Capistrano v3.4 deplyment

Gemfile

@@ -19,8 +19,6 @@ gem 'jquery-rails'
 # To use Jbuilder templates for JSON
 # gem 'jbuilder'
 
-# Use unicorn as the app server
-gem 'unicorn'
 
 # Deploy with Capistrano
 # gem 'capistrano'
@@ -57,3 +55,13 @@ gem 'logstash-logger'
 
 gem 'ontologies_api_client', :git => "https://github.com/ncbo/ontologies_api_ruby_client.git", branch: "staging"
 
+group :development do
+    #Capistrano
+    gem 'capistrano', '~> 3.4.0', require: false
+    # rails specific capistrano funcitons
+    gem 'capistrano-rails', '~> 1.1.0', require: false
+    # integrate bundler with capistrano
+    gem 'capistrano-bundler', require: false
+    # passenger reload
+    gem 'capistrano-passenger', require: false
+end

Gemfile.lock

@@ -61,6 +61,18 @@ GEM
       tzinfo (~> 1.1)
     arel (6.0.0)
     builder (3.2.2)
+    capistrano (3.4.0)
+      i18n
+      rake (>= 10.0.0)
+      sshkit (~> 1.3)
+    capistrano-bundler (1.1.4)
+      capistrano (~> 3.1)
+      sshkit (~> 1.2)
+    capistrano-passenger (0.1.1)
+      capistrano (~> 3.0)
+    capistrano-rails (1.1.3)
+      capistrano (~> 3.1)
+      capistrano-bundler (~> 1.1)
     coderay (1.1.0)
     coffee-rails (4.1.0)
       coffee-script (>= 2.2.0)
@@ -69,6 +81,7 @@ GEM
       coffee-script-source
       execjs
     coffee-script-source (1.9.1.1)
+    colorize (0.7.7)
     cube-ruby (0.0.3)
     dalli (2.7.4)
     domain_name (0.5.24)
@@ -100,7 +113,6 @@ GEM
     jquery-ui-rails (5.0.5)
       railties (>= 3.2.16)
     json (1.8.3)
-    kgio (2.9.3)
     logstash-event (1.1.5)
     logstash-logger (0.3.0)
       logstash-event
@@ -117,6 +129,9 @@ GEM
     multi_json (1.11.1)
     multipart-post (2.0.0)
     mysql (2.9.1)
+    net-scp (1.2.1)
+      net-ssh (>= 2.6.5)
+    net-ssh (2.9.2)
     netrc (0.10.3)
     newrelic_rpm (3.12.1.298)
     nokogiri (1.6.6.2)
@@ -157,7 +172,6 @@ GEM
       activesupport (= 4.2.1)
       rake (>= 0.8.7)
       thor (>= 0.18.1, < 2.0)
-    raindrops (0.13.0)
     rake (10.4.2)
     rake-compiler (0.9.5)
       rake
@@ -183,6 +197,10 @@ GEM
       actionpack (>= 3.0)
       activesupport (>= 3.0)
       sprockets (>= 2.8, < 4.0)
+    sshkit (1.7.1)
+      colorize (>= 0.7.0)
+      net-scp (>= 1.1.2)
+      net-ssh (>= 2.8.0)
     stackprof (0.2.7)
     thor (0.19.1)
     thread_safe (0.3.5)
@@ -195,16 +213,16 @@ GEM
     unf (0.1.4)
       unf_ext
     unf_ext (0.0.7.1)
-    unicorn (4.9.0)
-      kgio (~> 2.6)
-      rack
-      raindrops (~> 0.7)
     will_paginate (3.0.7)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
+  capistrano (~> 3.4.0)
+  capistrano-bundler
+  capistrano-passenger
+  capistrano-rails (~> 1.1.0)
   coffee-rails (~> 4.1.0)
   cube-ruby
   dalli
@@ -234,5 +252,7 @@ DEPENDENCIES
   sass-rails (~> 5.0)
   stackprof
   uglifier (>= 1.0.3)
-  unicorn
   will_paginate (~> 3.0)
+
+BUNDLED WITH
+   1.10.5

config/deploy.rb

@@ -1,38 +1,93 @@
-# required for typing in a password for sudo
-default_run_options[:pty] = true
+# config valid only for Capistrano 3.1
+lock '3.4.0'
 
