add capistrano deploy for biodiv

Capfile

@@ -0,0 +1,38 @@
+# Load DSL and set up stages
+require "capistrano/setup"
+
+# Include default deployment tasks
+require "capistrano/deploy"
+
+# Load the SCM plugin appropriate to your project:
+#
+# require "capistrano/scm/hg"
+# install_plugin Capistrano::SCM::Hg
+# or
+# require "capistrano/scm/svn"
+# install_plugin Capistrano::SCM::Svn
+# or
+require "capistrano/scm/git"
+install_plugin Capistrano::SCM::Git
+
+# Include tasks from other gems included in your Gemfile
+#
+# For documentation on these, see for example:
+#
+#   https://github.com/capistrano/rvm
+#   https://github.com/capistrano/rbenv
+#   https://github.com/capistrano/chruby
+#   https://github.com/capistrano/bundler
+#   https://github.com/capistrano/rails
+#   https://github.com/capistrano/passenger
+#
+# require "capistrano/rvm"
+# require "capistrano/rbenv"
+# require "capistrano/chruby"
+# require "capistrano/bundler"
+# require "capistrano/rails/assets"
+# require "capistrano/rails/migrations"
+# require "capistrano/passenger"
+
+# Load custom tasks from `lib/capistrano/tasks` if you have any defined
+Dir.glob("lib/capistrano/tasks/*.rake").each { |r| import r }

Gemfile

@@ -40,4 +40,14 @@ group :test do
   gem 'test-unit-minitest'
 end
 
+group :development do
+  # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42
+  gem 'bcrypt_pbkdf', '>= 1.0', '< 2.0', require: false
+  gem 'capistrano', '~> 3', require: false
+  gem 'capistrano-bundler', require: false
+  gem 'capistrano-locally', require: false
+  gem 'capistrano-rbenv', require: false
+  gem 'ed25519', '>= 1.2', '< 2.0', require: false
+end
+
 gem "binding_of_caller", "~> 1.0"

Gemfile.lock

@@ -74,17 +74,31 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (3.2.22.5)
-      i18n (~> 0.6, >= 0.6.4)
+    activesupport (3.1.12)
       multi_json (~> 1.0)
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
+    airbrussh (1.5.3)
+      sshkit (>= 1.6.1, != 1.7.0)
     base64 (0.2.0)
     bcrypt (3.1.20)
+    bcrypt_pbkdf (1.1.1)
     bigdecimal (3.1.8)
     binding_of_caller (1.0.1)
       debug_inspector (>= 1.2.0)
     builder (3.3.0)
+    capistrano (3.19.1)
+      airbrussh (>= 1.0.0)
+      i18n
+      rake (>= 10.0.0)
+      sshkit (>= 1.9.0)
+    capistrano-bundler (2.1.1)
+      capistrano (~> 3.1)
+    capistrano-locally (0.3.0)
+      capistrano (~> 3.0)
+    capistrano-rbenv (2.2.0)
+      capistrano (~> 3.1)
+      sshkit (~> 1.3)
     coderay (1.1.3)
     concurrent-ruby (1.3.4)
     connection_pool (2.4.1)
@@ -94,6 +108,7 @@ GEM
     declarative (0.0.20)
     docile (1.4.1)
     domain_name (0.6.20240107)
+    ed25519 (1.3.0)
     email_spec (2.1.1)
       htmlentities (~> 4.3.3)
       launchy (~> 2.1)
@@ -158,9 +173,9 @@ GEM
     http-cookie (1.0.7)
       domain_name (~> 0.5)
     httpclient (2.8.3)
-    i18n (0.9.5)
+    i18n (1.14.6)
       concurrent-ruby (~> 1.0)
-    json (2.7.6)
+    json (2.8.1)
     json-canonicalization (0.4.0)
     json-ld (3.2.5)
       htmlentities (~> 4.3)
@@ -184,7 +199,7 @@ GEM
     mime-types (3.6.0)
       logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.1001)
+    mime-types-data (3.2024.1105)
     mini_mime (1.1.5)
     minitest (4.7.5)
     mlanett-redis-lock (0.2.7)
@@ -193,6 +208,11 @@ GEM
     mutex_m (0.2.0)
     net-http-persistent (4.0.4)
       connection_pool (~> 2.2)
+    net-scp (4.0.0)
+      net-ssh (>= 2.6.5, < 8.0.0)
+    net-sftp (4.0.0)
+      net-ssh (>= 5.0.0, < 8.0.0)
+    net-ssh (7.3.0)
     netrc (0.11.0)
     oj (3.16.7)
       bigdecimal (>= 3.0)
@@ -267,6 +287,12 @@ GEM
       simplecov (~> 0.19)
     simplecov-html (0.13.1)
     simplecov_json_formatter (0.1.4)
+    sshkit (1.23.2)
+      base64
+      net-scp (>= 1.1.2)
+      net-sftp (>= 2.1.2)
+      net-ssh (>= 2.8.0)
+      ostruct
     sys-proctable (1.3.0)
       ffi (~> 1.1)
     systemu (2.6.5)
@@ -283,8 +309,14 @@ PLATFORMS
   x86_64-linux
 
 DEPENDENCIES
+  bcrypt_pbkdf (>= 1.0, < 2.0)
   binding_of_caller (~> 1.0)
+  capistrano (~> 3)
+  capistrano-bundler
+  capistrano-locally
+  capistrano-rbenv
   cube-ruby
+  ed25519 (>= 1.2, < 2.0)
   email_spec
   ffi (~> 1.16.3)
   goo!

config/deploy.rb

@@ -0,0 +1,26 @@
+set :repo_url, "[email protected]:biodivportal/ncbo_cron.git"
+set :user, 'ontoportal'
+
+set :deploy_to, '/srv/ontoportal/ncbo_cron_deployments'
+
+
+set :stages, %w[appliance]
+set :default_stage, 'appliance'
+set :stage, 'appliance'
+set :application, 'cron'
+
+# SSH parameters
+set :ssh_port, 22
+set :pty, true
+
+# Source code
+set :repository_cache, "git_cache"
+set :deploy_via, :remote_cache
+set :ssh_options, { :forward_agent => true }
+
+# Linked files and directories
+append :linked_files, "config/config.rb"
+append :linked_dirs, 'logs', '.bundle'
+set :keep_releases, 2
+
+

config/deploy/production.rb

@@ -0,0 +1,13 @@
+set :branch, 'master'
+set :server, '192.168.0.22'
+
+server fetch(:server), user: fetch(:user), roles: %w{web app}
+
+set :ssh_options, {
+  user: 'ontoportal',
+  forward_agent: 'true',
+  #keys: %w(config/deploy_id_rsa),
+  auth_methods: %w(publickey),
+  # use ssh proxy if UI servers are on a private network
+  proxy: Net::SSH::Proxy::Command.new('ssh [email protected] -W %h:%p')
+}

config/deploy/test.rb

@@ -0,0 +1,14 @@
+set :branch, 'master'
+set :server, 'biodivportal.gfbio.dev'
+
+server fetch(:server), user: fetch(:user), roles: %w{web app}
+
+set :ssh_options, {
+  user: 'ontoportal',
+  forward_agent: 'true',
+  port: 30082
+  #keys: %w(config/deploy_id_rsa),
+  #auth_methods: %w(publickey),
+  # use ssh proxy if UI servers are on a private network
+  #proxy: Net::SSH::Proxy::Command.new('ssh [email protected] -W %h:%p')
+}