From 141cbcedac92386711e0112849ad0c57ee271d3e Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Wed, 20 Mar 2024 09:05:46 +0100
Subject: [PATCH 1/2] update minitest, bigdecimal, and activesupport to newer
 versions

---
 Gemfile      | 15 +++++++++------
 Gemfile.lock | 48 +++++++++++++++++++++++++++---------------------
 2 files changed, 36 insertions(+), 27 deletions(-)

diff --git a/Gemfile b/Gemfile
index ec1f76f3..288250fa 100644
--- a/Gemfile
+++ b/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'
@@ -69,9 +69,12 @@ group :profiling do
 end
 
 group :test do
-  gem 'minitest', '~> 4.0'
+  gem 'minitest', '~> 5.0'
   gem 'minitest-stub_any_instance'
   gem 'rack-test'
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
+  gem 'crack', '0.4.5'
+  gem 'webmock'
+  gem "minitest-hooks", "~> 1.5"
 end
diff --git a/Gemfile.lock b/Gemfile.lock
index 37f2a36d..c17a0941 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -100,9 +100,11 @@ 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 (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
     airbrussh (1.5.1)
@@ -112,7 +114,7 @@ GEM
     base64 (0.2.0)
     bcrypt (3.1.20)
     bcrypt_pbkdf (1.1.0)
-    bigdecimal (1.4.2)
+    bigdecimal (3.1.6)
     builder (3.2.4)
     capistrano (3.18.1)
       airbrussh (>= 1.0.0)
@@ -128,7 +130,8 @@ GEM
       sshkit (~> 1.3)
     coderay (1.1.3)
     concurrent-ruby (1.2.3)
-    connection_pool (2.4.1)
+    crack (0.4.5)
+      rexml
     cube-ruby (0.0.3)
     dante (0.2.0)
     date (3.3.4)
@@ -168,7 +171,6 @@ GEM
     google-protobuf (3.25.3-aarch64-linux)
     google-protobuf (3.25.3-arm64-darwin)
     google-protobuf (3.25.3-x86_64-darwin)
-    google-protobuf (3.25.3-x86_64-linux)
     googleapis-common-protos (1.5.0)
       google-protobuf (~> 3.18)
       googleapis-common-protos-types (~> 1.7)
@@ -191,16 +193,14 @@ GEM
     grpc (1.62.0-x86_64-darwin)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.62.0-x86_64-linux)
-      google-protobuf (~> 3.25)
-      googleapis-common-protos-types (~> 1.0)
     haml (5.2.2)
       temple (>= 0.8.0)
       tilt
     http-accept (1.7.0)
     http-cookie (1.0.5)
       domain_name (~> 0.5)
-    i18n (0.9.5)
+    httpclient (2.8.3)
+    i18n (1.14.1)
       concurrent-ruby (~> 1.0)
     json (2.7.1)
     json-schema (2.8.1)
@@ -224,7 +224,9 @@ GEM
       mime-types-data (~> 3.2015)
     mime-types-data (3.2024.0305)
     mini_mime (1.1.5)
-    minitest (4.7.5)
+    minitest (5.22.2)
+    minitest-hooks (1.5.1)
+      minitest (> 5.3)
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
       redis
@@ -247,7 +249,8 @@ GEM
     net-ssh (7.2.1)
     netrc (0.11.0)
     newrelic_rpm (9.7.1)
-    oj (3.16.1)
+    oj (3.16.3)
+      bigdecimal (>= 3.0)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
@@ -357,11 +360,13 @@ GEM
       net-ssh (>= 2.8.0)
     systemu (2.6.5)
     temple (0.10.3)
+    thread_safe (0.3.6)
     tilt (2.3.0)
     timeout (0.4.1)
-    tzinfo (2.0.6)
-      concurrent-ruby (~> 1.0)
-    unicode-display_width (2.5.0)
+    trailblazer-option (0.1.2)
+    tzinfo (1.2.11)
+      thread_safe (~> 0.1)
+    uber (0.1.0)
     unicorn (6.1.0)
       kgio (~> 2.6)
       raindrops (~> 0.7)
@@ -377,30 +382,31 @@ PLATFORMS
   arm64-darwin-23
   x86_64-darwin-18
   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

