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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