Develop to Master merge, release v5.33.0

.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'
@@ -43,12 +43,12 @@ gem 'redcarpet'
 
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
-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 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
-gem 'goo', github: 'ncbo/goo', branch: 'master'
-gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master'
+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 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
+gem 'goo', github: 'ncbo/goo', branch: 'develop'
+gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop'
 
 
 group :development do
@@ -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

@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 2cec53c2d84179171def81d7dc0a18e462e78fc2
-  branch: master
+  revision: 74a012eebb9433d031eb00df5abbe488cb8b4512
+  branch: develop
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -16,8 +16,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 63c986880aa88c9384043e6611a682434a14aba7
-  branch: master
+  revision: b2731c98bfef0958fecb440c8648b7755a670895
+  branch: develop
   specs:
     ncbo_annotator (0.0.1)
       goo
@@ -27,8 +27,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_cron.git
-  revision: 15ccdaa2835be9f35f9c3afdcc4ed5bf5d130999
-  branch: master
+  revision: b279f9caa9a6a169bad7350890d7015d56e9e9b2
+  branch: develop
   specs:
     ncbo_cron (0.0.1)
       dante
@@ -45,8 +45,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: 013abea4af3b10910ec661dbb358a4b6cae198a4
-  branch: master
+  revision: 084cfc74a78b1c6334f3b74e228ddbf80d36e30a
+  branch: develop
   specs:
     ncbo_ontology_recommender (0.0.1)
       goo
@@ -56,8 +56,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: a9da0982eef16ea8272002d14d6b8851dc07fb0a
-  branch: master
+  revision: 812dd78f02b77c9c6d579b0febf1c2a42d513022
+  branch: develop
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -76,8 +76,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
-  branch: master
+  revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc
+  branch: develop
   specs:
     sparql-client (1.0.1)
       json_pure (>= 1.4)
@@ -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 +118,7 @@ GEM
     bcrypt (3.1.20)
     bcrypt_pbkdf (1.1.1)
     bcrypt_pbkdf (1.1.1-arm64-darwin)
-    bigdecimal (1.4.2)
+    bigdecimal (3.1.8)
     builder (3.3.0)
     capistrano (3.19.1)
       airbrussh (>= 1.0.0)
@@ -133,8 +135,7 @@ 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)
@@ -174,7 +175,7 @@ GEM
     google-cloud-core (1.7.1)
       google-cloud-env (>= 1.0, < 3.a)
       google-cloud-errors (~> 1.0)
-    google-cloud-env (2.2.0)
+    google-cloud-env (2.2.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.4.0)
     google-protobuf (3.25.5-aarch64-linux)
@@ -186,7 +187,7 @@ GEM
       grpc (~> 1.41)
     googleapis-common-protos-types (1.16.0)
       google-protobuf (>= 3.18, < 5.a)
-    googleauth (1.11.0)
+    googleauth (1.11.1)
       faraday (>= 1.0, < 3.a)
       google-cloud-env (~> 2.1)
       jwt (>= 1.4, < 3.0)
@@ -209,13 +210,13 @@ 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 (2.9.1)
+    jwt (2.9.3)
       base64
     kgio (2.11.4)
     language_server-protocol (3.17.0.3)
@@ -229,11 +230,14 @@ GEM
       net-pop
       net-smtp
     method_source (1.1.0)
-    mime-types (3.5.2)
+    mime-types (3.6.0)
+      logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0903)
+    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
@@ -254,10 +258,12 @@ GEM
       net-ssh (>= 5.0.0, < 8.0.0)
     net-smtp (0.5.0)
       net-protocol
-    net-ssh (7.2.3)
+    net-ssh (7.3.0)
     netrc (0.11.0)
-    newrelic_rpm (9.13.0)
-    oj (3.16.1)
+    newrelic_rpm (9.14.0)
+    oj (3.16.6)
+      bigdecimal (>= 3.0)
+      ostruct (>= 0.2)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
@@ -313,7 +319,7 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.3.7)
+    rexml (3.3.8)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -369,10 +375,11 @@ 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)
@@ -395,27 +402,29 @@ 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)
   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
@@ -447,4 +456,4 @@ DEPENDENCIES
   webrick
 
 BUNDLED WITH
-   2.5.19
+   2.5.20

controllers/recommender_v1_controller.rb

@@ -1,17 +1,10 @@
 class RecommenderController < ApplicationController
   namespace "/recommender_v1" do
 
-    # execute an annotator query
+    # Mark this route as deprecated
     get do
-      text = params["text"]
-      raise error 400, "A text to be analyzed by the recommender must be supplied using the argument text=<text>" if text.nil? || text.strip.empty?
-      acronyms = restricted_ontologies_to_acronyms(params)
-      display_classes = params['display_classes'].eql?('true')  # default will be false
-      recommender = Recommender::Models::NcboRecommender.new
-      recommendations = recommender.recommend(text, acronyms, display_classes)
-      reply 200, recommendations
+      reply 410, { message: "This API endpoint has been deprecated and is no longer available. Please use /recommender or refer to the API documentation for updated routes." }
     end
 
   end
 end
-

controllers/users_controller.rb

@@ -46,14 +46,24 @@ class UsersController < ApplicationController
       params["display"] = User.attributes.join(",") # used to serialize everything via the serializer
       user = LinkedData::Models::User.where(email: email, username: username).include(User.goo_attrs_to_load(includes_param)).first
       error 404, "User not found" unless user
+
+      user.bring(:resetToken)
+      user.bring(:resetTokenExpireTime)
+      user.bring(:passwordHash)
+
       if token.eql?(user.resetToken)
         error 401, "Invalid password reset token" if user.resetTokenExpireTime.nil?
         error 401, "The password reset token expired" if user.resetTokenExpireTime < Time.now.to_i
         user.resetToken = nil
         user.resetTokenExpireTime = nil
-        user.save(override_security: true) if user.valid?
-        user.show_apikey = true
-        reply user
+
+        if user.valid?
+          user.save(override_security: true)
+          user.show_apikey = true
+          reply user
+        else
+          error 422, "Error resetting password"
+        end
       else
         error 401, "Password reset not authorized with this token"
       end

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