[galaxy-dev] Galaxy reports crashing with the latest stable release
Hi, I encountered the following bug during my testing of the latest stable release: Error - type 'exceptions.AttributeError': 'SpecifiedDateListGrid' object has no attribute 'info_text' URL: http://galaxy.uni-freiburg.de:9001/jobs/specified_date_handler?specified_date=2014-06-04 File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/reports/controllers/jobs.py', line 177 in specified_date_handler return self.specified_date_list_grid( trans, **kwd ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 296 in __call__ message = message, File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1184 in fill_template def fill_template(self, filename, **kwargs): File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1199 in fill_template_mako template_lookup = template_lookup or self.webapp.mako_template_lookup File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ base.mako.py', line 66 in render_body __M_writer(unicode(next.body())) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 91 in render_body __M_writer(unicode(self.load())) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 120 in render_load __M_writer(unicode( h.to_json_string( self.get_grid_config( embedded=embedded, insert=insert ) ) )) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 193 in render_get_grid_config 'info_text' : grid.info_text, AttributeError: 'SpecifiedDateListGrid' object has no attribute 'info_text' Trello card is here: https://trello.com/c/EqQCAcIe Thanks, Bjoern ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy reports crashing with the latest stable release
I'm having trouble reproducing this. The base grid object that's used by the SpecifiedDateListGrid does have that info_text field -- it's almost as if you're somehow using an outdated grid module, while the rendering template is current. It's a bit brute force, but can you try (from the base of your galaxy directory) something like: find . -name '*.pyc' -delete and restart your reports app? On Wed, Jun 4, 2014 at 5:10 AM, bjoern.gruen...@googlemail.com bjoern.gruen...@gmail.com wrote: Hi, I encountered the following bug during my testing of the latest stable release: Error - type 'exceptions.AttributeError': 'SpecifiedDateListGrid' object has no attribute 'info_text' URL: http://galaxy.uni-freiburg.de:9001/jobs/specified_date_handler?specified_date=2014-06-04 File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/reports/controllers/jobs.py', line 177 in specified_date_handler return self.specified_date_list_grid( trans, **kwd ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 296 in __call__ message = message, File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1184 in fill_template def fill_template(self, filename, **kwargs): File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1199 in fill_template_mako template_lookup = template_lookup or self.webapp.mako_template_lookup File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ base.mako.py', line 66 in render_body __M_writer(unicode(next.body())) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 91 in render_body __M_writer(unicode(self.load())) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 120 in render_load __M_writer(unicode( h.to_json_string( self.get_grid_config( embedded=embedded, insert=insert ) ) )) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 193 in render_get_grid_config 'info_text' : grid.info_text, AttributeError: 'SpecifiedDateListGrid' object has no attribute 'info_text' Trello card is here: https://trello.com/c/EqQCAcIe Thanks, Bjoern ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy reports
Hi, We have recently updated our instance, I have noticed a bug display in the report page. In the section 'Jobs per Month', the month column does not contain any month name but number instead. Has anybody experienced the same thing ? Regards, Philip ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy reports