-set :stage, "stage-hostname"
-set :user, "SSHUserOnStage"
-set :flex_release, "stage"
+set :application, 'bioportal_web_ui'
 
-set :application, "BioPortal"
-set :repository,  "https://bmir-gforge.stanford.edu/svn/bioportalui/trunk"
-set :svn_username, "anonymous"
-set :svn_password, "anonymous_ncbo"
+set :repo_url, "git@github.com:ncbo/#{fetch(:application)}.git"
 
-set :scm, :subversion
+#set :deploy_via, :remote_cache
 
-# 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}"
+# Default branch is :master
+# ask :branch, proc { `git rev-parse --abbrev-ref HEAD`.chomp }
+NCBO_BRANCH = ENV.include?('NCBO_BRANCH') ? ENV['NCBO_BRANCH'] : 'staging'
+set :branch, "#{NCBO_BRANCH}"
 
-# stage
-server stage, :app, :web, :db, :primary => true
+# Default deploy_to directory is /var/www/my_app
+set :deploy_to, "/srv/rails/#{fetch(:application)}"
 
-# production
-#role :app, "ror-prod1.example.org"
-#role :web, "ror-prod1.example.org"
-#role :db,  "ror-prod1.example.org", :primary => true
+# Default value for :scm is :git
+# set :scm, :git
 
-# svn export --force --username anonymous --password anonymous_ncbo https://bmir-gforge.stanford.edu/svn/flexviz/tags/$flexrelease/flex $destination/public/flex
+# Default value for :format is :pretty
+# set :format, :pretty
+
+# Default value for :log_level is :debug
+# set :log_level, :debug
+
+# Default value for :pty is false
+# set :pty, true
+
+# Default value for :linked_files is []
+set :linked_files, %w{config/bioportal_config.rb config/database.yml public/robots.txt config/newrelic.yml}
+
+# Default value for linked_dirs is []
+set :linked_dirs, %w{bin log tmp/pids tmp/cache public/system public/assets config/locales}
+
+# Default value for default_env is {}
+# set :default_env, { path: "/opt/ruby/bin:$PATH" }
+
+# Default value for keep_releases is 5
+set :keep_releases, 5
+set :bundle_flags, '--without development test --deployment' 
+
+#If you want to restart using `touch tmp/restart.txt`, add this to your config/deploy.rb:
+
+set :passenger_restart_with_touch, true
+#If you want to restart using `passenger-config restart-app`, add this to your config/deploy.rb:
+#set :passenger_restart_with_touch, false # Note that `nil` is NOT the same as `false` here
+#If you don't set `:passenger_restart_with_touch`, capistrano-passenger will check what version of passenger you are running
+#and use `passenger-config restart-app` if it is available in that version.
 
-# 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')}"
+
+  desc 'Incorporate the bioportal_conf private repository content'
+  #Get cofiguration from repo if ENV NCBO_CONFIG_REPO is set 
+  #(should be set to NCBO private config repo)
+  task :get_config do
+    if ENV.include?('NCBO_CONFIG_REPO') 
+       PRIVATE_REPO = ENV['NCBO_CONFIG_REPO'] 
+       CONFIG_PATH = "/tmp/#{SecureRandom.hex(15)}"
+       on roles(:web) do
+          execute "git clone -q #{PRIVATE_REPO} #{CONFIG_PATH}"
+          execute "rsync -av #{CONFIG_PATH}/#{fetch(:application)}/ #{fetch(:deploy_to)}/shared"
+          execute "rm -rf #{CONFIG_PATH}"
+          ## Modify the bioportal_config.rb file for DEPLOY_TARGET on the remote system
+#	  cfg_file = File.join(release_path, "config", "bioportal_config.rb")
+#	  sed_cmd = "\'s/^deploy_target =.*/deploy_target = \"#{DEPLOY_TARGET}\"/\'"
+#	  execute "sed -i -e #{sed_cmd} #{cfg_file}"
+      end
+    end
   end
-end
 
