oor-dev
[Top] [All Lists]

Re: [oor-dev] BioPortal Ontology upload errors

To: OpenOntologyRepository-development <oor-dev@xxxxxxxxxxxxxxxx>
From: Paul R Alexander <palexander@xxxxxxxxxxxx>
Date: Fri, 15 Jan 2010 18:23:19 -0800
Message-id: <4B512317.2050904@xxxxxxxxxxxx>
I'm assuming that not all uploads are broken? It seems as though OOR has some ontologies hosted already, were those submitted via the UI?

There's a few things to consider here. First, upload size limits:
  • BioPortal UI restricts uploads to 20MB unless the user is an admin (no limit). This can be changed here:
    • File: app/controllers/ontologies_controller.rb
    • Code: if params[:isRemote].to_i.eql?(0) && params[:filePath].size.to_i > 20000000 && !session[:user].admin?
      • Change the 20000000 to your desired limit
  • Tomcat's default upload size limit is 2MB. This can be changed here:
This will likely fix problems related to the following errors:
NoMethodError in OntologiesController#create

undefined method `io' for #<REXML::ParseException:0x2b52c5ef1d50>
RAILS_ROOT: /usr/local/bioportal/bioportalui_oor

lib/BioPortalRestfulCore.rb:545:in `createOntology'

The ActiveRecord errors are associated with a missing table, I believe. Please try running the following from the Rails app root directory:
rake db:schema:load
WARNING: This is destructive and will wipe out any UI-related data (mappings, notes, etc) as it creates all of the necessary tables. You should backup the data and re-import it after the process is complete.

On 1/14/10 6:55 PM, Tejas Parikh wrote:
Yavuz was trying to upload ontologies on OOR sandbox
(oor-01f.cim3.net) and ran into couple of problems. He tried these
uploads on 12/29/2009.

I am attaching screenshots of the error and server logs. Please
provide feedback on whether this is an installation problem or
something else.

Thanks,
--Tejas
  
_________________________________________________________________ Message Archives: http://ontolog.cim3.net/forum/oor-dev/ Config/Unsubscribe: http://ontolog.cim3.net/mailman/listinfo/oor-dev/ Shared Files: http://ontolog.cim3.net/file/work/OOR/dev/ Wiki: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository

_________________________________________________________________
Message Archives: http://ontolog.cim3.net/forum/oor-dev/   
Config/Unsubscribe: http://ontolog.cim3.net/mailman/listinfo/oor-dev/   
Shared Files: http://ontolog.cim3.net/file/work/OOR/dev/ 
Wiki: http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository     (01)
<Prev in Thread] Current Thread [Next in Thread>