Switch to bundler for including gems

Capfile

@@ -1,2 +1,5 @@
-load 'deploy' if respond_to?(:namespace) # cap2 differentiator
-load 'config/deploy'
+load 'deploy'
+# Uncomment if you are using Rails' asset pipeline
+    # load 'deploy/assets'
+Dir['vendor/gems/*/recipes/*.rb','vendor/plugins/*/recipes/*.rb'].each { |plugin| load(plugin) }
+load 'config/deploy' # remove this line to skip loading any of the default tasks

Gemfile

@@ -0,0 +1,18 @@
+# Required gems
+source :gemcutter
+gem "rails", "2.3.14"
+
+gem "hpricot", "~> 0.8.6"
+gem "libxml-ruby", "~> 2.2.0"
+gem "recaptcha", "~> 0.3.1"
+gem "rest-client", "~> 1.6.1"
+gem "mysql", "~> 2.8.1"
+gem "ncbo_annotator", ">= 1.0.13"
+gem "memcache-client", "~> 1.8.5"
+gem "i18n", "~> 0.5.0"
+gem "airbrake"
+
+group :development do
+  gem "ruby-debug"
+  gem "mongrel"
+end

Gemfile.lock

@@ -0,0 +1,72 @@
+GEM
+  remote: http://rubygems.org/
+  specs:
+    actionmailer (2.3.14)
+      actionpack (= 2.3.14)
+    actionpack (2.3.14)
+      activesupport (= 2.3.14)
+      rack (~> 1.1.0)
+    activerecord (2.3.14)
+      activesupport (= 2.3.14)
+    activeresource (2.3.14)
+      activesupport (= 2.3.14)
+    activesupport (2.3.14)
+    airbrake (3.0.9)
+      activesupport
+      builder
+    builder (3.0.0)
+    cgi_multipart_eof_fix (2.5.0)
+    columnize (0.3.6)
+    daemons (1.1.8)
+    fastthread (1.0.7)
+    gem_plugin (0.2.3)
+    hpricot (0.8.6)
+    i18n (0.5.0)
+    libxml-ruby (2.2.2)
+    linecache (0.46)
+      rbx-require-relative (> 0.0.4)
+    memcache-client (1.8.5)
+    mime-types (1.18)
+    mongrel (1.1.5)
+      cgi_multipart_eof_fix (>= 2.4)
+      daemons (>= 1.0.3)
+      fastthread (>= 1.0.1)
+      gem_plugin (>= 0.2.3)
+    mysql (2.8.1)
+    ncbo_annotator (1.0.13)
+      libxml-ruby (~> 2.2.0)
+    rack (1.1.3)
+    rails (2.3.14)
+      actionmailer (= 2.3.14)
+      actionpack (= 2.3.14)
+      activerecord (= 2.3.14)
+      activeresource (= 2.3.14)
+      activesupport (= 2.3.14)
+      rake (>= 0.8.3)
+    rake (0.9.2.2)
+    rbx-require-relative (0.0.9)
+    recaptcha (0.3.4)
+    rest-client (1.6.7)
+      mime-types (>= 1.16)
+    ruby-debug (0.10.4)
+      columnize (>= 0.1)
+      ruby-debug-base (~> 0.10.4.0)
+    ruby-debug-base (0.10.4)
+      linecache (>= 0.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  airbrake
+  hpricot (~> 0.8.6)
+  i18n (~> 0.5.0)
+  libxml-ruby (~> 2.2.0)
+  memcache-client (~> 1.8.5)
+  mongrel
+  mysql (~> 2.8.1)
+  ncbo_annotator (>= 1.0.13)
+  rails (= 2.3.14)
+  recaptcha (~> 0.3.1)
+  rest-client (~> 1.6.1)
+  ruby-debug

config/boot.rb

@@ -106,5 +106,19 @@ def read_environment_rb
   end
 end
 
+class Rails::Boot
+  def run
+    load_initializer
+
+    Rails::Initializer.class_eval do
+      def load_gems
+        @bundler_loaded ||= Bundler.require :default, Rails.env
+      end
+    end
+
+    Rails::Initializer.run(:set_load_path)
+  end
+end
+
 # All that for this:
 Rails.boot!

