Merge branch 'master' into feature/biodivportal/align-to-agroportal-3.0

.dockerignore

@@ -1,6 +1,7 @@
 # Git
 .git
 .gitignore
+.github
 create_permissions.log
 # Logs
 log/*
@@ -9,4 +10,8 @@ tmp/*
 # Editor temp files
 *.swp
 *.swo
-test/solr
+coverage
+# Ignore generated test data
+test/data/uploaded_ontologies/**/*
+test/data/ontology_files/repo/**/*
+test/log

.gitignore

@@ -56,8 +56,6 @@ test/data/ontology_files/repo/**/*
 
 *.swp
 
-.ruby-version
-
 config/environments/console.rb
 
 config/environments/development.rb.sample

Capfile

@@ -22,6 +22,6 @@ require 'capistrano/bundler'
 # require 'capistrano/rails/assets'
 # require 'capistrano/rails/migrations'
 require 'capistrano/locally'
-
+require 'new_relic/recipes' # announce deployments in NewRelic
 # Loads custom tasks from `lib/capistrano/tasks' if you have any defined.
 Dir.glob('lib/capistrano/tasks/*.cap').each { |r| import r }

Dockerfile

@@ -1,4 +1,4 @@
-ARG RUBY_VERSION
+ARG RUBY_VERSION=3.0
 ARG DISTRO_NAME=bullseye
 
 FROM ruby:$RUBY_VERSION-$DISTRO_NAME

Gemfile

@@ -1,15 +1,15 @@
 source 'https://rubygems.org'
-
-gem 'activesupport', '~> 3.2'
+gem 'activesupport', '~> 5'
 # see https://github.com/ncbo/ontologies_api/issues/69
-gem 'bigdecimal', '1.4.2'
-gem 'faraday', '~> 1.9'
+gem 'bigdecimal'
+# gem 'faraday', '~> 1.9'
 gem 'json-schema', '~> 2.0'
-gem 'multi_json', '~> 1.0'
+gem 'multi_json'
 gem 'oj'
 gem 'parseconfig'
 gem 'rack'
 gem 'rake', '~> 10.0'
+gem 'rexml' # Investigate why unicorn fails to start under ruby 3 without adding rexml gem to the Gemfile
 gem 'sinatra', '~> 1.0'
 gem 'sinatra-advanced-routes'
 gem 'sinatra-contrib', '~> 1.0'
@@ -19,7 +19,7 @@ gem 'json-ld'
 gem 'google-protobuf', '3.25.3'
 
 # Rack middleware
-gem 'ffi'
+gem 'ffi', '~> 1.16.3'
 gem 'rack-accept', '~> 0.4'
 gem 'rack-attack', '~> 6.6.1', require: 'rack/attack'
 gem 'rack-cache', '~> 1.13.0'
@@ -35,7 +35,7 @@ gem 'redis-store', '~>1.10'
 
 # Monitoring
 gem 'cube-ruby', require: 'cube'
-gem 'newrelic_rpm'
+gem 'newrelic_rpm', group: [:default, :deployment]
 
 # HTTP server
 gem 'unicorn'
@@ -46,28 +46,28 @@ gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
 gem 'redcarpet'
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', git: 'https://github.com/ontoportal-lirmm/goo.git', branch: 'master'
 gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'development'
 gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'master'
-gem 'ncbo_ontology_recommender', git: 'https://github.com/ncbo/ncbo_ontology_recommender.git', branch: 'master'
+gem 'ncbo_ontology_recommender', git: 'https://github.com/ontoportal-lirmm/ncbo_ontology_recommender.git', branch: 'development'
+gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development'
-gem 'ontologies_linked_data', git: 'https://github.com/BiodivPortal/ontologies_linked_data.git', branch: 'master'
+gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'development'
+
 
 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 'shotgun', github: 'palexander/shotgun', branch: 'ncbo'
+  gem 'rubocop'
+end
+
+group :deployment 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
-  gem 'pry'
-  gem 'shotgun', github: 'palexander/shotgun', branch: 'ncbo'
-
-  gem 'solargraph'
-  gem 'solargraph-rails'
-  gem 'rufo', require: false
-  gem 'reek', require: false
 end
 
 
@@ -76,10 +76,13 @@ group :profiling do
 end
 
 group :test do
-  gem 'minitest', '~> 4.0'
+  gem 'crack', '0.4.5'
+  gem 'minitest', '~> 5.0'
+  gem 'minitest-hooks', "~> 1.5"
   gem 'minitest-stub_any_instance'
   gem 'rack-test'
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
   gem 'webmock', '~> 3.19.1'
+  gem 'webrick'
 end