Re: [galaxy-dev] Error in Galaxy Reports

[Nikos Sidiropoulos]

Thanks so much Martin!


2014-02-14 19:32 GMT+01:00 Martin Čech :

> Hi,
>
> this has been resolved in galaxy-central repo (not dist). You can apply
> the patch manualy, it is less than one-liner.
>
>
> https://bitbucket.org/galaxy/galaxy-central/commits/3691fd3e12ef8160ae993cef5ebd51ddeee95da1
>
> Martin
>
>
> On Fri, Feb 14, 2014 at 1:28 PM, Nikos Sidiropoulos <
> nikos.sid...@gmail.com> wrote:
>
>> Hi Sam,
>>
>> thank you for the quick reply but I can't seem to find the revision, or
>> maybe don't know how to pull it.
>>
>> I tried to check galaxy-dist on BitBucket but couldn't find any updates
>> related to Galaxy Reports.
>>
>> Bests,
>> Nikos
>>
>>
>> 2014-02-13 17:35 GMT+01:00 sam guerler :
>>
>> Hi Nikos,
>>>
>>> Thank you so much for your report. This issue should be fixed now.
>>> Please update your revision and try again.
>>>
>>> Thanks,
>>> Sam
>>>
>>>
>>> On Thu, Feb 13, 2014 at 7:52 AM, Nikos Sidiropoulos <
>>> nikos.sid...@gmail.com> wrote:
>>>
 Hi all,

 after the February 2014 galaxy update I'm experiencing errors in Galaxy
 Reports.

 It only occurs when I'm trying to see which jobs were ran at a specific
 date (e.g. I can see how many jobs were ran today, but when I click on the
 number to see which ones it returns the following error):

 URL:
 http://localhost:9001/jobs/specified_date_handler?webapp=reports&specified_date=2014-02-13
 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.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.jobs:*177* in
 specified_date_handler
 >>  
 >> 
 *return* self*.*specified_date_list_grid*(* trans*,* kwd *)*
 Module galaxy.web.framework.helpers.grids:*296* in __call__
 >>  
 >> 
 kwargs*=*kwargs *)*
 Module galaxy.web.framework:*1184* in fill_template
 >>  
 >> 
 *return* self*.*fill_template_mako*(* filename*,* kwargs *)*
 Module galaxy.web.framework:*1199* in fill_template_mako
 >>  
 >> 
 *return* template*.*render*(* data *)*
 Module mako.template:*296* in render
 >>  
 >> 
 *return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data
 *)*
 Module mako.runtime:*660* in _render
 >>  
 >> 
 _kwargs_for_callable*(*callable_*,* data*)**)*
 Module mako.runtime:*692* in _render_context
 >>  
 >> 
 _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*
 kwargs*)*
 Module mako.runtime:*718* in _exec_template
 >>  
 >> 
 callable_*(*context*,* ***args*,* kwargs*)*
 Module _base_mako:*45* in render_body
 >>  
 >> 
 _

Re: [galaxy-dev] Error in Galaxy Reports

[Martin Čech]

Hi,

this has been resolved in galaxy-central repo (not dist). You can apply the
patch manualy, it is less than one-liner.

https://bitbucket.org/galaxy/galaxy-central/commits/3691fd3e12ef8160ae993cef5ebd51ddeee95da1

Martin


On Fri, Feb 14, 2014 at 1:28 PM, Nikos Sidiropoulos
wrote:

> Hi Sam,
>
> thank you for the quick reply but I can't seem to find the revision, or
> maybe don't know how to pull it.
>
> I tried to check galaxy-dist on BitBucket but couldn't find any updates
> related to Galaxy Reports.
>
> Bests,
> Nikos
>
>
> 2014-02-13 17:35 GMT+01:00 sam guerler :
>
> Hi Nikos,
>>
>> Thank you so much for your report. This issue should be fixed now. Please
>> update your revision and try again.
>>
>> Thanks,
>> Sam
>>
>>
>> On Thu, Feb 13, 2014 at 7:52 AM, Nikos Sidiropoulos <
>> nikos.sid...@gmail.com> wrote:
>>
>>> Hi all,
>>>
>>> after the February 2014 galaxy update I'm experiencing errors in Galaxy
>>> Reports.
>>>
>>> It only occurs when I'm trying to see which jobs were ran at a specific
>>> date (e.g. I can see how many jobs were ran today, but when I click on the
>>> number to see which ones it returns the following error):
>>>
>>> URL:
>>> http://localhost:9001/jobs/specified_date_handler?webapp=reports&specified_date=2014-02-13
>>> 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.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.jobs:*177* in
>>> specified_date_handler
>>> >>  
>>> >> 
>>> *return* self*.*specified_date_list_grid*(* trans*,* kwd *)*
>>> Module galaxy.web.framework.helpers.grids:*296* in __call__
>>> >>  
>>> >> 
>>> kwargs*=*kwargs *)*
>>> Module galaxy.web.framework:*1184* in fill_template
>>> >>  
>>> >> 
>>> *return* self*.*fill_template_mako*(* filename*,* kwargs *)*
>>> Module galaxy.web.framework:*1199* in fill_template_mako
>>> >>  
>>> >> 
>>> *return* template*.*render*(* data *)*
>>> Module mako.template:*296* in render
>>> >>  
>>> >> 
>>> *return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)*
>>> Module mako.runtime:*660* in _render
>>> >>  
>>> >> 
>>> _kwargs_for_callable*(*callable_*,* data*)**)*
>>> Module mako.runtime:*692* in _render_context
>>> >>  
>>> >> 
>>> _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs
>>> *)*
>>> Module mako.runtime:*718* in _exec_template
>>> >>  
>>> >> 
>>> callable_*(*context*,* ***args*,* kwargs*)*
>>> Module _base_mako:*45* in render_body
>>> >>  
>>> >> 
>>> __M_writer*(*unicode*(*next*.*body*(**)**)**)*
>>> Module _grid_base_mako:*134* in render_body
>>> >>  
>>> >> 
>>> __M_writer*(*uni

Re: [galaxy-dev] Error in Galaxy Reports

[Nikos Sidiropoulos]

Hi Sam,

thank you for the quick reply but I can't seem to find the revision, or
maybe don't know how to pull it.