config/deploy.rb

@@ -1,34 +1,53 @@
+# required for typing in a password for sudo
+default_run_options[:pty] = true
+
+set :stage, "ncbostage-ror1"
+set :user, "palexand"
+set :flex_release, "stage"
 
 set :application, "BioPortal"
 set :repository,  "https://bmir-gforge.stanford.edu/svn/bioportalui/trunk"
-set :svn_username, "ngriff"
-set :svn_password, Proc.new {Capistrano::CLI::password_prompt('SVN Password:')}
+set :svn_username, "anonymous"
+set :svn_password, "anonymous_ncbo"
+
+set :scm, :subversion
 
 # If you aren't deploying to /u/apps/#{application} on the target
 # servers (which is the default), you can specify the actual location
 # via the :deploy_to variable:
 set :deploy_to, "/var/rails/#{application}"
-set :user,"ngriff"
-# If you aren't using Subversion to manage your source code, specify
-# your SCM below:
-# set :scm, :subversion
-
-#alpha
-#role :app, "ncbo-ror1.stanford.edu"
-#role :web, "ncbo-ror1.stanford.edu"
-#role :db,  "ncbo-ror1.stanford.edu", :primary => true
 
-#stage
-role :app, "ncbo-ror-stage1.stanford.edu"
-role :web, "ncbo-ror-stage1.stanford.edu"
-role :db,  "ncbo-ror-stage1.stanford.edu", :primary => true
+# stage
+server stage, :app, :web, :db, :primary => true
 
-
-#production
+# production
 #role :app, "ncbo-ror-prod1.stanford.edu"
 #role :web, "ncbo-ror-prod1.stanford.edu"
 #role :db,  "ncbo-ror-prod1.stanford.edu", :primary => true
 
+# svn export --force --username anonymous --password anonymous_ncbo https://bmir-gforge.stanford.edu/svn/flexviz/tags/$flexrelease/flex $destination/public/flex
+
+# #fix logs
+# #we want to store logs in /var/logs/rails
+# if [ ! -d /var/log/rails/$bpinstance ];
+# then
+#  mkdir -p /var/log/rails/$bpinstance
+#  chown -R $user:$user /var/log/rails/$bpinstance
+# fi
+# #update sym link
+# rm -Rf $destination/log
+# ln -s /var/log/rails/$bpinstance/ $destination/log
+
+
+# If you are using Passenger mod_rails uncomment this:
+namespace :deploy do
+  task :start do ; end
+  task :stop do ; end
+  task :restart, :roles => :app, :except => { :no_release => true } do
+    run "#{try_sudo} touch #{File.join(current_path,'tmp','restart.txt')}"
+  end
+end
+
 Dir[File.join(File.dirname(__FILE__), '..', 'vendor', 'gems', 'airbrake-*')].each do |vendored_notifier|
   $: << File.join(vendored_notifier, 'lib')
 end

config/environment.rb

@@ -57,15 +57,5 @@
   # Make Active Record use UTC-base instead of local time
   # config.active_record.default_timezone = :utc
 
-  # Gem configuration
-  config.gem "hpricot", :version => "~> 0.8.4"
-  config.gem "libxml-ruby", :lib => "libxml", :version => "~> 2.2.0"
-  config.gem "recaptcha", :version => "~> 0.3.1"
-  config.gem "rest-client", :version => "~> 1.6.1"
-  config.gem "mysql", :version => "~> 2.8.1"
-  config.gem "ncbo_annotator", :version => ">= 1.0.13"
-  config.gem "memcache-client", :lib => "memcache", :version => "~> 1.8.5"
-  config.gem "i18n", :version => "~> 0.5.0"
-  config.gem "airbrake"
 end
 

config/preinitializer.rb

@@ -0,0 +1,21 @@
+# Bundler init
+begin
+  require "rubygems"
+  require "bundler"
+rescue LoadError
+  raise "Could not load the bundler gem. Install it with `gem install bundler`."
+end
+
+if Gem::Version.new(Bundler::VERSION) <= Gem::Version.new("0.9.24")
+  raise RuntimeError, "Your bundler version is too old for Rails 2.3." +
+   "Run `gem install bundler` to upgrade."
+end
+
+begin
+  # Set up load paths for all bundled gems
+  ENV["BUNDLE_GEMFILE"] = File.expand_path("../../Gemfile", __FILE__)
+  Bundler.setup
+rescue Bundler::GemNotFound
+  raise RuntimeError, "Bundler couldn't find some gems." +
+    "Did you run `bundle install`?"
+end