update the tests files to use the new minitest framework

ncbo · Mar 21, 2024 · b3c5eb7 · b3c5eb7
1 parent 141cbce
commit b3c5eb7
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Showing 30 changed files with 167 additions and 122 deletions.
diff --git a/.env 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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