Hello Philip, the page you are talking about should look like this: https://www.dropbox.com/s/r97zvgl8a5h1u4z/Screenshot%202014-03-06%2017.07.52.png How does yours look like? Martin On Thu, Mar 6, 2014 at 4:43 PM, Philippe Moncuquet philippe.m...@gmail.comwrote: Hi, We have recently updated our instance, I have noticed a bug display in the report page. In the section 'Jobs per Month', the month column does not contain any month name but number instead. Has anybody experienced the same thing ? Regards, Philip ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy reports
Hi Martin, [image: Images intégrées 1] Cheers, Philip 2014-03-07 9:08 GMT+11:00 Martin Čech mar...@bx.psu.edu: Hello Philip, the page you are talking about should look like this: https://www.dropbox.com/s/r97zvgl8a5h1u4z/Screenshot%202014-03-06%2017.07.52.png How does yours look like? Martin On Thu, Mar 6, 2014 at 4:43 PM, Philippe Moncuquet philippe.m...@gmail.com wrote: Hi, We have recently updated our instance, I have noticed a bug display in the report page. In the section 'Jobs per Month', the month column does not contain any month name but number instead. Has anybody experienced the same thing ? Regards, Philip ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ inline: Report_screenshot.jpg___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy reports
Hi Philippe, I realised we hadn’t restarted the reports application after the upgrade. I’ve done that it seems to be working fine. Cheers. Steve McMahon Solution Architect and Senior System Administrator | Scientific Computing Information Management and Technology CSIRO T +61 2 6214 2968 Alt +61 4 0077 9318 steve.mcma...@csiro.aumailto:steve.mcma...@csiro.au | www.csiro.au 1 Wilf Crane Crescent, Yarralumla ACT 2600 PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email. From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Martin Cech Sent: Friday, 7 March 2014 9:09 AM To: Philippe Moncuquet Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy reports Hello Philip, the page you are talking about should look like this: https://www.dropbox.com/s/r97zvgl8a5h1u4z/Screenshot%202014-03-06%2017.07.52.png How does yours look like? Martin On Thu, Mar 6, 2014 at 4:43 PM, Philippe Moncuquet philippe.m...@gmail.commailto:philippe.m...@gmail.com wrote: Hi, We have recently updated our instance, I have noticed a bug display in the report page. In the section 'Jobs per Month', the month column does not contain any month name but number instead. Has anybody experienced the same thing ? Regards, Philip ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy reports
Awesome, I am glad it is working for you. Thank you for using Galaxy! regards Martin On Thu, Mar 6, 2014 at 5:18 PM, steve.mcma...@csiro.au wrote: Hi Philippe, I realised we hadn’t restarted the reports application after the upgrade. I’ve done that it seems to be working fine. Cheers. *Steve McMahon* Solution Architect and Senior System Administrator | Scientific Computing *Information Management and Technology* CSIRO T +61 2 6214 2968 Alt +61 4 0077 9318 steve.mcma...@csiro.au | www.csiro.au 1 Wilf Crane Crescent, Yarralumla ACT 2600 *PLEASE NOTE* The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. *Please consider the environment before printing this email.* *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto: galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Martin Cech *Sent:* Friday, 7 March 2014 9:09 AM *To:* Philippe Moncuquet *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] Galaxy reports Hello Philip, the page you are talking about should look like this: https://www.dropbox.com/s/r97zvgl8a5h1u4z/Screenshot%202014-03-06%2017.07.52.png How does yours look like? Martin On Thu, Mar 6, 2014 at 4:43 PM, Philippe Moncuquet philippe.m...@gmail.com wrote: Hi, We have recently updated our instance, I have noticed a bug display in the report page. In the section 'Jobs per Month', the month column does not contain any month name but number instead. Has anybody experienced the same thing ? Regards, Philip ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy Reports link - registed users per month - does not work
Hello,
First..I love the Galaxy Reports tool...thanks so much for this.
