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

nestor vb nestorvb at gmail.com
Tue Jul 13 21:52:32 PDT 2010


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.
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