+  desc 'Restart application'
+  task :restart do
+    on roles(:web), in: :sequence, wait: 5 do
+      # Your restart mechanism here, for example:
+      execute :touch, release_path.join('tmp/restart.txt')
+    end
+  end
+
+  before :started, :get_config
+  after :publishing, :restart
+
+  after :restart, :clear_cache do
+    on roles(:web), in: :groups, limit: 3, wait: 10 do
+      # Here we can do anything such as:
+      # within release_path do
+      #   execute :rake, 'cache:clear'
+      # end
+    end
+  end
+
+
+end

config/deploy/production.rb

@@ -0,0 +1,39 @@
+# Simple Role Syntax
+# ==================
+# Supports bulk-adding hosts to roles, the primary
+# server in each group is considered to be the first
+# unless any hosts have the primary property set.
+# Don't declare `role :all`, it's a meta role
+role :app, %w{deploy@example.com}
+role :web, %w{deploy@example.com}
+role :db,  %w{deploy@example.com}
+
+# Extended Server Syntax
+# ======================
+# This can be used to drop a more detailed server
+# definition into the server list. The second argument
+# something that quacks like a hash can be used to set
+# extended properties on the server.
+server 'example.com', user: 'deploy', roles: %w{web app}, my_property: :my_value
+
+# you can set custom ssh options
+# it's possible to pass any option but you need to keep in mind that net/ssh understand limited list of options
+# you can see them in [net/ssh documentation](http://net-ssh.github.io/net-ssh/classes/Net/SSH.html#method-c-start)
+# set it globally
+#  set :ssh_options, {
+#    keys: %w(/home/rlisowski/.ssh/id_rsa),
+#    forward_agent: false,
+#    auth_methods: %w(password)
+#  }
+# and/or per server
+# server 'example.com',
+#   user: 'user_name',
+#   roles: %w{web app},
+#   ssh_options: {
+#     user: 'user_name', # overrides user setting above
+#     keys: %w(/home/user_name/.ssh/id_rsa),
+#     forward_agent: false,
+#     auth_methods: %w(publickey password)
+#     # password: 'please use keys'
+#   }
+# setting per server overrides global ssh_options

config/deploy/staging.rb

@@ -0,0 +1,39 @@
+# Simple Role Syntax
+# ==================
+# Supports bulk-adding hosts to roles, the primary
+# server in each group is considered to be the first
+# unless any hosts have the primary property set.
+# Don't declare `role :all`, it's a meta role
+role :app, %w{deploy@example.com}
+role :web, %w{deploy@example.com}
+role :db,  %w{deploy@example.com}
+
+# Extended Server Syntax
+# ======================
+# This can be used to drop a more detailed server
+# definition into the server list. The second argument
+# something that quacks like a hash can be used to set
+# extended properties on the server.
+server 'example.com', user: 'deploy', roles: %w{web app}, my_property: :my_value
+
+# you can set custom ssh options
+# it's possible to pass any option but you need to keep in mind that net/ssh understand limited list of options
+# you can see them in [net/ssh documentation](http://net-ssh.github.io/net-ssh/classes/Net/SSH.html#method-c-start)
+# set it globally
+#  set :ssh_options, {
+#    keys: %w(/home/rlisowski/.ssh/id_rsa),
+#    forward_agent: false,
+#    auth_methods: %w(password)
+#  }
+# and/or per server
+# server 'example.com',
+#   user: 'user_name',
+#   roles: %w{web app},
+#   ssh_options: {
+#     user: 'user_name', # overrides user setting above
+#     keys: %w(/home/user_name/.ssh/id_rsa),
+#     forward_agent: false,
+#     auth_methods: %w(publickey password)
+#     # password: 'please use keys'
+#   }
+# setting per server overrides global ssh_options