From b3c5eb795875ff884c5c9b1ceb12affb5d67f5d0 Mon Sep 17 00:00:00 2001
From: Syphax bouazzouni <gs_bouazzouni@esi.dz>
Date: Wed, 20 Mar 2024 09:06:05 +0100
Subject: [PATCH 2/2] update the tests files to use the new minitest framework

---
 .env                                          |  6 ++
 Gemfile                                       | 12 +--
 Gemfile.lock                                  | 85 ++++++++++++-------
 test/controllers/test_annotator_controller.rb |  4 +-
 test/controllers/test_batch_controller.rb     |  2 +-
 test/controllers/test_classes_controller.rb   |  2 +-
 test/controllers/test_instances_controller.rb |  2 +-
 test/controllers/test_mappings_controller.rb  |  4 +-
 test/controllers/test_metrics_controller.rb   |  2 +-
 test/controllers/test_notes_controller.rb     |  6 +-
 .../controllers/test_ontologies_controller.rb | 10 +--
 .../test_ontology_analytics_controller.rb     |  8 +-
 .../test_ontology_submissions_controller.rb   |  9 +-
 .../controllers/test_properties_controller.rb |  4 +-
 .../test_properties_search_controller.rb      |  6 +-
 .../test_provisional_classes_controller.rb    |  8 +-
 .../test_provisional_relations_controller.rb  |  8 +-
 .../test_recommender_controller.rb            |  2 +-
 .../test_recommender_v1_controller.rb         |  2 +-
 test/controllers/test_replies_controller.rb   |  4 +-
 test/controllers/test_search_controller.rb    |  5 +-
 test/controllers/test_slices_controller.rb    | 13 ++-
 test/controllers/test_users_controller.rb     |  2 +-
 test/helpers/test_access_control_helper.rb    | 11 +--
 test/helpers/test_application_helper.rb       |  2 +-
 test/helpers/test_http_cache_helper.rb        |  8 +-
 test/helpers/test_slices_helper.rb            | 11 ++-
 test/helpers/test_users_helper.rb             |  9 +-
 test/middleware/test_rack_attack.rb           |  6 +-
 test/test_case.rb                             | 36 +++++---
 30 files changed, 167 insertions(+), 122 deletions(-)
 create mode 100644 .env

