diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml
index 16d8357e..39d28a8c 100644
--- a/.github/workflows/ruby-unit-tests.yml
+++ b/.github/workflows/ruby-unit-tests.yml
@@ -2,15 +2,14 @@ name: Ruby Unit Tests
 
 on:
   push:
-  pull_request:
 
 jobs:
   test:
     strategy:
       fail-fast: false
       matrix:
-        goo-slice: [ '20', '100', '500' ]
-        ruby-version: [ '2.7' ]
+        goo-slice: [ '100' ]
+        ruby-version: [ '3.2.0' ]
         triplestore: [ 'fs', 'ag', 'vo', 'gb' ]
     runs-on: ubuntu-latest
     steps:
@@ -28,11 +27,10 @@ jobs:
           ruby-version: ${{ matrix.ruby-version }}
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
       - name: Run unit tests
-        # unit tests are run inside a container
-        # http://docs.codecov.io/docs/testing-with-docker
         run: |
           ci_env=`bash <(curl -s https://codecov.io/env)`
-          GOO_SLICES=${{ matrix.goo-slice }} bundle exec rake test:docker:${{ matrix.triplestore }} TESTOPTS="-v"
+          GOO_SLICES=${{ matrix.goo-slice }} bundle exec rake test:docker:${{ matrix.triplestore }}
+
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
         with:
diff --git a/Gemfile b/Gemfile
index bf0d2af8..bf659419 100644
--- a/Gemfile
+++ b/Gemfile
@@ -1,40 +1,43 @@
 source 'https://rubygems.org'
-gem 'activesupport', '~> 5'
-# see https://github.com/ncbo/ontologies_api/issues/69
+gem 'activesupport'
 gem 'bigdecimal'
-# gem 'faraday', '~> 1.9'
-gem 'json-schema', '~> 2.0'
+gem 'json-schema'
 gem 'multi_json'
 gem 'oj'
 gem 'parseconfig'
 gem 'rack'
-gem 'rake', '~> 10.0'
+gem 'rake'
 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'
+gem 'sinatra'
+gem 'rackup'
+
+github 'sinatra/sinatra' do
+  gem 'sinatra-contrib'
+end
+
 gem 'request_store'
 gem 'parallel'
-gem 'json-ld'
-gem 'google-protobuf', '3.25.3'
+gem 'google-protobuf'
+gem 'net-ftp'
+gem 'json-ld', '~> 3.2.0'
+gem 'rdf-raptor', github:'ruby-rdf/rdf-raptor', ref: '6392ceabf71c3233b0f7f0172f662bd4a22cd534' # use version 3.3.0 when available
 
 # Rack middleware
-gem 'ffi', '~> 1.16.3'
-gem 'rack-accept', '~> 0.4'
-gem 'rack-attack', '~> 6.6.1', require: 'rack/attack'
-gem 'rack-cache', '~> 1.13.0'
+gem 'ffi'
+gem 'rack-accept'
+gem 'rack-attack', require: 'rack/attack'
+gem 'rack-cache'
 gem 'rack-cors', require: 'rack/cors'
 # GitHub dependency can be removed when https://github.com/niko/rack-post-body-to-params/pull/6 is merged and released
 gem 'rack-post-body-to-params', github: 'palexander/rack-post-body-to-params', branch: 'multipart_support'
 gem 'rack-timeout'
-gem 'redis-rack-cache', '~> 2.0'
+gem 'redis-rack-cache'
 
 # Data access (caching)
 gem 'redis'
-gem 'redis-store', '~>1.10'
+gem 'redis-store'
 
 # Monitoring
-gem 'cube-ruby', require: 'cube'
 gem 'newrelic_rpm', group: [:default, :deployment]
 
 # HTTP server
@@ -42,16 +45,16 @@ gem 'unicorn'
 gem 'unicorn-worker-killer'
 
 # Templating
-gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
+gem 'haml'
 gem 'redcarpet'
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
 gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'development'
-gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'development'
+gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'feature/migrate-to-ruby-3.2'
 gem 'ncbo_ontology_recommender', git: 'https://github.com/ontoportal-lirmm/ncbo_ontology_recommender.git', branch: 'development'
-gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
+gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'feature/migrate-ruby-3.2'
+gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'feature/migrate-ruby-3.2'
 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
@@ -77,12 +80,14 @@ end
 