I tried to check galaxy-dist on BitBucket but couldn't find any updates
related to Galaxy Reports.

Bests,
Nikos


2014-02-13 17:35 GMT+01:00 sam guerler :

> Hi Nikos,
>
> Thank you so much for your report. This issue should be fixed now. Please
> update your revision and try again.
>
> Thanks,
> Sam
>
>
> On Thu, Feb 13, 2014 at 7:52 AM, Nikos Sidiropoulos <
> nikos.sid...@gmail.com> wrote:
>
>> Hi all,
>>
>> after the February 2014 galaxy update I'm experiencing errors in Galaxy
>> Reports.
>>
>> It only occurs when I'm trying to see which jobs were ran at a specific
>> date (e.g. I can see how many jobs were ran today, but when I click on the
>> number to see which ones it returns the following error):
>>
>> URL:
>> http://localhost:9001/jobs/specified_date_handler?webapp=reports&specified_date=2014-02-13
>> 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.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.jobs:*177* in
>> specified_date_handler
>> >>  
>> >> 
>> *return* self*.*specified_date_list_grid*(* trans*,* kwd *)*
>> Module galaxy.web.framework.helpers.grids:*296* in __call__
>> >>  
>> >> 
>> kwargs*=*kwargs *)*
>> Module galaxy.web.framework:*1184* in fill_template
>> >>  
>> >> 
>> *return* self*.*fill_template_mako*(* filename*,* kwargs *)*
>> Module galaxy.web.framework:*1199* in fill_template_mako
>> >>  
>> >> 
>> *return* template*.*render*(* data *)*
>> Module mako.template:*296* in render
>> >>  
>> >> 
>> *return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)*
>> Module mako.runtime:*660* in _render
>> >>  
>> >> 
>> _kwargs_for_callable*(*callable_*,* data*)**)*
>> Module mako.runtime:*692* in _render_context
>> >>  
>> >> 
>> _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs
>> *)*
>> Module mako.runtime:*718* in _exec_template
>> >>  
>> >> 
>> callable_*(*context*,* ***args*,* kwargs*)*
>> Module _base_mako:*45* in render_body
>> >>  
>> >> 
>> __M_writer*(*unicode*(*next*.*body*(**)**)**)*
>> Module _grid_base_mako:*134* in render_body
>> >>  
>> >> 
>> __M_writer*(*unicode*(*self*.*load*(**)**)**)*
>> Module _grid_base_mako:*108* in render_load
>> >>  
>> >> 
>> self*.*grid_javascripts*(**)*
>> Module _grid_base_mako:*517* in render_grid_javascripts
>> >>  
>> >> 
>> __M_writer*(

Re: [galaxy-dev] Error in Galaxy Reports

[sam guerler]

Hi Nikos,

Thank you so much for your report. This issue should be fixed now. Please
update your revision and try again.

Thanks,
Sam


On Thu, Feb 13, 2014 at 7:52 AM, Nikos Sidiropoulos
wrote:

> Hi all,
>
> after the February 2014 galaxy update I'm experiencing errors in Galaxy
> Reports.
>
> It only occurs when I'm trying to see which jobs were ran at a specific
> date (e.g. I can see how many jobs were ran today, but when I click on the
> number to see which ones it returns the following error):
>
> URL:
> http://localhost:9001/jobs/specified_date_handler?webapp=reports&specified_date=2014-02-13
> 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.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.jobs:*177* in
> specified_date_handler
> >>  
> >> 
> *return* self*.*specified_date_list_grid*(* trans*,* kwd *)*
> Module galaxy.web.framework.helpers.grids:*296* in __call__
> >>  
> >> 
> kwargs*=*kwargs *)*
> Module galaxy.web.framework:*1184* in fill_template
> >>  
> >> 
> *return* self*.*fill_template_mako*(* filename*,* kwargs *)*
> Module galaxy.web.framework:*1199* in fill_template_mako
> >>  
> >> 
> *return* template*.*render*(* data *)*
> Module mako.template:*296* in render
> >>  
> >> 
> *return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)*
> Module mako.runtime:*660* in _render
> >>  
> >> 
> _kwargs_for_callable*(*callable_*,* data*)**)*
> Module mako.runtime:*692* in _render_context
> >>  
> >> 
> _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs
> *)*
> Module mako.runtime:*718* in _exec_template
> >>  
> >> 
> callable_*(*context*,* ***args*,* kwargs*)*
> Module _base_mako:*45* in render_body
> >>  
> >> 
> __M_writer*(*unicode*(*next*.*body*(**)**)**)*
> Module _grid_base_mako:*134* in render_body
> >>  
> >> 
> __M_writer*(*unicode*(*self*.*load*(**)**)**)*
> Module _grid_base_mako:*108* in render_load
> >>  
> >> 
> self*.*grid_javascripts*(**)*
> Module _grid_base_mako:*517* in render_grid_javascripts
> >>  
> >> 
> __M_writer*(*unicode*(*h*.*to_json_string*(*self*.*grid_config*)**)**)*
> Module json:*231* in dumps
> >>  
> >> 
> *return* _default_encoder*.*encode*(*obj*)*
> Module json.encoder:*200* in encode
> >>  
> >> 
> chunks *=* self*.*i