diff --git a/.env b/.env
new file mode 100644
index 00000000..2b53fceb
--- /dev/null
+++ b/.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
diff --git a/Gemfile b/Gemfile
index 288250fa..3048681d 100644
--- a/Gemfile
+++ b/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
diff --git a/Gemfile.lock b/Gemfile.lock
index c17a0941..a64ad257 100644
--- a/Gemfile.lock
+++ b/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)
@@ -114,7 +114,7 @@ GEM
     base64 (0.2.0)
     bcrypt (3.1.20)
     bcrypt_pbkdf (1.1.0)
-    bigdecimal (3.1.6)
+    bigdecimal (3.1.7)
     builder (3.2.4)
     capistrano (3.18.1)
       airbrussh (>= 1.0.0)
@@ -130,6 +130,7 @@ GEM
       sshkit (~> 1.3)
     coderay (1.1.3)
     concurrent-ruby (1.2.3)
+    connection_pool (2.4.1)
     crack (0.4.5)
       rexml
     cube-ruby (0.0.3)
@@ -138,13 +139,29 @@ GEM
     docile (1.4.0)
     domain_name (0.6.20240107)
     ed25519 (1.3.0)
-    faraday (2.8.1)
-      base64
-      faraday-net_http (>= 2.0, < 3.1)
+    faraday (1.10.3)
+      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)
       ruby2_keywords (>= 0.0.4)
-    faraday-net_http (3.0.2)
-    faraday-retry (2.2.0)
-      faraday (~> 2.0)
+    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 (1.0.1)
+    faraday-net_http_persistent (1.2.0)
+    faraday-patron (1.0.0)
+    faraday-rack (1.0.0)
+    faraday-retry (1.0.3)
     ffi (1.16.3)
     gapic-common (0.21.1)
       faraday (>= 1.9, < 3.a)
@@ -168,14 +185,14 @@ GEM
     google-cloud-env (2.1.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.4.0)
-    google-protobuf (3.25.3-aarch64-linux)
     google-protobuf (3.25.3-arm64-darwin)
     google-protobuf (3.25.3-x86_64-darwin)
+    google-protobuf (3.25.3-x86_64-linux)
     googleapis-common-protos (1.5.0)
       google-protobuf (~> 3.18)
       googleapis-common-protos-types (~> 1.7)
       grpc (~> 1.41)
-    googleapis-common-protos-types (1.13.0)
+    googleapis-common-protos-types (1.14.0)
       google-protobuf (~> 3.18)
     googleauth (1.11.0)
       faraday (>= 1.0, < 3.a)
@@ -184,23 +201,23 @@ GEM
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.62.0-aarch64-linux)
-      google-protobuf (~> 3.25)
-      googleapis-common-protos-types (~> 1.0)
     grpc (1.62.0-arm64-darwin)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
     grpc (1.62.0-x86_64-darwin)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
+    grpc (1.62.0-x86_64-linux)
+      google-protobuf (~> 3.25)
+      googleapis-common-protos-types (~> 1.0)
     haml (5.2.2)
       temple (>= 0.8.0)
       tilt
+    hashdiff (1.1.0)
     http-accept (1.7.0)
     http-cookie (1.0.5)
       domain_name (~> 0.5)
-    httpclient (2.8.3)
-    i18n (1.14.1)
+    i18n (1.14.4)
       concurrent-ruby (~> 1.0)
     json (2.7.1)
     json-schema (2.8.1)
@@ -224,13 +241,14 @@ GEM
       mime-types-data (~> 3.2015)
     mime-types-data (3.2024.0305)
     mini_mime (1.1.5)
-    minitest (5.22.2)
+    minitest (5.22.3)
     minitest-hooks (1.5.1)
       minitest (> 5.3)
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
+    multipart-post (2.4.0)
     mutex_m (0.2.0)
     net-http-persistent (2.9.4)
     net-imap (0.4.10)
@@ -363,10 +381,9 @@ GEM
     thread_safe (0.3.6)
     tilt (2.3.0)
     timeout (0.4.1)
-    trailblazer-option (0.1.2)
     tzinfo (1.2.11)
       thread_safe (~> 0.1)
-    uber (0.1.0)
+    unicode-display_width (2.5.0)
     unicorn (6.1.0)
       kgio (~> 2.6)
       raindrops (~> 0.7)
@@ -375,13 +392,15 @@ GEM
       unicorn (>= 4, < 7)
     uuid (2.3.9)
       macaddr (~> 1.0)
+    webmock (3.23.0)
+      addressable (>= 2.8.0)
+      crack (>= 0.3.2)
+      hashdiff (>= 0.4.0, < 2.0.0)
 
 PLATFORMS
-  aarch64-linux
   arm64-darwin-22
-  arm64-darwin-23
   x86_64-darwin-18
-  x86_64-darwin-23
+  x86_64-linux
 
 DEPENDENCIES
   activesupport (~> 5)
@@ -394,6 +413,7 @@ DEPENDENCIES
   crack (= 0.4.5)
   cube-ruby
   ed25519 (>= 1.2, < 2.0)
+  faraday (~> 1.9)
   ffi
   goo!
   haml (~> 5.2.2)
@@ -433,6 +453,7 @@ DEPENDENCIES
   sparql-client!
   unicorn
   unicorn-worker-killer
+  webmock
 