I did however come across an error when trying to few the Registered Users
per month link. It would be really nice to have this working :)
Thanks in advance,
Liisa
URL: http://domain:9001/users/registered_users_per_month
Module paste.exceptions.errormiddleware:144 in __call__
app_iter = self.application(environ, sr_checker)
Module paste.debug.prints:106 in __call__
environ, self.app)
Module paste.wsgilib:543 in intercept_output
app_iter = application(environ, replacement_start_response)
Module paste.lint:170 in lint_app
iterator = application(environ, start_response_wrapper)
Module paste.recursive:84 in __call__
return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
body = method( trans, **kwargs )
Module galaxy.webapps.reports.controllers.users:29 in
registered_users_per_month
for row in q.execute():
Module sqlalchemy.sql.expression:2841 in execute
Module sqlalchemy.engine.base:2453 in _execute_clauseelement
Module sqlalchemy.engine.base:1584 in _execute_clauseelement
Module sqlalchemy.engine.base:1698 in _execute_context
Module sqlalchemy.engine.base:1691 in _execute_context
Module sqlalchemy.engine.default:331 in do_execute
Module MySQLdb.cursors:173 in execute
Module MySQLdb.connections:36 in defaulterrorhandler
OperationalError: (OperationalError) (1305, 'FUNCTION
galaxy_production.date_trunc does not exist') 'SELECT date_trunc(%s,
date(galaxy_user.create_time)) AS date, count(galaxy_user.id) AS num_users
\nFROM galaxy_user GROUP BY date_trunc(%s, date(galaxy_user.create_time))
ORDER BY date DESC' ('month', 'month')
___
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Galaxy Reports link - registed users per month - does not work
Hi Liisa
This rings a bell
I assume you use a MYSQL database? and I guess other pages are broken as
well?
We are also using MySQL and I had to fix several lines in several files
in order to get all report pages to work.
To do the fixes, have a look at this old (but still valid) e-mail from
Assaf Gordon:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2009-August/000641.html
I can send you all my fixed files next week
Regards, Hans-Rudolf
On 01/17/2014 05:38 PM, Liisa Koski wrote:
Hello,
First..I love the Galaxy Reports tool...thanks so much for this.
I did however come across an error when trying to few the Registered
Users per month link. It would be really nice to have this working :)
Thanks in advance,
Liisa
URL: http://domain:9001/users/registered_users_per_month
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month
Module paste.exceptions.errormiddleware:*144* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#app_iter*=*
self*.*application*(*environ*,* sr_checker*)*
Module paste.debug.prints:*106* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#environ*,*
self*.*app*)*
Module paste.wsgilib:*543* in intercept_output_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#app_iter*=*
application*(*environ*,* replacement_start_response*)*
Module paste.lint:*170* in lint_app_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#iterator*=*
application*(*environ*,* start_response_wrapper*)*
Module paste.recursive:*84* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#*return*self*.*application*(*environ*,*
start_response*)*
Module paste.httpexceptions:*633* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#*return*self*.*application*(*environ*,*
start_response*)*
Module galaxy.web.framework.base:*132* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#*return*self*.*handle_request*(*
environ*,* start_response*)*
Module galaxy.web.framework.base:*190* in handle_request_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#body*=*
method*(* trans*,* kwargs*)*
Module galaxy.webapps.reports.controllers.users:*29* in
registered_users_per_month_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#*for*row*in*q*.*execute*():*
Module sqlalchemy.sql.expression:*2841* in execute
Module sqlalchemy.engine.base:*2453* in _execute_clauseelement
Module sqlalchemy.engine.base:*1584* in _execute_clauseelement
Module sqlalchemy.engine.base:*1698* in _execute_context
Module sqlalchemy.engine.base:*1691* in _execute_context
Module sqlalchemy.engine.default:*331* in do_execute
Module MySQLdb.cursors:*173* in execute
Module MySQLdb.connections:*36* in defaulterrorhandler*
OperationalError: (OperationalError) (1305, 'FUNCTION
galaxy_production.date_trunc does not exist') 'SELECT date_trunc(%s,
date(galaxy_user.create_time)) AS date, count(galaxy_user.id) AS
num_users \nFROM galaxy_user GROUP BY date_trunc(%s,
date(galaxy_user.create_time)) ORDER BY date DESC' ('month', 'month')*
___
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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___
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:
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Galaxy Reports
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Well! This is the first I've heard of a Galaxy Reports page. Too bad I
already re-invented the wheel because I hadn't ever heard of this tool...
Anyway, since run_reports.sh was only mentioned once anywhere in the
wiki (according to search, in a DevNewsBrief from 2008), I've added a
wiki page for the report tool.
