[BioRuby] BioRuby Shell Rails Generator Bug ?

Toshiaki Katayama ktym at hgc.jp
Fri Feb 1 00:15:03 UTC 2008


Hmm, it is working in my environment without any changes.
What version of rails are you using?

By the way, rails mode (bioruby -r) is not yet tested
with Rails 2.x and may not work.

Regards,
Toshiaki Katayama

On 2008/01/29, at 19:40, Raoul Jean Pierre Bonnal wrote:

> [root at Graco febo]# gem install bio
> Updating metadata for 30 gems from http://gems.rubyforge.org
> ..............................
> complete
> Successfully installed bio-1.2.1
> 1 gem installed
> ----
> [febo at Graco Projects]$ bioruby -r testrb
> Creating directory (/home/febo/Work/Projects/testrb/shell/session) ...
> done
> Creating directory (/home/febo/Work/Projects/testrb/shell/plugin) ...
> done
> Creating directory (/home/febo/Work/Projects/testrb/data) ... done
> Installing Rails application for BioRuby shell ... 
>      exists  
> a lot of create ....
>
> done
> Installing Rails plugin for BioRuby shell ... 
> Couldn't find 'bioruby' generator
> done
> Then Rails starts.
> ----------
>
> So digging into the installation tree I
> found  /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/generators/bioruby/
>
> and taking as example uniprot plugins
>
>
> [root at Graco febo]#
> ll /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/generators/bioruby/
> [root at Graco febo]#
> mkdir /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/bioruby
> [root at Graco febo]#
> mv /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/generators /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/bioruby
> [root at Graco febo]#
> ll /usr/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/shell/rails/vendor/plugins/
> totale 1
> drwxr-xr-x 3 root root 1024 2008-01-29 11:37 bioruby/
>
>
> [febo at Graco Projects]$ bioruby -r testrb
> Creating directory (/home/febo/Work/Projects/testrb/shell/session) ...
> done
> Creating directory (/home/febo/Work/Projects/testrb/shell/plugin) ...
> done
> Creating directory (/home/febo/Work/Projects/testrb/data) ... done
> Installing Rails application for BioRuby shell ... 
>      exists  
>      create  app/controllers
>      create  app/helpers
>      create  app/models
>      create  app/views/layouts
>      create  config/environments
>      create  config/initializers
>      create  db
>      create  doc
>      create  lib
>      create  lib/tasks
>      create  log
>      create  public/images
>      create  public/javascripts
>      create  public/stylesheets
>      create  script/performance
>      create  script/process
>      create  test/fixtures
>      create  test/functional
>      create  test/integration
>      create  test/mocks/development
>      create  test/mocks/test
>      create  test/unit
>      create  vendor
>      create  vendor/plugins
>      create  tmp/sessions
>      create  tmp/sockets
>      create  tmp/cache
>      create  tmp/pids
>      create  Rakefile
>      create  README
>      create  app/controllers/application.rb
>      create  app/helpers/application_helper.rb
>      create  test/test_helper.rb
>      create  config/database.yml
>      create  config/routes.rb
>      create  public/.htaccess
>      create  config/initializers/inflections.rb
>      create  config/initializers/mime_types.rb
>      create  config/boot.rb
>      create  config/environment.rb
>      create  config/environments/production.rb
>      create  config/environments/development.rb
>      create  config/environments/test.rb
>      create  script/about
>      create  script/console
>      create  script/destroy
>      create  script/generate
>      create  script/performance/benchmarker
>      create  script/performance/profiler
>      create  script/performance/request
>      create  script/process/reaper
>      create  script/process/spawner
>      create  script/process/inspector
>      create  script/runner
>      create  script/server
>      create  script/plugin
>      create  public/dispatch.rb
>      create  public/dispatch.cgi
>      create  public/dispatch.fcgi
>      create  public/404.html
>      create  public/422.html
>      create  public/500.html
>      create  public/index.html
>      create  public/favicon.ico
>      create  public/robots.txt
>      create  public/images/rails.png
>      create  public/javascripts/prototype.js
>      create  public/javascripts/effects.js
>      create  public/javascripts/dragdrop.js
>      create  public/javascripts/controls.js
>      create  public/javascripts/application.js
>      create  doc/README_FOR_APP
>      create  log/server.log
>      create  log/production.log
>      create  log/development.log
>      create  log/test.log
> done
> Installing Rails plugin for BioRuby shell ... 
>      exists  app/controllers
>      exists  app/helpers
>      create  app/views/bioruby
>      exists  app/views/layouts
>      create  public/images/bioruby
>      exists  public/stylesheets
>      create  app/controllers/bioruby_controller.rb
>      create  app/helpers/bioruby_helper.rb
>      create  app/views/bioruby/_methods.rhtml
>      create  app/views/bioruby/_classes.rhtml
>      create  app/views/bioruby/_modules.rhtml
>      create  app/views/bioruby/_log.rhtml
>      create  app/views/bioruby/_variables.rhtml
>      create  app/views/bioruby/commands.rhtml
>      create  app/views/bioruby/history.rhtml
>      create  app/views/bioruby/index.rhtml
>      create  app/views/layouts/bioruby.rhtml
>      create  public/images/bioruby/spinner.gif
>      create  public/images/bioruby/gem.png
>      create  public/images/bioruby/link.gif
>      create  public/images/bioruby/bg.gif
>      create  public/stylesheets/bioruby.css
> done
>
>>>>
>>>> open http://localhost:3000/bioruby
>>>>
>
> (You can change the port number by adding "-- -p 4000" option)
>
>
> . . . B i o R u b y   i n   t h e   s h e l l . . .
>
>  Version : BioRuby 1.2.1 / Ruby 1.8.6
>
> => Booting WEBrick...
> => Rails application started on http://0.0.0.0:3000
> => Ctrl-C to shutdown server; call with --help for options
> [2008-01-29 11:37:51] INFO  WEBrick 1.3.1
> [2008-01-29 11:37:51] INFO  ruby 1.8.6 (2007-03-13) [i586-linux-gnu]
> [2008-01-29 11:37:51] INFO  WEBrick::HTTPServer#start: pid=9210
> port=3000
>
>
> WORKS ! 
>
> --
> Ra
>





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