 BUNDLED WITH
    2.4.22
diff --git a/test/controllers/test_annotator_controller.rb b/test/controllers/test_annotator_controller.rb
index 3b21b9e7..751176f6 100644
--- a/test/controllers/test_annotator_controller.rb
+++ b/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
@@ -20,7 +20,7 @@ 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
diff --git a/test/controllers/test_batch_controller.rb b/test/controllers/test_batch_controller.rb
index 55d9cee9..a4da9766 100644
--- a/test/controllers/test_batch_controller.rb
+++ b/test/controllers/test_batch_controller.rb
@@ -1,7 +1,7 @@
 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
   end
diff --git a/test/controllers/test_classes_controller.rb b/test/controllers/test_classes_controller.rb
index a918ece0..b88ec369 100644
--- a/test/controllers/test_classes_controller.rb
+++ b/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],
diff --git a/test/controllers/test_instances_controller.rb b/test/controllers/test_instances_controller.rb
index 4e9b8a5c..1735455f 100644
--- a/test/controllers/test_instances_controller.rb
+++ b/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',
diff --git a/test/controllers/test_mappings_controller.rb b/test/controllers/test_mappings_controller.rb
index 44bfa032..d8c6f619 100644
--- a/test/controllers/test_mappings_controller.rb
+++ b/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
diff --git a/test/controllers/test_metrics_controller.rb b/test/controllers/test_metrics_controller.rb
index 1b8890a6..94e55af8 100644
--- a/test/controllers/test_metrics_controller.rb
+++ b/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
diff --git a/test/controllers/test_notes_controller.rb b/test/controllers/test_notes_controller.rb
index d9223669..0c7d2bcb 100644
--- a/test/controllers/test_notes_controller.rb
+++ b/test/controllers/test_notes_controller.rb
@@ -3,9 +3,9 @@
 
 class TestNotesController < TestCase
 
-  def self.before_suite
-    self.new("before_suite").delete_ontologies_and_submissions
-    @@ontology, @@cls = self.new("before_suite")._ontology_and_class
+  def before_suite
+    self.delete_ontologies_and_submissions
+    @@ontology, @@cls = self._ontology_and_class
 
     @@note_user = "test_note_user"
     @@user = LinkedData::Models::User.new(
diff --git a/test/controllers/test_ontologies_controller.rb b/test/controllers/test_ontologies_controller.rb
index 4f61256b..1f99912d 100644
--- a/test/controllers/test_ontologies_controller.rb
+++ b/test/controllers/test_ontologies_controller.rb
@@ -2,11 +2,11 @@
 require_relative '../test_case'
 
 class TestOntologiesController < TestCase
-  def self.before_suite
-    _set_vars
-    _delete
-    _create_user
-    _create_onts
+  def before_suite
+    self.class._set_vars
+    self.class._delete
+    self.class._create_user
+    self.class._create_onts
   end
 
   def teardown
diff --git a/test/controllers/test_ontology_analytics_controller.rb b/test/controllers/test_ontology_analytics_controller.rb
index b8e36dce..721efea6 100644
--- a/test/controllers/test_ontology_analytics_controller.rb
+++ b/test/controllers/test_ontology_analytics_controller.rb
@@ -196,7 +196,7 @@ class TestOntologyAnalyticsController < 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
@@ -212,9 +212,9 @@ def self.before_suite
         "SNOMEDCT" => "SNOMEDCT Ontology",
         "TST" => "TST Ontology"
     }
-    _delete
-    _create_user
-    _create_onts
+    self.class._delete
+    self.class._create_user
+    self.class._create_onts
   end
 
   def teardown
diff --git a/test/controllers/test_ontology_submissions_controller.rb b/test/controllers/test_ontology_submissions_controller.rb
index 40532cd0..4660e10b 100644
--- a/test/controllers/test_ontology_submissions_controller.rb
+++ b/test/controllers/test_ontology_submissions_controller.rb
@@ -2,10 +2,11 @@
 
 class TestOntologySubmissionsController < TestCase
 
-  def self.before_suite
-    _set_vars
-    _create_user
-    _create_onts
+  def before_suite
+    self.backend_4s_delete
+    self.class._set_vars
+    self.class._create_user
+    self.class._create_onts
   end
 
   def self._set_vars
diff --git a/test/controllers/test_properties_controller.rb b/test/controllers/test_properties_controller.rb
index 8248403c..1bd30d5b 100644
--- a/test/controllers/test_properties_controller.rb
+++ b/test/controllers/test_properties_controller.rb
@@ -2,7 +2,7 @@
 
 class TestPropertiesController < TestCase
 
-  def self.before_suite
+  def before_suite
     count, acronyms, bro = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
                                                                                                   process_submission: true,
                                                                                                   acronym: "BROSEARCHTEST",
@@ -25,7 +25,7 @@ def self.before_suite
     @@acronyms = @@ontologies.map { |ont| ont.bring_remaining; ont.acronym }
   end
 