Please add whatever information you all feel I've left out.
https://wiki.galaxyproject.org/Admin/Usage%20Reports
Cheers,
Eric Rasche
On 01/17/2014 10:38 AM, Liisa Koski wrote:
Hello,
First..I love the Galaxy Reports tool...thanks so much for this.
I did however come across an error when trying to few the Registered
Users per month link. It would be really nice to have this working :)
Thanks in advance,
Liisa
URL: http://domain:9001/users/registered_users_per_month
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month
Module paste.exceptions.errormiddleware:*144* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#app_iter*=*
self*.*application*(*environ*,* sr_checker*)*
Module paste.debug.prints:*106* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#environ*,*
self*.*app*)*
Module paste.wsgilib:*543* in intercept_output_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#app_iter*=*
application*(*environ*,* replacement_start_response*)*
Module paste.lint:*170* in lint_app_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#iterator*=*
application*(*environ*,* start_response_wrapper*)*
Module paste.recursive:*84* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#*return*self*.*application*(*environ*,*
start_response*)*
Module paste.httpexceptions:*633* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#*return*self*.*application*(*environ*,*
start_response*)*
Module galaxy.web.framework.base:*132* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#*return*self*.*handle_request*(*
environ*,* start_response*)*
Module galaxy.web.framework.base:*190* in handle_request_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#body*=*
method*(* trans*,* kwargs*)*
Module galaxy.webapps.reports.controllers.users:*29* in
registered_users_per_month_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#*for*row*in*q*.*execute*():*
Module sqlalchemy.sql.expression:*2841* in execute
Module sqlalchemy.engine.base:*2453* in _execute_clauseelement
Module sqlalchemy.engine.base:*1584* in _execute_clauseelement
Module sqlalchemy.engine.base:*1698* in _execute_context
Module sqlalchemy.engine.base:*1691* in _execute_context
Module sqlalchemy.engine.default:*331* in do_execute
Module MySQLdb.cursors:*173* in execute
Module MySQLdb.connections:*36* in defaulterrorhandler*
OperationalError: (OperationalError) (1305, 'FUNCTION
galaxy_production.date_trunc does not exist') 'SELECT date_trunc(%s,
date(galaxy_user.create_time)) AS date, count(galaxy_user.id) AS
num_users \nFROM galaxy_user GROUP BY date_trunc(%s,
date(galaxy_user.create_time)) ORDER BY date DESC' ('month', 'month')*
___
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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] Galaxy Reports
Thank you Eric for the wiki page.
I agree that Galaxy Reports are not visible enough and this might help.
Martin, Galaxy Team
On Fri, Jan 17, 2014 at 12:29 PM, Eric Rasche rasche.e...@yandex.ru wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Well! This is the first I've heard of a Galaxy Reports page. Too bad I
already re-invented the wheel because I hadn't ever heard of this tool...
Anyway, since run_reports.sh was only mentioned once anywhere in the
wiki (according to search, in a DevNewsBrief from 2008), I've added a
wiki page for the report tool.
Please add whatever information you all feel I've left out.
https://wiki.galaxyproject.org/Admin/Usage%20Reports
Cheers,
Eric Rasche
On 01/17/2014 10:38 AM, Liisa Koski wrote:
Hello,
First..I love the Galaxy Reports tool...thanks so much for this.
