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[bioontology-support] Problems with Bioportal's ui deployment

Paul R Alexander palexander at stanford.edu
Wed Jul 14 13:00:27 PDT 2010


  Nestor,

Can you check to make sure that the db/schema.rb file that you have 
contains the following?

   create_table "notes_indices", :force => true do |t|
     t.string   "note_id",                      :null => false
     t.integer  "ontology_id",                  :null => false
     t.integer  "author",                       :null => false
     t.string   "note_type",                    :null => false
     t.string   "subject",                      :null => false
     t.string   "applies_to",                   :null => false
     t.string   "applies_to_type",              :null => false
     t.text     "body"
     t.integer  "created",         :limit => 8, :null => false
     t.datetime "timestamp"
   end

   add_index "notes_indices", ["note_id"], :name => "note_id", :unique 
=> true

If not, please update your code from the SVN repository and try running 
the rake commands again.

Thanks,
Paul Alexander
Web / UI Developer
NCBO BioPortal


On 7/13/10 9:52 PM, nestor vb wrote:
> Hi:
>
> My name is Nestor Velasco, I'm a PhD student from mexico, I'm working 
> on adapting a java SPARQL endpoint tool, but before doing that I would 
> want to have my own Bioportal installation locally to make the needed 
> adjustments in order to test it later against the online version of 
> Bioportal. I write to you because Mr.Nigam Shah gave me the following 
> email address since the plan is to share my sparql tool with you.
>
> My main problem is that I download the source code for the core and ui 
> releases from the svn, I follow the deployment recommendations and 
> notes and everything works fine until I try to access it. When testing 
> it via http://localhost:3000/ there's an error shown, such error 
> refers to a MySQL table missing (see the following part of the log)
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> nestorvb at nestorvb-laptop:~/BioPortal ui$ ./script/server
> => Booting Mongrel
> => Rails 2.3.5 application starting on http://0.0.0.0:3000
> => Call with -d to detach
> => Ctrl-C to shutdown server
>   SQL (0.2ms)   SET NAMES 'utf8'
>   SQL (0.1ms)   SET SQL_AUTO_IS_NULL=0
>
>
> Processing HomeController#index (for 127.0.0.1 at 2010-07-13 23:32:13) 
> [GET]
>   SQL (0.0ms)   Mysql::Error: Table 
> 'bioportal_ui_development.notes_indices' doesn't exist: select 
> ontology_id,count(ontology_id) as note_count from notes_indices as 
> note group by ontology_id order by note_count desc
>
> ActiveRecord::StatementInvalid (Mysql::Error: Table 
> 'bioportal_ui_development.notes_indices' doesn't exist: select 
> ontology_id,count(ontology_id) as note_count from notes_indices as 
> note  group by ontology_id order by note_count desc):
>   app/controllers/home_controller.rb:10:in `index'
>
> Rendered rescues/_trace (62.1ms)
> Rendered rescues/_request_and_response (31.2ms)
> Rendering rescues/layout (internal_server_error)
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> I create the table "notes_indices" but then it asks for more columns, 
> and so on... I ran all the needed sql scripts and the rake db:create 
> and rake db:migrate commands but still nothing solves the conflict. 
> I've already repeated all the installation twice on a Linux computer 
> (Linux 2.6.32-23-generic Intel(R) Pentium(R) M processor 1.86GHz 
> 1600.000 MHz, 1.0 GB RAM )
>
> Can you help me please? am I missing something? what must I do in 
> order to solve the problem.
>
> Thank you for your time and help.
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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