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:25.0) Gecko/20100101
Firefox/25.0
Error - type 'exceptions.AttributeError': 'NoQuotaAgent' object has
no attribute 'set_entity_quota_associations'
URL: 
http://ppserver/galaxy/admin/manage_users_and_groups_for_quota?id=7a72206f0ccffc2e
File '/mnt/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File '/mnt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py',
line 84 in __call__
  return self.application(environ, start_response)
File 
'/mnt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
line 633 in __call__
  return self.application(environ, start_response)
File '/mnt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
132 in __call__
  return self.handle_request( environ, start_response )
File '/mnt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
190 in handle_request
  body = method( trans, **kwargs )
File '/mnt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 229 in decorator
  return func( self, trans, *args, **kwargs )
File '/mnt/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin.py',
line 531 in manage_users_and_groups_for_quota
  quota, params = self._quota_op( trans, 'quota_members_edit_button',
self._manage_users_and_groups_for_quota, kwd )
File '/mnt/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin.py',
line 664 in _quota_op
  message = op_method( quota, params )
File '/mnt/galaxy/galaxy-dist/lib/galaxy/actions/admin.py', line 80 in
_manage_users_and_groups_for_quota
  self.app.quota_agent.set_entity_quota_associations( quotas=[ quota
], users=in_users, groups=in_groups )
AttributeError: 'NoQuotaAgent' object has no attribute
'set_entity_quota_associations'


CGI Variables
-
  CONTENT_LENGTH: '-1'
  CONTENT_TYPE: 'application/x-www-form-urlencoded'
  HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
  HTTP_ACCEPT_ENCODING: 'gzip, deflate'
  HTTP_ACCEPT_LANGUAGE: 'en-gb,en;q=0.7,en-us;q=0.3'
  HTTP_CONNECTION: 'Keep-Alive'
  HTTP_COOKIE: 
'galaxysession=fed9265fae01dfd85c30fe1bbf5a988ae27edcb17a4961e7cef7bef77b0eeb9be91a902d5f0aacdf'
  HTTP_DNT: '1'
  HTTP_HOST: 'ppserver'
  HTTP_REFERER:
'http://ppserver/galaxy/admin/manage_users_and_groups_for_quota?webapp=galaxyid=7a72206f0ccffc2e'
  HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9;
rv:25.0) Gecko/20100101 Firefox/25.0'
  PATH_INFO: '/admin/manage_users_and_groups_for_quota'
  QUERY_STRING: 'id=7a72206f0ccffc2e'
  REMOTE_ADDR: '143.234.97.120'
  REQUEST_METHOD: 'POST'
  SCRIPT_NAME: '/galaxy'
  SERVER_NAME: 'xxx'
  SERVER_PORT: '8080'
  SERVER_PROTOCOL: 'HTTP/1.1'


WSGI Variables
--
  application: paste.recursive.RecursiveMiddleware object at 0x910c890
  is_api_request: False
  paste.cookies: (SimpleCookie:
galaxysession='fed9265fae01dfd85c30fe1bbf5a988ae27edcb17a4961e7cef7bef77b0eeb9be91a902d5f0aacdf',
'galaxysession=fed9265fae01dfd85c30fe1bbf5a988ae27edcb17a4961e7cef7bef77b0eeb9be91a902d5f0aacdf')
  paste.expected_exceptions: [class 'paste.httpexceptions.HTTPException']
  paste.httpexceptions: paste.httpexceptions.HTTPExceptionHandler
object at 0x783fd50
  paste.httpserver.thread_pool: paste.httpserver.ThreadPool object at
0x30eea90
  paste.parsed_querystring: ([('id', '7a72206f0ccffc2e')],
'id=7a72206f0ccffc2e')
  paste.recursive.forward: paste.recursive.Forwarder from /galaxy
  paste.recursive.include: paste.recursive.Includer from /galaxy
  paste.recursive.include_app_iter: paste.recursive.IncluderAppIter
from /galaxy
  paste.recursive.script_name: '/galaxy'
  paste.throw_errors: True
  request_id: '744ee0cc4ac911e3bbcc0026b95a4d69'

Re: [galaxy-dev] Error editing users associated with a quota

2013-11-11 Thread John Chilton 
Hey Peter,

  Does your universe_wsgi.ini have enable_quotas = True set?

-John

On Mon, Nov 11, 2013 at 6:08 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
 Hi all,

 I'm trying to remove a user from our default quota (while they
 run a large analysis), but am getting an error:

 Internal Server Error
 Galaxy was unable to successfully complete your request
 An error occurred.
 This may be an intermittent problem due to load or other unpredictable
 factors, reloading the page may address the problem.
 The error has been logged to our team.

 Has anyone else seen this?