 group :test do
   gem 'crack', '0.4.5'
-  gem 'minitest', '~> 5.0'
-  gem 'minitest-hooks', "~> 1.5"
+  gem 'minitest'
+  gem 'minitest-hooks'
   gem 'minitest-stub_any_instance'
+  gem 'minitest-reporters'
+  gem 'minitest-fail-fast'
   gem 'rack-test'
   gem 'simplecov', require: false
   gem 'simplecov-cobertura' # for codecov.io
-  gem 'webmock', '~> 3.19.1'
+  gem 'webmock'
   gem 'webrick'
 end
diff --git a/Gemfile.lock b/Gemfile.lock
index f0708f5a..eda9337a 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,12 +1,12 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: 5825dc1f9d0ff439b1ba9d8f78fa7bb20b1c65d0
-  branch: development
+  revision: dd3ea6c0f583c2044622a9f872a0bd18e898bb79
+  branch: feature/migrate-ruby-3.2
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
       pry
-      rdf (= 3.2.11)
+      rdf
       rdf-raptor
       rdf-rdfxml
       rdf-vocab
@@ -29,8 +29,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ncbo_cron.git
-  revision: dd736917974f13ac7558e0d2a61a84030d82acaa
-  branch: development
+  revision: 9cbc8b9ea384350597412c24e3dffb96b7d650ff
+  branch: feature/migrate-to-ruby-3.2
   specs:
     ncbo_cron (0.0.1)
       dante
@@ -42,7 +42,7 @@ GIT
       ncbo_annotator
       ontologies_linked_data
       redis
-      rufus-scheduler (~> 2.0.24)
+      rufus-scheduler
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ncbo_ontology_recommender.git
@@ -57,8 +57,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 6cb18910e322645e3cc3490951d10f19468da52f
-  branch: development
+  revision: d5f5a439fdec58a9f0ac074f263dc18ff78f3df0
+  branch: feature/migrate-ruby-3.2
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -77,7 +77,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/sparql-client.git
-  revision: d4a226e75eb4aeaaf42720eac4f23f55380a0bd3
+  revision: 736b7650e28db3ce5e3e49511ac30f958a29e8f1
   branch: development
   specs:
     sparql-client (3.2.2)
@@ -100,23 +100,58 @@ GIT
     shotgun (0.9)
       rack (>= 1.0)
 
