Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] [BioPortal] Feedback from brycemecum

Jennifer Leigh Vendetti vendetti at
Wed Apr 5 17:23:57 PDT 2017

Hi again Bryce,

I did a bit more digging and found the occurrence of the 500 error in our production log files:

I, [2017-04-05T10:47:07.646950 #21412]  INFO -- : Completed 500 Internal Server Error in 60274ms (ActiveRecord: 0.0ms)
F, [2017-04-05T10:47:07.649109 #21412] FATAL -- :
Faraday::TimeoutError (read timeout reached):
  app/controllers/ontologies_controller.rb:398:in `update'

I, [2017-04-05T10:47:07.650174 #21412]  INFO -- : Processing by ErrorsController#internal_server_error as HTML
I, [2017-04-05T10:47:07.650307 #21412]  INFO -- :   Parameters: {"utf8"=>"✓", "authenticity_token"=>"", "ontology"=>{"name"=>"The Ecosystem Ontology", "administeredBy"=>["", "", "", ""], "viewingRestriction"=>"public", "acl"=>["", "", "", "", "", ""], "hasDomain"=>["", "", ""], "isView"=>"0", "subscribe_notifications"=>"1"}, "commit"=>"Save ontology", "id"=>"ECSO"}
I, [2017-04-05T10:47:07.655224 #21412]  INFO -- :   Rendered errors/internal_server_error.html.erb within layouts/ontology (2.0ms)
I, [2017-04-05T10:47:07.658264 #21412]  INFO -- :   Rendered layouts/_topnav.html.haml (1.8ms)
I, [2017-04-05T10:47:07.658598 #21412]  INFO -- :   Rendered layouts/_notices.html.erb (0.2ms)
I, [2017-04-05T10:47:07.658686 #21412]  INFO -- :   Rendered layouts/_header.html.erb (3.2ms)
I, [2017-04-05T10:47:07.659514 #21412]  INFO -- :   Rendered layouts/_footer.html.erb (0.7ms)
I, [2017-04-05T10:47:07.659725 #21412]  INFO -- : Completed 500 Internal Server Error in 9ms (Views: 7.5ms | ActiveRecord: 0.0ms)

It looks like a read timeout occurred when you tried to update your ontology.  Since I’m not able to reproduce this behavior, I went ahead and entered an issue in our GitHub tracker:

We’ll need to do some investigation with regard to why these timeouts may occasionally occur.

Perhaps more than you wanted to know.  :)

Kind regards,

> On Apr 5, 2017, at 4:14 PM, Jennifer Leigh Vendetti <vendetti at> wrote:
> Hi Bryce,
>> On Apr 5, 2017, at 11:40 AM, Bryce Mecum <mecum at> wrote:
>> Hey Jennifer, thanks for getting back. The account I'm trying to remove is ‘leinfelder'
> I looked at ECSO just now.  The ‘leinfelder’ account is no longer an administrator.  I tried adding and removing my own user account, as well as “schild” a couple of times, and I haven’t been able to reproduce the 500 error you saw earlier.
> I’ll keep an eye out for this behavior in the hope that we can track down a reliably reproducible case for debugging purposes.
> Apologies for the inconvenience.
> Kind regards,
> Jennifer
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at

More information about the bioontology-support mailing list