-  def self.after_suite
+  def after_suite
     LinkedData::SampleData::Ontology.delete_ontologies_and_submissions
   end
 
diff --git a/test/controllers/test_properties_search_controller.rb b/test/controllers/test_properties_search_controller.rb
index f93a90a1..4302eb97 100644
--- a/test/controllers/test_properties_search_controller.rb
+++ b/test/controllers/test_properties_search_controller.rb
@@ -2,7 +2,9 @@
 
 class TestPropertiesSearchController < TestCase
 
-  def self.before_suite
+  def before_suite
+    self.backend_4s_delete
+
     count, acronyms, bro = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
                                                                                                   process_submission: true,
                                                                                                   acronym: "BROSEARCHTEST",
@@ -24,7 +26,7 @@ def self.before_suite
     @@ontologies = bro.concat(mccl)
   end
 
-  def self.after_suite
+  def after_suite
     LinkedData::SampleData::Ontology.delete_ontologies_and_submissions
     LinkedData::Models::Ontology.indexClear(:property)
     LinkedData::Models::Ontology.indexCommit(nil, :property)
diff --git a/test/controllers/test_provisional_classes_controller.rb b/test/controllers/test_provisional_classes_controller.rb
index 7225d772..e54c7805 100644
--- a/test/controllers/test_provisional_classes_controller.rb
+++ b/test/controllers/test_provisional_classes_controller.rb
@@ -1,9 +1,9 @@
 require_relative '../test_case'
 
 class TestProvisionalClassesController < TestCase
-  def self.before_suite
-    self.new("before_suite").delete_ontologies_and_submissions
-    @@ontology, classes = self.new("before_suite")._ontology_and_classes
+  def before_suite
+    self.delete_ontologies_and_submissions
+    @@ontology, classes = self._ontology_and_classes
 
     @@cls = classes[0]
     @@cls1 = classes[1]
@@ -32,7 +32,7 @@ def self.before_suite
     end
   end
 
-  def self.after_suite
+  def after_suite
     3.times do |i|
       @@pcs[i].delete
     end
diff --git a/test/controllers/test_provisional_relations_controller.rb b/test/controllers/test_provisional_relations_controller.rb
index 83f2761d..f097dde9 100644
--- a/test/controllers/test_provisional_relations_controller.rb
+++ b/test/controllers/test_provisional_relations_controller.rb
@@ -1,9 +1,9 @@
 require_relative '../test_case'
 
 class TestProvisionalRelationsController < TestCase
-  def self.before_suite
-    self.new("before_suite").delete_ontologies_and_submissions
-    @@ontology, classes = self.new("before_suite")._ontology_and_classes
+  def before_suite
+    self.delete_ontologies_and_submissions
+    @@ontology, classes = self._ontology_and_classes
 
     @@cls1 = classes[0]
     @@cls2 = classes[1]
@@ -39,7 +39,7 @@ def self.before_suite
     @@test_rel.save
   end
 