+GIT
+  remote: https://github.com/ruby-rdf/rdf-raptor.git
+  revision: 6392ceabf71c3233b0f7f0172f662bd4a22cd534
+  ref: 6392ceabf71c3233b0f7f0172f662bd4a22cd534
+  specs:
+    rdf-raptor (3.3.0)
+      ffi (~> 1.15)
+      rdf (~> 3.3)
+
+GIT
+  remote: https://github.com/sinatra/sinatra.git
+  revision: c4b7c04e6d23ef8e17404d64cc731bece268acea
+  specs:
+    rack-protection (4.1.1)
+      base64 (>= 0.1.0)
+      logger (>= 1.6.0)
+      rack (>= 3.0.0, < 4)
+    sinatra-contrib (4.1.1)
+      multi_json (>= 0.0.2)
+      mustermann (~> 3.0)
+      rack-protection (= 4.1.1)
+      sinatra (= 4.1.1)
+      tilt (~> 2.0)
+
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (5.2.8.1)
-      concurrent-ruby (~> 1.0, >= 1.0.2)
-      i18n (>= 0.7, < 2)
-      minitest (~> 5.1)
-      tzinfo (~> 1.1)
+    activesupport (8.0.1)
+      base64
+      benchmark (>= 0.3)
+      bigdecimal
+      concurrent-ruby (~> 1.0, >= 1.3.1)
+      connection_pool (>= 2.2.5)
+      drb
+      i18n (>= 1.6, < 2)
+      logger (>= 1.4.2)
+      minitest (>= 5.1)
+      securerandom (>= 0.3)
+      tzinfo (~> 2.0, >= 2.0.5)
+      uri (>= 0.13.1)
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
     airbrussh (1.5.3)
       sshkit (>= 1.6.1, != 1.7.0)
+    ansi (1.5.0)
     ast (2.4.2)
-    backports (3.25.0)
     base64 (0.2.0)
+    bcp47_spec (0.2.1)
     bcrypt (3.1.20)
     bcrypt_pbkdf (1.1.1)
+    bcrypt_pbkdf (1.1.1-arm64-darwin)
+    benchmark (0.4.0)
     bigdecimal (3.1.9)
     builder (3.3.0)
     capistrano (3.19.2)
@@ -136,36 +171,45 @@ GEM
     connection_pool (2.5.0)
     crack (0.4.5)
       rexml
-    cube-ruby (0.0.3)
     dante (0.2.0)
     date (3.4.1)
     declarative (0.0.20)
     docile (1.4.1)
     domain_name (0.6.20240107)
+    drb (2.2.1)
     ed25519 (1.3.0)
-    faraday (2.8.1)
-      base64
-      faraday-net_http (>= 2.0, < 3.1)
-      ruby2_keywords (>= 0.0.4)
-    faraday-net_http (3.0.2)
+    et-orbi (1.2.11)
+      tzinfo
+    faraday (2.12.2)
+      faraday-net_http (>= 2.0, < 3.5)
+      json
+      logger
+    faraday-net_http (3.4.0)
+      net-http (>= 0.5.0)
     faraday-retry (2.2.1)
       faraday (~> 2.0)
-    ffi (1.16.3)
-    gapic-common (0.21.1)
+    ffi (1.17.1-arm64-darwin)
+    ffi (1.17.1-x86_64-linux-gnu)
+    fugit (1.11.1)
+      et-orbi (~> 1, >= 1.2.11)
+      raabro (~> 1.4)
+    gapic-common (0.25.0)
       faraday (>= 1.9, < 3.a)
       faraday-retry (>= 1.0, < 3.a)
-      google-protobuf (~> 3.18)
-      googleapis-common-protos (>= 1.4.0, < 2.a)
-      googleapis-common-protos-types (>= 1.11.0, < 2.a)
-      googleauth (~> 1.9)
-      grpc (~> 1.59)
+      google-cloud-env (~> 2.2)
+      google-logging-utils (~> 0.1)
+      google-protobuf (>= 3.25, < 5.a)
+      googleapis-common-protos (~> 1.6)
+      googleapis-common-protos-types (~> 1.15)
+      googleauth (~> 1.12)
+      grpc (~> 1.66)
     get_process_mem (0.2.7)
       ffi (~> 1.0)
-    google-analytics-data (0.6.1)
+    google-analytics-data (0.7.0)
       google-analytics-data-v1beta (>= 0.11, < 2.a)
       google-cloud-core (~> 1.6)
-    google-analytics-data-v1beta (0.14.0)
-      gapic-common (>= 0.21.1, < 2.a)
+    google-analytics-data-v1beta (0.16.0)
+      gapic-common (>= 0.25.0, < 2.a)
       google-cloud-errors (~> 1.0)
     google-apis-analytics_v3 (0.16.0)
       google-apis-core (>= 0.15.0, < 2.a)
@@ -180,28 +224,39 @@ GEM
     google-cloud-core (1.7.1)
       google-cloud-env (>= 1.0, < 3.a)
       google-cloud-errors (~> 1.0)
-    google-cloud-env (2.1.1)
+    google-cloud-env (2.2.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.4.0)
-    google-protobuf (3.25.3-x86_64-linux)
+    google-logging-utils (0.1.0)
+    google-protobuf (4.29.3-arm64-darwin)
+      bigdecimal
+      rake (>= 13)
+    google-protobuf (4.29.3-x86_64-linux)
+      bigdecimal
+      rake (>= 13)
     googleapis-common-protos (1.6.0)
       google-protobuf (>= 3.18, < 5.a)
       googleapis-common-protos-types (~> 1.7)
       grpc (~> 1.41)
     googleapis-common-protos-types (1.18.0)
       google-protobuf (>= 3.18, < 5.a)
-    googleauth (1.11.2)
+    googleauth (1.13.1)
       faraday (>= 1.0, < 3.a)
-      google-cloud-env (~> 2.1)
+      google-cloud-env (~> 2.2)
+      google-logging-utils (~> 0.1)
       jwt (>= 1.4, < 3.0)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.65.2-x86_64-linux)
