Feature: Migrate to minitest 5 (#102)

* Merge remote-tracking branch 'ncbo/ontoportal-lirmm-pr/refactor/migrate-to-minitest-5' into feature/migrate-to-minitest-5

* add password reset token expiration

* deprecate recommender_v1 endpoint

.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

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

.ruby-version

@@ -0,0 +1 @@
+3.0.6

Capfile

@@ -16,12 +16,12 @@ 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'
 # 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'
@@ -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'
@@ -53,16 +53,21 @@ 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/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'
 end
 
 
@@ -71,10 +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

Gemfile.lock

@@ -57,7 +57,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 793c4fde592e6db91d8d103c15afe993c3472aae
+  revision: c0f8697529ebfca2c3fe90d46d9482ac72f13362
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -103,18 +103,21 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (3.2.22.5)
-      i18n (~> 0.6, >= 0.6.4)
-      multi_json (~> 1.0)
+    activesupport (5.2.8.1)
+      concurrent-ruby (~> 1.0, >= 1.0.2)
+      i18n (>= 0.7, < 2)
+      minitest (~> 5.1)
+      tzinfo (~> 1.1)
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
     airbrussh (1.5.3)
       sshkit (>= 1.6.1, != 1.7.0)
+    ast (2.4.2)
     backports (3.25.0)
     base64 (0.2.0)
     bcrypt (3.1.20)
     bcrypt_pbkdf (1.1.1)
-    bigdecimal (1.4.2)
+    bigdecimal (3.1.8)
     builder (3.3.0)
     capistrano (3.19.1)
       airbrussh (>= 1.0.0)
@@ -131,8 +134,7 @@ GEM
     coderay (1.1.3)
     concurrent-ruby (1.3.4)
     connection_pool (2.4.1)
-    crack (1.0.0)
-      bigdecimal
+    crack (0.4.5)
       rexml
     cube-ruby (0.0.3)
     dante (0.2.0)
@@ -141,29 +143,13 @@ GEM
     docile (1.4.1)
     domain_name (0.6.20240107)
     ed25519 (1.3.0)
-    faraday (1.10.4)
-      faraday-em_http (~> 1.0)
-      faraday-em_synchrony (~> 1.0)
-      faraday-excon (~> 1.1)
-      faraday-httpclient (~> 1.0)
-      faraday-multipart (~> 1.0)
-      faraday-net_http (~> 1.0)
-      faraday-net_http_persistent (~> 1.0)
-      faraday-patron (~> 1.0)
-      faraday-rack (~> 1.0)
-      faraday-retry (~> 1.0)
+    faraday (2.8.1)
+      base64
+      faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
-    faraday-em_http (1.0.0)
-    faraday-em_synchrony (1.0.0)
-    faraday-excon (1.1.0)
-    faraday-httpclient (1.0.1)
-    faraday-multipart (1.0.4)
-      multipart-post (~> 2)
-    faraday-net_http (1.0.2)
-    faraday-net_http_persistent (1.2.0)
-    faraday-patron (1.0.0)
-    faraday-rack (1.0.0)
-    faraday-retry (1.0.3)
+    faraday-net_http (3.0.2)
+    faraday-retry (2.2.1)
+      faraday (~> 2.0)
     ffi (1.16.3)
     gapic-common (0.21.1)
       faraday (>= 1.9, < 3.a)
@@ -223,7 +209,7 @@ 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 (2.7.3)
     json-ld (3.0.2)
@@ -234,6 +220,7 @@ GEM
     jwt (2.9.3)
       base64
     kgio (2.11.4)
+    language_server-protocol (3.17.0.3)
     libxml-ruby (5.0.3)
     link_header (0.0.8)
     logger (1.6.1)
@@ -250,12 +237,13 @@ GEM
       mime-types-data (~> 3.2015)
     mime-types-data (3.2024.1001)
     mini_mime (1.1.5)
-    minitest (4.7.5)
+    minitest (5.25.1)
+    minitest-hooks (1.5.2)
+      minitest (> 5.3)
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
-    multipart-post (2.4.1)
     mutex_m (0.2.0)
     net-http-persistent (4.0.4)
       connection_pool (~> 2.2)
@@ -275,19 +263,25 @@ GEM
     net-ssh (7.3.0)
     netrc (0.11.0)
     newrelic_rpm (9.14.0)
-    oj (3.16.1)
+    oj (3.16.6)
+      bigdecimal (>= 3.0)
+      ostruct (>= 0.2)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
     ostruct (0.6.0)
     parallel (1.26.3)
     parseconfig (1.1.2)
+    parser (3.3.5.0)
+      ast (~> 2.4.1)
+      racc
     pony (1.13.1)
       mail (>= 2.0)
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.1.1)
+    racc (1.8.1)
     rack (1.6.13)
     rack-accept (0.4.5)
       rack (>= 0.4)
@@ -304,6 +298,7 @@ GEM
     rack-test (2.1.0)
       rack (>= 1.3)
     rack-timeout (0.7.0)
+    rainbow (3.1.1)
     raindrops (0.20.1)
     rake (10.5.0)
     rdf (3.2.11)
@@ -331,6 +326,7 @@ GEM
       redis-store (>= 1.6, < 2)
     redis-store (1.11.0)
       redis (>= 4, < 6)
+    regexp_parser (2.9.2)
     representable (3.2.0)
       declarative (< 0.1.0)
       trailblazer-option (>= 0.1.1, < 0.2.0)
@@ -347,6 +343,19 @@ GEM
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
+    rubocop (1.67.0)
+      json (~> 2.3)
+      language_server-protocol (>= 3.17.0)
+      parallel (~> 1.10)
+      parser (>= 3.3.0.2)
+      rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 2.4, < 3.0)
+      rubocop-ast (>= 1.32.2, < 2.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (>= 2.4.0, < 3.0)
+    rubocop-ast (1.32.3)
+      parser (>= 3.3.1.0)
+    ruby-progressbar (1.13.0)
     ruby-xxHash (0.4.0.2)
     ruby2_keywords (0.0.5)
     rubyzip (2.3.2)
@@ -387,12 +396,14 @@ GEM
       ostruct
     systemu (2.6.5)
     temple (0.10.3)
+    thread_safe (0.3.6)
     tilt (2.4.0)
     timeout (0.4.1)
     trailblazer-option (0.1.2)
-    tzinfo (2.0.6)
-      concurrent-ruby (~> 1.0)
+    tzinfo (1.2.11)
+      thread_safe (~> 0.1)
     uber (0.1.0)
+    unicode-display_width (2.6.0)
     unicorn (6.1.0)
       kgio (~> 2.6)
       raindrops (~> 0.7)
@@ -405,30 +416,32 @@ GEM
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
+    webrick (1.8.2)
 
