Merge develop -> master, release 5.29.1

.github/workflows/deploy.yml

@@ -63,7 +63,6 @@ jobs:
     - uses: actions/checkout@v4
     - uses: ruby/setup-ruby@v1
       with:
-        ruby-version: 2.7.8 # Not needed with a .ruby-version file
         bundler-cache: true # runs 'bundle install' and caches installed gems automatically
     - name: get-deployment-config
       uses: actions/checkout@v4

.gitignore

@@ -55,8 +55,6 @@ test/data/ontology_files/repo/**/*
 
 *.swp
 
-.ruby-version
-
 config/environments/console.rb
 
 config/environments/stage.rb

.ruby-version

@@ -0,0 +1 @@
+2.7.8

Capfile

@@ -16,7 +16,7 @@ install_plugin Capistrano::SCM::Git
 #   https://github.com/capistrano/rails
 #
 # require 'capistrano/rvm'
-# require 'capistrano/rbenv'
+require 'capistrano/rbenv'
 # require 'capistrano/chruby'
 require 'capistrano/bundler'
 # require 'capistrano/rails/assets'

Gemfile

@@ -41,12 +41,12 @@ gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
 gem 'redcarpet'
 
 # NCBO
-gem 'goo', github: 'ncbo/goo', branch: 'master'
-gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master'
-gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'master'
-gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'master'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'goo', github: 'ncbo/goo', branch: 'develop'
+gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop'
+gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'develop'
+gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'develop'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
 
 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

Gemfile.lock

@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 75436fe8e387febc53e34ee31ff0e6dd837a9d3f
-  branch: master
+  revision: 87e991b0e720c580a71e2c2c10f9ab44183db322
+  branch: develop
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -15,8 +15,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 63c986880aa88c9384043e6611a682434a14aba7
-  branch: master
+  revision: fe0783c542479ed0a12da5663ef28e1673e80eba
+  branch: develop
   specs:
     ncbo_annotator (0.0.1)
       goo
@@ -26,8 +26,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: b5764cc314758dbfdbb855b2b63c1c53b1325f6f
-  branch: master
+  revision: 2f8b1c1cff9a00da06ff68c1449f049e3f59c5ce
+  branch: develop
   specs:
     ncbo_cron (0.0.1)
       dante
@@ -42,8 +42,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: 013abea4af3b10910ec661dbb358a4b6cae198a4
-  branch: master
+  revision: d047de0a9650df321db47300eba8ff8c195e0854
+  branch: develop
   specs:
     ncbo_ontology_recommender (0.0.1)
       goo
@@ -53,8 +53,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: b6df920d03af15ee35a3a7c31078c6ea263ba41d
-  branch: master
+  revision: a466d530877cb48cdfb811d0b61ecaabd2b835eb
+  branch: develop
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -73,8 +73,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: d418d56a6c9ff5692f925b45739a2a1c66bca851
-  branch: master
+  revision: 55e7dbf858eb571c767bc67868f9af61663859cb
+  branch: develop
   specs:
     sparql-client (1.0.1)
       json_pure (>= 1.4)
@@ -376,6 +376,7 @@ PLATFORMS
   arm64-darwin-22
   arm64-darwin-23
   x86_64-darwin-18
+  x86_64-darwin-21
   x86_64-darwin-23
   x86_64-linux
 

config/deploy.rb

@@ -34,7 +34,8 @@
 set :linked_dirs, %w{log vendor/bundle tmp/pids tmp/sockets public/system}
 
 # rbenv
-# set :rbenv_type, :system #or :user
+set :rbenv_type, :system
+set :rbenv_ruby, File.read('.ruby-version').strip
 # set :rbenv_ruby, '2.2.5'
 # set :rbenv_roles, :all # default value
 
@@ -43,8 +44,7 @@
 # required for restarting unicorn with sudo
 set :pty, true
 # Default value for default_env is {}
-set :default_env, {
-}
+# set :default_env, { path: "/opt/ruby/bin:$PATH" }
 
 # Default value for keep_releases is 5
 set :keep_releases, 5

config/deploy/production.rb

@@ -4,7 +4,7 @@
 # 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
-ole :app, %w{api1.prd.ontoportal.org api2.prd.ontoportal.org/}
+pole :app, %w{api1.prd.ontoportal.org api2.prd.ontoportal.org/}
 
 # Extended Server Syntax
 # ======================

config/deploy/staging.rb

@@ -4,7 +4,7 @@
 # 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
-ole :app, %w{api1.stg.ontoportal.org api2.stg.ontoportal.org}
+role :app, %w{api1.stg.ontoportal.org api2.stg.ontoportal.org}
 
 # Extended Server Syntax
 # ======================