I did however come across an error when trying to few the Registered
Users per month link. It would be really nice to have this working :)
Thanks in advance,
Liisa
URL: http://domain:9001/users/registered_users_per_month
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month
Module paste.exceptions.errormiddleware:*144* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
app_iter*=*
self*.*application*(*environ*,* sr_checker*)*
Module paste.debug.prints:*106* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
environ*,*
self*.*app*)*
Module paste.wsgilib:*543* in intercept_output_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
app_iter*=*
application*(*environ*,* replacement_start_response*)*
Module paste.lint:*170* in lint_app_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
iterator*=*
application*(*environ*,* start_response_wrapper*)*
Module paste.recursive:*84* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
*return*self*.*application*(*environ*,*
start_response*)*
Module paste.httpexceptions:*633* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
*return*self*.*application*(*environ*,*
start_response*)*
Module galaxy.web.framework.base:*132* in __call___
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
*return*self*.*handle_request*(*
environ*,* start_response*)*
Module galaxy.web.framework.base:*190* in handle_request_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
body*=*
method*(* trans*,* kwargs*)*
Module galaxy.webapps.reports.controllers.users:*29* in
registered_users_per_month_
__ _
http://martin.dnalandmarks.ca:9001/users/registered_users_per_month#
*for*row*in*q*.*execute*():*
Module sqlalchemy.sql.expression:*2841* in execute
Module sqlalchemy.engine.base:*2453* in _execute_clauseelement
Module sqlalchemy.engine.base:*1584* in _execute_clauseelement
Module sqlalchemy.engine.base:*1698* in _execute_context
Module sqlalchemy.engine.base:*1691* in _execute_context
Module sqlalchemy.engine.default:*331* in do_execute
Module MySQLdb.cursors:*173* in execute
Module MySQLdb.connections:*36* in defaulterrorhandler*
OperationalError: (OperationalError) (1305, 'FUNCTION
galaxy_production.date_trunc does not exist') 'SELECT date_trunc(%s,
date(galaxy_user.create_time)) AS date, count(galaxy_user.id) AS
num_users \nFROM galaxy_user GROUP BY date_trunc(%s,
date(galaxy_user.create_time)) ORDER BY date DESC' ('month', 'month')*
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[galaxy-dev] Galaxy Reports: 'unfinished jobs' seems not to do the job
Hi all, I make increasingly use of the Galaxy Reports tool. Until recently I started it and shut it down again. Now I run it continuously. I have noticed that a lot of the jobs listed in 'unfinished jobs' are actually finished. Any hint on how to clean up the database? Which table? Perhaps I can make a Trello card: 'Provide a button to remove the jobs from the unfinished jobs page' ? Thanks for taking me further, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy Reports: 'unfinished jobs' seems not to do the job
Hi Joachim I make increasingly use of the Galaxy Reports tool. Until recently I started it and shut it down again. Now I run it continuously. I have noticed that a lot of the jobs listed in 'unfinished jobs' are actually finished. Any hint on how to clean up the database? Which table? Perhaps I can make a Trello card: 'Provide a button to remove the jobs from the unfinished jobs page' ? Well, you can modify the entries in the 'job' table.As always, be very careful when you directly access the MySQL or PostgreSQL database. In your case I would set the state to 'error', eg: update job set state='error' where id=123456789; Once again be careful. I would examine each job individually. And try to figure out, why you consider the job as being finished, and Galaxy thinks the job is still running Regards, Hans-Rudolf Thanks for taking me further, Joachim ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy Reports: 'unfinished jobs' seems not to do the job
Hi Hans, OK, thanks: diving into the job table. Your question: why you consider the job as being finished, and Galaxy thinks the job is still running is the core issue that I need to find out. None of those jobs have entries in the ps list. Currently, I think that those jobs are still listed because they were not nicely shut down by Galaxy, but because of a crash (e.g. of the virtual machine). Upon restarting Galaxy, Galaxy seems not to check whether those jobs are currently running, but seems to depend entirely on the job table to fill the 'unfinished jobs' table. Cheers, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 03/07/2013 11:21 AM, Hans-Rudolf Hotz wrote: Hi Joachim I make increasingly use of the Galaxy Reports tool. Until recently I started it and shut it down again. Now I run it continuously. I have noticed that a lot of the jobs listed in 'unfinished jobs' are actually finished. Any hint on how to clean up the database? Which table? Perhaps I can make a Trello card: 'Provide a button to remove the jobs from the unfinished jobs page' ? Well, you can modify the entries in the 'job' table.As always, be very careful when you directly access the MySQL or PostgreSQL database. In your case I would set the state to 'error', eg: update job set state='error' where id=123456789; Once again be careful. I would examine each job individually. And try to figure out, why you consider the job as being finished, and Galaxy thinks the job is still running Regards, Hans-Rudolf Thanks for taking me further, Joachim ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy Reports no longer functions
