Merge pull request #165 from ncbo/ontoportal-lirmm-pr/refactor/migrat…

…e-to-minitest-5

Refactor: Migrate to Minitest 5 and ActiveSupport 5

.env

@@ -0,0 +1,6 @@
+API_URL=http://localhost:9393
+ONTOLOGIES_LINKED_DATA_PATH=
+GOO_PATH=
+SPARQL_CLIENT_PATH=
+ONTOPORTAL_KB=ontoportal_kb
+REDIS_HOST=redis-ut

Gemfile

@@ -1,11 +1,11 @@
 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 'bigdecimal'
+# gem 'faraday', '~> 1.9'
 gem 'json-schema', '~> 2.0'
-gem 'multi_json', '~> 1.0'
-gem 'oj', '~> 3.0'
+gem 'multi_json'
+gem 'oj'
 gem 'parseconfig'
 gem 'rack'
 gem 'rake', '~> 10.0'
@@ -72,7 +72,9 @@ 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

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 70007faf43d0d96292809f89f15a27a757ccaa25
+  revision: aaa3941b48edbc317ec42ba4ecb44c0defeccef6
   branch: develop
   specs:
     goo (0.0.2)
@@ -16,7 +16,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 2fb892f92f66b876b9793944124f72821f3b3eb8
+  revision: b2731c98bfef0958fecb440c8648b7755a670895
   branch: develop
   specs:
     ncbo_annotator (0.0.1)
@@ -27,7 +27,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: 3bb491139267efc37d3b752888824ca3dd976e85
+  revision: cf66e7d076a94e6d669ffeb09c6bcd988226ece3
   branch: develop
   specs:
     ncbo_cron (0.0.1)
@@ -56,7 +56,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: c30887ee907acd39500cae6c12f45edb06fe0802
+  revision: a22fae3150d8e84e3b6fd19223a5ce2111e8ce94
   branch: develop
   specs:
     ontologies_linked_data (0.0.1)
@@ -103,9 +103,11 @@ 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)
@@ -116,7 +118,8 @@ GEM
     bcrypt (3.1.20)
     bcrypt_pbkdf (1.1.1)
     bcrypt_pbkdf (1.1.1-arm64-darwin)
-    bigdecimal (1.4.2)
+    bcrypt_pbkdf (1.1.1-x86_64-darwin)
+    bigdecimal (3.1.8)
     builder (3.3.0)
     capistrano (3.19.1)
       airbrussh (>= 1.0.0)
@@ -133,8 +136,7 @@ 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)
@@ -154,6 +156,7 @@ GEM
       faraday (~> 2.0)
     ffi (1.17.0-aarch64-linux-gnu)
     ffi (1.17.0-arm64-darwin)
+    ffi (1.17.0-x86_64-darwin)
     ffi (1.17.0-x86_64-linux-gnu)
     gapic-common (0.22.0)
       faraday (>= 1.9, < 3.a)
@@ -179,6 +182,7 @@ GEM
     google-cloud-errors (1.4.0)
     google-protobuf (3.25.5-aarch64-linux)
     google-protobuf (3.25.5-arm64-darwin)
+    google-protobuf (3.25.5-x86_64-darwin)
     google-protobuf (3.25.5-x86_64-linux)
     googleapis-common-protos (1.6.0)
       google-protobuf (>= 3.18, < 5.a)
@@ -199,6 +203,9 @@ GEM
     grpc (1.66.0-arm64-darwin)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
+    grpc (1.66.0-x86_64-darwin)
+      google-protobuf (>= 3.25, < 5.0)
+      googleapis-common-protos-types (~> 1.0)
     grpc (1.66.0-x86_64-linux)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
@@ -209,13 +216,13 @@ GEM
     http-accept (1.7.0)
     http-cookie (1.0.7)
       domain_name (~> 0.5)
-    i18n (0.9.5)
+    i18n (1.14.6)
       concurrent-ruby (~> 1.0)
     json (2.7.2)
     json-schema (2.8.1)
       addressable (>= 2.4)
     json_pure (2.7.2)
-    jwt (2.9.0)
+    jwt (2.9.1)
       base64
     kgio (2.11.4)
     language_server-protocol (3.17.0.3)
@@ -233,7 +240,9 @@ GEM
       mime-types-data (~> 3.2015)
     mime-types-data (3.2024.0903)
     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
@@ -257,7 +266,9 @@ GEM
     net-ssh (7.2.3)
     netrc (0.11.0)
     newrelic_rpm (9.13.0)
-    oj (3.16.1)
+    oj (3.16.6)
+      bigdecimal (>= 3.0)
+      ostruct (>= 0.2)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
@@ -369,10 +380,11 @@ GEM
       ostruct
     systemu (2.6.5)
     temple (0.10.3)
+    thread_safe (0.3.6)
     tilt (2.4.0)
     timeout (0.4.1)
-    tzinfo (2.0.6)
-      concurrent-ruby (~> 1.0)
+    tzinfo (1.2.11)
+      thread_safe (~> 0.1)
     unicode-display_width (2.6.0)
     unicorn (6.1.0)
       kgio (~> 2.6)
@@ -387,35 +399,38 @@ GEM
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
-    webrick (1.8.1)
+    webrick (1.8.2)
 
