W. Augustine Dunn III wrote:
> I am starting to really get the hang of customizing my new galaxy instance,
> and please just let me THANK YOU GUYS!
> 
> However, I am also running into a problem.  I am trying to link genome fasta
> files that i obtained through metazoa.ensembl.org.  I created a library
> called "Genome Sequences" with sub-folders to house them.  Everything was
> going fine until I tried to change the info on a couple so that they were
> fasta not so other randomly autoassigned type.
> 
> Now I get this error msg when ever i try to browse ANY of the "Genome Seq"
> Library:
> 
> Error attempting to display contents of library (Genome Sequences):
> 'NoneType' object has no attribute 'dataset'.
> 
> I am running this instance using a postgresql backend but the default paste
> web-server since its mostly gonna me me and one or two other lab-mates using
> it.
> 
> I can NOT figure out whats up.

Hi Gus,

Sorry for the delay in response.  If you're still experiencing this
problem, I have a couple ideas.

It looks like somehow you've gotten a LibraryDataset or
LibraryDatasetDatasetAssociation that is not properly associated,
possibly due to an unhandled exception when you were populating the
library.  If this is the case, it's certainly a bug, but may be
difficult to track down.

Could you check the contents of your database for the following:

select * from library_dataset_dataset_association where library_dataset_id is 
null;
select * from library_dataset where library_dataset_dataset_association_id is 
null;

Thanks,
--nate

> 
> Relevant excerpt of Server log follows:
> xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:03 -0700] "GET / HTTP/1.1" 200 -
> "http://xxx.xxx.xxx.xxx/library"; "Mozilla/5.0 (X11; Linux x86_64)
> AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30"
> xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:04 -0700] "GET /root/tool_menu
> HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/"; "Mozilla/5.0 (X11; Linux x86_64)
> AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30"
> xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:04 -0700] "GET /history HTTP/1.1" 200
> - "http://xxx.xxx.xxx.xxx/"; "Mozilla/5.0 (X11; Linux x86_64)
> AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30"
> xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:07 -0700] "GET /admin HTTP/1.1" 200 -
> "http://vlad.bio.uci.edu:8081/"; "Mozilla/5.0 (X11; Linux x86_64)
> AppleWebKit/534.30 (KHTML, like Gecko) Chrome/12.0.742.112 Safari/534.30"
> xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:07 -0700] "GET
> /admin/center?webapp=galaxy HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/admin";
> "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko)
> Chrome/12.0.742.112 Safari/534.30"
> xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:10 -0700] "GET
> /library_admin/browse_libraries HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/admin";
> "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko)
> Chrome/12.0.742.112 Safari/534.30"
> xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET
> /library_admin/browse_libraries?f-deleted=False&f-name=All&f-description=All&sort=name&show_item_checkboxes=false&async=false&page=1&webapp=galaxy&operation=browse&id=9a8774fee61dd122&
> HTTP/1.1" 302 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries";
> "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko)
> Chrome/12.0.742.112 Safari/534.30"
> xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET
> /library_common/browse_library?sort=name&operation=browse&f-description=All&f-name=All&f-deleted=False&cntrller=library_admin&async=false&show_item_checkboxes=false&webapp=galaxy&id=9a8774fee61dd122&page=1
> HTTP/1.1" 302 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries";
> "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko)
> Chrome/12.0.742.112 Safari/534.30"
> xxx.xxx.xxx.xxx - - [10/Jul/2011:13:31:12 -0700] "GET
> /library_admin/browse_libraries?status=error&use_panels=False&message=Error+attempting+to+display+contents+of+library+%28Genome+Sequences%29%3A+__sq__NoneType__sq__+object+has+no+attribute+__sq__dataset__sq__.
> HTTP/1.1" 200 - "http://xxx.xxx.xxx.xxx/library_admin/browse_libraries";
> "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/534.30 (KHTML, like Gecko)
> Chrome/12.0.742.112 Safari/534.30"
> 
> 
> Thanks in advance!  And thanks for this priceless tool!
> 
> Gus
> 
> -- 
> In science, "fact" can only mean "confirmed to such a degree that it would
> be perverse to withhold provisional assent." I suppose that apples might
> start to rise tomorrow, but the possibility does not merit equal time in
> physics classrooms.
> *-Stephen Jay Gould*

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