 PLATFORMS
   x86_64-linux
 
 DEPENDENCIES
-  activesupport (~> 3.2)
+  activesupport (~> 5)
   bcrypt_pbkdf (>= 1.0, < 2.0)
-  bigdecimal (= 1.4.2)
+  bigdecimal
   capistrano (~> 3)
   capistrano-bundler
   capistrano-locally
   capistrano-rbenv
+  crack (= 0.4.5)
   cube-ruby
   ed25519 (>= 1.2, < 2.0)
-  faraday (~> 1.9)
   ffi (~> 1.16.3)
   goo!
   google-protobuf (= 3.25.3)
   haml (~> 5.2.2)
   json-ld
   json-schema (~> 2.0)
-  minitest (~> 4.0)
+  minitest (~> 5.0)
+  minitest-hooks (~> 1.5)
   minitest-stub_any_instance
-  multi_json (~> 1.0)
+  multi_json
   ncbo_annotator!
   ncbo_cron!
   ncbo_ontology_recommender!
@@ -437,7 +450,6 @@ DEPENDENCIES
   ontologies_linked_data!
   parallel
   parseconfig
-  pry
   rack
   rack-accept (~> 0.4)
   rack-attack (~> 6.6.1)
@@ -453,6 +465,8 @@ DEPENDENCIES
   redis-rack-cache (~> 2.0)
   redis-store (~> 1.10)
   request_store
+  rexml
+  rubocop
   shotgun!
   simplecov
   simplecov-cobertura
@@ -463,6 +477,7 @@ DEPENDENCIES
   unicorn
   unicorn-worker-killer
   webmock (~> 3.19.1)
+  webrick
 
 BUNDLED WITH
    2.4.22