 PLATFORMS
   aarch64-linux
   arm64-darwin-22
+  x86_64-darwin-23
   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)
   ffi
   goo!
   haml (~> 5.2.2)
   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!
   newrelic_rpm
-  oj (~> 3.0)
+  oj
   ontologies_linked_data!
   parseconfig
   rack

test/controllers/test_annotator_controller.rb

@@ -2,7 +2,7 @@
 
 class TestAnnotatorController < TestCase
 
-  def self.before_suite
+  def before_suite
     @@redis = Redis.new(:host => Annotator.settings.annotator_redis_host, :port => Annotator.settings.annotator_redis_port)
     db_size = @@redis.dbsize
     if db_size > MAX_TEST_REDIS_SIZE
@@ -25,7 +25,7 @@ def self.before_suite
     annotator = Annotator::Models::NcboAnnotator.new
     annotator.init_redis_for_tests()
     annotator.create_term_cache_from_ontologies(@@ontologies, false)
-    mapping_test_set
+    self.class.mapping_test_set
   end
 
   def test_annotate

test/controllers/test_batch_controller.rb

@@ -1,7 +1,8 @@
 require_relative '../test_case'
 
 class TestBatchController < TestCase
-  def self.before_suite
+  def before_suite
+    LinkedData::SampleData::Ontology.delete_ontologies_and_submissions
     @@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies(process_submission: true)
   end
 
@@ -25,7 +26,7 @@ def test_class_batch_one_ontology
     assert last_response.ok?
     data = MultiJson.load(last_response.body)
     classes = data["http://www.w3.org/2002/07/owl#Class"]
-    assert classes.length == 4
+    assert_equal 4, classes.length
     classes.each do |klass|
       assert_instance_of String, klass["prefLabel"]
       assert_instance_of Array, klass["synonym"]
@@ -75,18 +76,19 @@ def test_class_batch_multiple
     assert last_response.ok?
     data = MultiJson.load(last_response.body)
     classes = data["http://www.w3.org/2002/07/owl#Class"]
-    assert classes.length == 6
+    assert_equal 6, classes.length
     classes.each do |klass|
       assert_instance_of String, klass["prefLabel"]
-      assert !klass["synonym"]
-      assert klass["prefLabel"] == class_ids[klass["@id"]]
+      refute klass["synonym"]
+      assert_equal klass["prefLabel"], class_ids[klass["@id"]]
     end
   end
 
 
   def test_class_all_bro
     mccl = @@ontologies.select { |y| y.id.to_s.include? "MCCL"}.first
     assert mccl, "mccl is not found to execute batch test."
+    # binding.pry
     classes = LinkedData::Models::Class.in(mccl.latest_submission).include(:prefLabel).page(1,500).read_only.all
     class_ids = {}
     classes.each do |klass|
@@ -101,9 +103,10 @@ def test_class_all_bro
     }
     post "/batch/", call_params
     assert last_response.ok?
+#    refute last_response.ok?
     data = MultiJson.load(last_response.body)
     classes_response = data["http://www.w3.org/2002/07/owl#Class"]
-    assert classes_response.length == classes.length
+    assert_equal classes.length, classes_response.length
     classes_response.each do |klass|
       assert_instance_of String, klass["prefLabel"]
       assert klass["prefLabel"] == class_ids[klass["@id"]]

test/controllers/test_classes_controller.rb

@@ -2,7 +2,7 @@
 
 class TestClassesController < TestCase
 
-  def self.before_suite
+  def before_suite
     options = {ont_count: 1,
                submission_count: 3,
                submissions_to_process: [1, 2],

test/controllers/test_instances_controller.rb

@@ -2,7 +2,7 @@
 
 class TestInstancesController < TestCase
 
-  def self.before_suite
+  def before_suite
     LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
       process_submission: true,
       acronym: 'XCT-TEST-INST',

test/controllers/test_mappings_controller.rb

@@ -2,8 +2,8 @@
 
 class TestMappingsController < TestCase
 
-  def self.before_suite
-
+  def before_suite
+    self.backend_4s_delete
     ["BRO-TEST-MAP-0","CNO-TEST-MAP-0","FAKE-TEST-MAP-0"].each do |acr|
       LinkedData::Models::OntologySubmission.where(ontology: [acronym: acr]).to_a.each do |s|
         s.delete

test/controllers/test_metrics_controller.rb

@@ -2,7 +2,7 @@
 
 class TestMetricsController < TestCase
 
-  def self.before_suite
+  def before_suite
     if OntologySubmission.all.count > 100
       puts "this test is going to wipe out all submission and ontologies. probably this is not a test env."
       return