Hi Iry The last but one line: socket.error: [Errno 98] Address already in use holds probably the clue. Looks like something else is running on the same port or you didn't stop the reports server before restarting it (after the upgrade) Regards, Hans On 08/17/2012 11:08 PM, Iry Witham wrote: Hi Team, Since I upgraded to the latest galaxy-dist I can no longer get the reports interface to function. When I go to galaxy:9001 I get the following server error: An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). The reports_webapp.log is as follows: python path is: /hpcdata/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip, /usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages/Numeric, /usr/lib64/python2.6/site-packages/gtk-2.0, /usr/local/lib64/python2.6/site-packages galaxy.model.custom_types DEBUG 2012-08-07 17:13:53,219 psycopg2 egg successfully loaded for postgres dialect galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,792 Enabling 'users' controller, class: Users galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,815 Enabling 'system' controller, class: System galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,909 Enabling 'sample_tracking' controller, class: SampleTracking galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,922 Enabling 'jobs' controller, class: Jobs galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,942 Enabling 'workflows' controller, class: Workflows galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,947 Enabling 'root' controller, class: Report galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,950 Enabling 'httpexceptions' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,971 Enabling 'recursive' middleware /hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/serial_number_generator.py:11: DeprecationWarning: the md5 module is deprecated; use hashlib instead import md5 galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,708 Enabling 'error' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,749 Enabling 'trans logger' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,750 Enabling 'config' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,888 Enabling 'x-forwarded-host' middleware Starting server in PID 6345. Traceback (most recent call last): File ./scripts/paster.py, line 34, in module command.run() File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 123, in invoke exit_code = runner.run(args) File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 218, in run result = self.command() File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 303, in command serve() File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 287, in serve server(app) File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 151, in server_wrapper **context.local_conf) File
[galaxy-dev] Galaxy Reports no longer functions
Hi Team, Since I upgraded to the latest galaxy-dist I can no longer get the reports interface to function. When I go to galaxy:9001 I get the following server error: An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). The reports_webapp.log is as follows: python path is: /hpcdata/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /hpcdata/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip, /usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages/Numeric, /usr/lib64/python2.6/site-packages/gtk-2.0, /usr/local/lib64/python2.6/site-packages galaxy.model.custom_types DEBUG 2012-08-07 17:13:53,219 psycopg2 egg successfully loaded for postgres dialect galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,792 Enabling 'users' controller, class: Users galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,815 Enabling 'system' controller, class: System galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,909 Enabling 'sample_tracking' controller, class: SampleTracking galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,922 Enabling 'jobs' controller, class: Jobs galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,942 Enabling 'workflows' controller, class: Workflows galaxy.web.framework.base DEBUG 2012-08-07 17:13:59,947 Enabling 'root' controller, class: Report galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,950 Enabling 'httpexceptions' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:13:59,971 Enabling 'recursive' middleware /hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/serial_number_generator.py:11: DeprecationWarning: the md5 module is deprecated; use hashlib instead import md5 galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,708 Enabling 'error' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,749 Enabling 'trans logger' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,750 Enabling 'config' middleware galaxy.webapps.reports.buildapp DEBUG 2012-08-07 17:14:00,888 Enabling 'x-forwarded-host' middleware Starting server in PID 6345. Traceback (most recent call last): File ./scripts/paster.py, line 34, in module command.run() File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 123, in invoke exit_code = runner.run(args) File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py, line 218, in run result = self.command() File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 303, in command serve() File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py, line 287, in serve server(app) File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py, line 151, in server_wrapper **context.local_conf) File /hpcdata/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/util/fixtypeerror.py, line 57, in fix_call val = callable(*args, **kw) File /hpcdata/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 1314, in server_runner