-  def self.after_suite
+  def after_suite
     @@test_pc.delete
     @@test_user.delete
   end
diff --git a/test/controllers/test_recommender_controller.rb b/test/controllers/test_recommender_controller.rb
index 29caf28c..96b6e106 100644
--- a/test/controllers/test_recommender_controller.rb
+++ b/test/controllers/test_recommender_controller.rb
@@ -2,7 +2,7 @@
 
 class TestRecommenderController < 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
diff --git a/test/controllers/test_recommender_v1_controller.rb b/test/controllers/test_recommender_v1_controller.rb
index 7b14a63d..074cda8f 100644
--- a/test/controllers/test_recommender_v1_controller.rb
+++ b/test/controllers/test_recommender_v1_controller.rb
@@ -2,7 +2,7 @@
 
 class TestRecommenderController < TestCase
 
-  def self.before_suite
+  def before_suite
     LinkedData::SampleData::Ontology.delete_ontologies_and_submissions
     @@ontologies = LinkedData::SampleData::Ontology.sample_owl_ontologies
     @@text = <<eos
diff --git a/test/controllers/test_replies_controller.rb b/test/controllers/test_replies_controller.rb
index 41b15e2e..19a6ddd0 100644
--- a/test/controllers/test_replies_controller.rb
+++ b/test/controllers/test_replies_controller.rb
@@ -2,8 +2,8 @@
 
 class TestRepliesController < TestCase
 
-  def self.before_suite
-    ontologies = self.new("before_suite").create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: false)[2]
+  def before_suite
+    ontologies = self.create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: false)[2]
     @@ontology = ontologies.first
 
     @@reply_user = "test_reply_user"
diff --git a/test/controllers/test_search_controller.rb b/test/controllers/test_search_controller.rb
index 70bf246e..5ffb9ecf 100644
--- a/test/controllers/test_search_controller.rb
+++ b/test/controllers/test_search_controller.rb
@@ -2,7 +2,8 @@
 
 class TestSearchController < TestCase
 
-  def self.before_suite
+  def before_suite
+     self.backend_4s_delete
      count, acronyms, bro = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
       process_submission: true,
       acronym: "BROSEARCHTEST",
@@ -54,7 +55,7 @@ def self.before_suite
     @@test_pc_child.save
   end
 
-  def self.after_suite
+  def after_suite
     @@test_pc_root.delete
     @@test_pc_child.delete
     LinkedData::SampleData::Ontology.delete_ontologies_and_submissions
diff --git a/test/controllers/test_slices_controller.rb b/test/controllers/test_slices_controller.rb
index 308b9fb7..e1250ba2 100644
--- a/test/controllers/test_slices_controller.rb
+++ b/test/controllers/test_slices_controller.rb
@@ -2,12 +2,11 @@
 
 class TestSlicesController < TestCase
 
-  def self.before_suite
+  def before_suite
     ont_count, ont_acronyms, @@onts = LinkedData::SampleData::Ontology.create_ontologies_and_submissions(ont_count: 1, submission_count: 0)
-
     @@slice_acronyms = ["tst-a", "tst-b"].sort
-    _create_slice(@@slice_acronyms[0], "Test Slice A", @@onts)
-    _create_slice(@@slice_acronyms[1], "Test Slice B", @@onts)
+    self.class._create_slice(@@slice_acronyms[0], "Test Slice A", @@onts)
+    self.class._create_slice(@@slice_acronyms[1], "Test Slice B", @@onts)
 
     @@user = User.new({
                         username: "test-slice",
@@ -15,13 +14,13 @@ def self.before_suite
                         password: "12345"
                       }).save
     @@new_slice_data = { acronym: 'tst-c', name: "Test Slice C", ontologies: ont_acronyms}
-    enable_security
+    self.class.enable_security
   end
 
-  def self.after_suite
+  def after_suite
     LinkedData::Models::Slice.all.each(&:delete)
     @@user.delete
-    reset_security
+    self.class.reset_security
   end
 
   def setup
diff --git a/test/controllers/test_users_controller.rb b/test/controllers/test_users_controller.rb
index 53bf520f..4a33a79a 100644
--- a/test/controllers/test_users_controller.rb
+++ b/test/controllers/test_users_controller.rb
@@ -1,7 +1,7 @@
 require_relative '../test_case'
 
 class TestUsersController < TestCase
-  def self.before_suite
+  def before_suite
     # Create a bunch of test users
     @@usernames = %w(fred goerge henry ben mark matt charlie)
 
diff --git a/test/helpers/test_access_control_helper.rb b/test/helpers/test_access_control_helper.rb
index 1e3807d5..19b0ae0f 100644
--- a/test/helpers/test_access_control_helper.rb
+++ b/test/helpers/test_access_control_helper.rb
@@ -2,8 +2,8 @@
 
 class TestAccessControlHelper < TestCaseHelpers
 
-  def self.before_suite
-    self.new("before_suite").delete_ontologies_and_submissions
+  def before_suite
+    self.backend_4s_delete
 
