Data library fails to display contents
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. 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*
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*
___________________________________________________________ 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:
participants (2)
-
Nate Coraor -
W. Augustine Dunn III