search

geneontology / go-site

A collection of metadata, tools, and files associated with the Gene Ontology public web presence.
http://geneontology.org
BSD 3-Clause "New" or "Revised" License
46 stars 89 forks source link

Term Enrichment tool error with viewer for originating resource. #55

Closed monicacecilia closed 9 years ago

monicacecilia commented 9 years ago

When using the Term Enrichment tool at http://amigo.geneontology.org/rte

When entering a list of genes to analyze, if the user chooses the option "Originating Resource" from the "Results Viewer" menu, as seen in the first figure, a server error is reported. ("The server encountered an internal error and was unable to complete your request. Error message: Premature end of script headers: rte If you think this is a server error, please contact the webmaster.").

screen shot 2015-03-20 at 11 51 00 am

screen shot 2015-03-20 at 11 50 53 am

kltm commented 9 years ago

Huh. Something generally seems to be very wrong as I now no longer get a results page either, but rather a form that doesn't seem to work. I'm adding @mugitty for comment.

kltm commented 9 years ago

Also pinging on @cmungall, I'm still trying to figure out if this is upstream or not. There is at least some upstream component since I don't seem to be able to contact the server in some cases. As well, directly trying the URL:

http://pantherdb.org/webservices/go/overrep.jsp?ontology=biological_process&input=P31946%0AP62258%0AQ04917%0AP61981%0AP31947%0Abaxter%0AP27348%0AP63104%0AQ96QU6%0AQ8NCW5&species=HUMAN&correction=bonferroni&format=html

Takes me to a page with a submit button that is unresponsive, rather than results:

panther-te

kltm commented 9 years ago

One consistent issue I seem to be able to reproduce is that the previous test URL always seems to go to an unresponsive form page (above):

http://pantherdb.org/webservices/go/overrep.jsp?ontology=biological_process&input=P31946%0AP62258%0AQ04917%0AP61981%0AP31947%0Abaxter%0AP27348%0AP63104%0AQ96QU6%0AQ8NCW5&species=HUMAN&correction=bonferroni&format=html

kltm commented 9 years ago

I believe the 500 error comes from production using a branch that doesn't have the fix from geneontology/amigo#171. I've added a fix to 2.1.x and will see if they can get that out.

I believe that this means that the only remaining issue is the (unresponsive) interstitial form.

mugitty commented 9 years ago

Unresponsive interstitial form has been fixed.

monicacecilia commented 9 years ago

Thank you @kltm :+1: @mugitty Until the 500 error has been cleared (visible until the change is pushed), I think this issue should remain as "Open". thanks for fixing the other form! :+1:

kltm commented 9 years ago

I've added unit tests to AmiGO to cover both labs and production TE situations. I'll tests in a bit to check the actual return data.

Since the upstream issue has been cleared, any further problems are AmiGO's. I've reopened the relevant ticket there: geneontology/amigo#171

Production is currently looking to get a hotfix out (and then maybe clean it permanently with the release of 2.2.x).