     @@usernames = ["user1", "user2", "user3", "admin"]
     @@usernames.each do |username|
@@ -14,7 +14,7 @@ def self.before_suite
       )
       user.save
       user.bring_remaining
-      self.class_variable_set(:"@@#{username}", user)
+      self.class.class_variable_set(:"@@#{username}", user)
     end
 
     @@admin.role = [LinkedData::Models::Users::Role.find(LinkedData::Models::Users::Role::ADMIN).first]
@@ -42,8 +42,9 @@ def self.before_suite
     LinkedData.settings.enable_security = true
   end
 
-  def self.after_suite
-    LinkedData.settings.enable_security = @@old_security_setting if class_variable_defined?("@@old_security_setting")
+  def after_suite
+    self.backend_4s_delete
+    LinkedData.settings.enable_security = @@old_security_setting unless @@old_security_setting.nil?
   end
 
   def test_filtered_list
diff --git a/test/helpers/test_application_helper.rb b/test/helpers/test_application_helper.rb
index b90aa30f..2315a677 100644
--- a/test/helpers/test_application_helper.rb
+++ b/test/helpers/test_application_helper.rb
@@ -3,7 +3,7 @@
 
 class TestApplicationHelper < TestCaseHelpers
 
-  def self.before_suite
+  def before_suite
     @@ontologies = LinkedData::SampleData::Ontology.create_ontologies_and_submissions[2]
   end
 
diff --git a/test/helpers/test_http_cache_helper.rb b/test/helpers/test_http_cache_helper.rb
index 944198a6..8a88cc55 100644
--- a/test/helpers/test_http_cache_helper.rb
+++ b/test/helpers/test_http_cache_helper.rb
@@ -2,10 +2,10 @@
 
 class TestHTTPCacheHelper < TestCaseHelpers
 
-  def self.before_suite
+  def before_suite
     raise Exception, "Redis is unavailable, caching will not function" if LinkedData::HTTPCache.redis.ping.nil?
-    self.new("before_suite").delete_ontologies_and_submissions
-    ontologies = self.new("before_suite")._ontologies
+    self.delete_ontologies_and_submissions
+    ontologies = self._ontologies
     @@ontology = ontologies.shift
     @@ontology_alt = ontologies.shift
     @@ontology.bring_remaining
@@ -39,7 +39,7 @@ def self.before_suite
     LinkedData.settings.enable_http_cache = true
   end
 
-  def self.after_suite
+  def after_suite
     LinkedData.settings.enable_http_cache = @orig_enable_cache
     LinkedData::HTTPCache.invalidate_all
   end
diff --git a/test/helpers/test_slices_helper.rb b/test/helpers/test_slices_helper.rb
index 165a2a7e..e776c155 100644
--- a/test/helpers/test_slices_helper.rb
+++ b/test/helpers/test_slices_helper.rb
@@ -2,13 +2,14 @@
 
 class TestSlicesHelper < TestCaseHelpers
 
-  def self.before_suite
-    self.new("before_suite").delete_ontologies_and_submissions
+  def before_suite
+    self.backend_4s_delete
+
     @@orig_slices_setting = LinkedData.settings.enable_slices
     LinkedData.settings.enable_slices = true
     @@onts = LinkedData::SampleData::Ontology.create_ontologies_and_submissions(ont_count: 5, submission_count: 0)[2]
     @@group_acronym = "test-group"
-    @@group = _create_group
+    @@group = self.class._create_group
     @@onts[0..2].each do |o|
       o.bring_remaining
       o.group = [@@group]
@@ -30,6 +31,10 @@ def self.before_suite
     LinkedData::Models::Slice.synchronize_groups_to_slices
   end
 