 Thanks,

 Peter


 $ hg branch
 stable
 [galaxy@ppserver galaxy-dist]$ hg head | more
 changeset:   11219:5c789ab4144a
 branch:  stable
 tag: tip
 user:Nate Coraor n...@bx.psu.edu
 date:Mon Nov 04 15:04:42 2013 -0500
 summary: Added tag release_2013.11.04 for changeset 26f58e05aa10

 changeset:   11216:c458a0fe1ba8
 parent:  11213:6d633418ecfa
 parent:  11215:f79149dd3d35
 user:Nate Coraor n...@bx.psu.edu
 date:Mon Nov 04 14:56:57 2013 -0500
 summary: Merge security fix for filtering tools from stable/next-stable.

 From the pasteur.log file,

 xxx.xxx.xxx.xxx - - [11/Nov/2013:12:04:45 +0100] POST
 /galaxy/admin/manage_users_and_groups_for_quota?id=7a72206f0ccffc2e
 HTTP/1.1 500 -
 http://xxx/galaxy/admin/manage_users_and_groups_for_quota?webapp=galaxyid=7a72206f0ccffc2e;
 Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9; rv:25.0) Gecko/20100101
 Firefox/25.0
 Error - type 'exceptions.AttributeError': 'NoQuotaAgent' object has
 no attribute 'set_entity_quota_associations'
 URL: 
 http://ppserver/galaxy/admin/manage_users_and_groups_for_quota?id=7a72206f0ccffc2e
 File '/mnt/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
 line 149 in __call__
   app_iter = self.application(environ, sr_checker)
 File 
 '/mnt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py',
 line 84 in __call__
   return self.application(environ, start_response)
 File 
 '/mnt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
 line 633 in __call__
   return self.application(environ, start_response)
 File '/mnt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
 132 in __call__
   return self.handle_request( environ, start_response )
 File '/mnt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
 190 in handle_request
   body = method( trans, **kwargs )
 File '/mnt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
 line 229 in decorator
   return func( self, trans, *args, **kwargs )
 File '/mnt/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin.py',
 line 531 in manage_users_and_groups_for_quota
   quota, params = self._quota_op( trans, 'quota_members_edit_button',
 self._manage_users_and_groups_for_quota, kwd )
 File '/mnt/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin.py',
 line 664 in _quota_op
   message = op_method( quota, params )
 File '/mnt/galaxy/galaxy-dist/lib/galaxy/actions/admin.py', line 80 in
 _manage_users_and_groups_for_quota
   self.app.quota_agent.set_entity_quota_associations( quotas=[ quota
 ], users=in_users, groups=in_groups )
 AttributeError: 'NoQuotaAgent' object has no attribute
 'set_entity_quota_associations'


 CGI Variables
 -
   CONTENT_LENGTH: '-1'
   CONTENT_TYPE: 'application/x-www-form-urlencoded'
   HTTP_ACCEPT: 
 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
   HTTP_ACCEPT_ENCODING: 'gzip, deflate'
   HTTP_ACCEPT_LANGUAGE: 'en-gb,en;q=0.7,en-us;q=0.3'
   HTTP_CONNECTION: 'Keep-Alive'
   HTTP_COOKIE: 
 'galaxysession=fed9265fae01dfd85c30fe1bbf5a988ae27edcb17a4961e7cef7bef77b0eeb9be91a902d5f0aacdf'
   HTTP_DNT: '1'
   HTTP_HOST: 'ppserver'
   HTTP_REFERER:
 'http://ppserver/galaxy/admin/manage_users_and_groups_for_quota?webapp=galaxyid=7a72206f0ccffc2e'
   HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9;
 rv:25.0) Gecko/20100101 Firefox/25.0'
   PATH_INFO: '/admin/manage_users_and_groups_for_quota'
   QUERY_STRING: 'id=7a72206f0ccffc2e'
   REMOTE_ADDR: '143.234.97.120'
   REQUEST_METHOD: 'POST'
   SCRIPT_NAME: '/galaxy'
   SERVER_NAME: 'xxx'
   SERVER_PORT: '8080'
   SERVER_PROTOCOL: 'HTTP/1.1'


 WSGI Variables
 --
   application: paste.recursive.RecursiveMiddleware object at 0x910c890
   is_api_request: False
   paste.cookies: (SimpleCookie:
 galaxysession='fed9265fae01dfd85c30fe1bbf5a988ae27edcb17a4961e7cef7bef77b0eeb9be91a902d5f0aacdf',
 'galaxysession=fed9265fae01dfd85c30fe1bbf5a988ae27edcb17a4961e7cef7bef77b0eeb9be91a902d5f0aacdf')
   paste.expected_exceptions: [class 'paste.httpexceptions.HTTPException']
   paste.httpexceptions: paste.httpexceptions.HTTPExceptionHandler
 object at 0x783fd50
   paste.httpserver.thread_pool: paste.httpserver.ThreadPool object at
 0x30eea90
   paste.parsed_querystring: ([('id', '7a72206f0ccffc2e')],
 'id=7a72206f0ccffc2e')
   paste.recursive.forward: paste.recursive.Forwarder from