+  def after_suite
+    self.backend_4s_delete
+  end
+
   def test_filtered_list
     get "http://#{@@group_acronym}.dev/ontologies"
     assert last_response.ok?
diff --git a/test/helpers/test_users_helper.rb b/test/helpers/test_users_helper.rb
index 6cd5bd50..9f1614f1 100644
--- a/test/helpers/test_users_helper.rb
+++ b/test/helpers/test_users_helper.rb
@@ -2,9 +2,10 @@
 
 class TestUsersHelper < TestCaseHelpers
 
-  def self.before_suite
-    @@user = _create_user
-    @@non_custom_user = _create_user("notcustom")
+  def before_suite
+    self.backend_4s_delete
+    @@user = self.class._create_user
+    @@non_custom_user = self.class._create_user("notcustom")
 
     @@onts = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
       ont_count: 5,
@@ -29,7 +30,7 @@ def self.before_suite
     LinkedData.settings.enable_security = true
   end
 
-  def self.after_suite
+  def after_suite
     LinkedData.settings.enable_security = @@old_security_setting
   end
 
diff --git a/test/middleware/test_rack_attack.rb b/test/middleware/test_rack_attack.rb
index 42b1ddf2..7f2f990e 100644
--- a/test/middleware/test_rack_attack.rb
+++ b/test/middleware/test_rack_attack.rb
@@ -5,8 +5,8 @@
 RACK_CONFIG = File.join([settings.root, "config.ru"])
 
 class TestRackAttack < TestCase
-
-  def self.before_suite
+  
+  def before_suite
     # Store app settings
     @@auth_setting = LinkedData.settings.enable_security
     @@throttling_setting = LinkedData.settings.enable_throttling
@@ -61,7 +61,7 @@ def self.before_suite
     sleep(5)
   end
 
-  def self.after_suite
+  def after_suite
     # Restore app settings
     LinkedData.settings.enable_security = @@auth_setting
     LinkedData::OntologiesAPI.settings.enable_throttling = @@throttling_setting
diff --git a/test/test_case.rb b/test/test_case.rb
index 98b02442..4b029b61 100644
--- a/test/test_case.rb
+++ b/test/test_case.rb
@@ -20,8 +20,10 @@
 
 require_relative 'test_log_file'
 require_relative '../app'
-require 'minitest/unit'
-MiniTest::Unit.autorun
+require 'minitest/autorun'
+require 'minitest/hooks/test'
+require 'webmock/minitest'
+WebMock.allow_net_connect!
 require 'rack/test'
 require 'multi_json'
 require 'oj'
@@ -60,7 +62,9 @@ def safe_redis_hosts?(sh)
   $stdout.flush
 end
 
-class AppUnit < MiniTest::Unit
+class AppUnit < Minitest::Test
+  include Minitest::Hooks
+
   def count_pattern(pattern)
     q = "SELECT (count(DISTINCT ?s) as ?c) WHERE { #{pattern} }"
     rs = Goo.sparql_query_client.query(q)
@@ -88,23 +92,27 @@ def backend_4s_delete
     end
   end
 
-  def before_suites
+  def before_suite
     # code to run before the first test (gets inherited in sub-tests)
   end
 
-  def after_suites
+  def after_suite
     # code to run after the last test (gets inherited in sub-tests)
   end
 
-  def _run_suites(suites, type)
-    begin
-      before_suites
-      super(suites, type)
-    ensure
-      after_suites
-    end
+  def before_all
+    super
+    backend_4s_delete
+    before_suite
   end
 
+  def after_all
+    after_suite
+    super
+  end
+
+
+
   def _run_suite(suite, type)
     begin
       backend_4s_delete
@@ -122,12 +130,12 @@ def _run_suite(suite, type)
   end
 end
 
-AppUnit.runner = AppUnit.new
+
 
 # All tests should inherit from this class.
 # Use 'rake test' from the command line to run tests.
 # See http://www.sinatrarb.com/testing.html for testing information
-class TestCase < MiniTest::Unit::TestCase
+class TestCase < AppUnit
   include Rack::Test::Methods