+    grpc (1.70.1-arm64-darwin)
+      google-protobuf (>= 3.25, < 5.0)
+      googleapis-common-protos-types (~> 1.0)
+    grpc (1.70.1-x86_64-linux)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    haml (5.2.2)
-      temple (>= 0.8.0)
+    haml (6.3.0)
+      temple (>= 0.8.2)
+      thor
       tilt
     hashdiff (1.1.2)
     htmlentities (4.3.4)
@@ -212,15 +267,21 @@ GEM
     i18n (1.14.7)
       concurrent-ruby (~> 1.0)
     json (2.9.1)
-    json-ld (3.0.2)
-      multi_json (~> 1.12)
-      rdf (>= 2.2.8, < 4.0)
-    json-schema (2.8.1)
-      addressable (>= 2.4)
+    json-canonicalization (0.4.0)
+    json-ld (3.2.5)
+      htmlentities (~> 4.3)
+      json-canonicalization (~> 0.3, >= 0.3.2)
+      link_header (~> 0.0, >= 0.0.8)
+      multi_json (~> 1.15)
+      rack (>= 2.2, < 4)
+      rdf (~> 3.2, >= 3.2.10)
+    json-schema (5.1.1)
+      addressable (~> 2.8)
+      bigdecimal (~> 3.1)
     jwt (2.10.1)
       base64
     kgio (2.11.4)
-    language_server-protocol (3.17.0.3)
+    language_server-protocol (3.17.0.4)
     libxml-ruby (5.0.3)
     link_header (0.0.8)
     logger (1.6.5)
@@ -235,19 +296,33 @@ GEM
     mime-types (3.6.0)
       logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2025.0107)
+    mime-types-data (3.2025.0204)
     mini_mime (1.1.5)
     minitest (5.25.4)
+    minitest-fail-fast (0.1.0)
+      minitest (~> 5)
     minitest-hooks (1.5.2)
       minitest (> 5.3)
+    minitest-reporters (1.7.1)
+      ansi
+      builder
+      minitest (>= 5.0)
+      ruby-progressbar
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
+    mustermann (3.0.3)
+      ruby2_keywords (~> 0.0.1)
     mutex_m (0.3.0)
+    net-ftp (0.3.8)
+      net-protocol
+      time
+    net-http (0.6.0)
+      uri
     net-http-persistent (4.0.5)
       connection_pool (~> 2.2)
-    net-imap (0.4.18)
+    net-imap (0.5.5)
       date
       net-protocol
     net-pop (0.1.2)
@@ -258,11 +333,11 @@ GEM
       net-ssh (>= 2.6.5, < 8.0.0)
     net-sftp (4.0.0)
       net-ssh (>= 5.0.0, < 8.0.0)
-    net-smtp (0.5.0)
+    net-smtp (0.5.1)
       net-protocol
     net-ssh (7.3.0)
     netrc (0.11.0)
-    newrelic_rpm (9.16.1)
+    newrelic_rpm (9.17.0)
     oj (3.16.9)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
@@ -272,7 +347,7 @@ GEM
     ostruct (0.6.1)
     parallel (1.26.3)
     parseconfig (1.1.2)
-    parser (3.3.7.0)
+    parser (3.3.7.1)
       ast (~> 2.4.1)
       racc
     pony (1.13.1)
@@ -280,41 +355,44 @@ GEM
     pry (0.15.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.1.1)
+    public_suffix (6.0.1)
+    raabro (1.4.0)
     racc (1.8.1)
-    rack (1.6.13)
+    rack (3.1.9)
     rack-accept (0.4.5)
       rack (>= 0.4)
-    rack-attack (6.6.1)
-      rack (>= 1.0, < 3)
-    rack-cache (1.13.0)
+    rack-attack (6.7.0)
+      rack (>= 1.0, < 4)
+    rack-cache (1.17.0)
       rack (>= 0.4)
-    rack-cors (1.0.6)
-      rack (>= 1.6.0)
+    rack-cors (2.0.2)
+      rack (>= 2.0.0)
     rack-mini-profiler (3.3.1)
       rack (>= 1.2.0)
-    rack-protection (1.5.5)
-      rack
+    rack-session (2.1.0)
+      base64 (>= 0.1.0)
+      rack (>= 3.0.0)
     rack-test (2.2.0)
       rack (>= 1.3)
     rack-timeout (0.7.0)
+    rackup (2.2.1)
+      rack (>= 3)
     rainbow (3.1.1)
     raindrops (0.20.1)
-    rake (10.5.0)
-    rdf (3.2.11)
+    rake (13.2.1)
+    rdf (3.3.2)
+      bcp47_spec (~> 0.2)
+      bigdecimal (~> 3.1, >= 3.1.5)
       link_header (~> 0.0, >= 0.0.8)
-    rdf-raptor (3.2.0)
-      ffi (~> 1.15)
-      rdf (~> 3.2)
-    rdf-rdfxml (3.2.2)
-      builder (~> 3.2)
+    rdf-rdfxml (3.3.0)
+      builder (~> 3.2, >= 3.2.4)
       htmlentities (~> 4.3)
-      rdf (~> 3.2)
-      rdf-xsd (~> 3.2)
-    rdf-vocab (3.2.7)
-      rdf (~> 3.2, >= 3.2.4)
-    rdf-xsd (3.2.1)
-      rdf (~> 3.2)
+      rdf (~> 3.3)
+      rdf-xsd (~> 3.3)
+    rdf-vocab (3.3.2)
+      rdf (~> 3.3)
+    rdf-xsd (3.3.0)
+      rdf (~> 3.3)
       rexml (~> 3.2)
     redcarpet (3.6.0)
     redis (5.3.0)
@@ -343,24 +421,25 @@ GEM
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.71.0)
+    rubocop (1.71.2)
       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 (>= 2.9.3, < 3.0)
-      rubocop-ast (>= 1.36.2, < 2.0)
+      rubocop-ast (>= 1.38.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 4.0)
-    rubocop-ast (1.37.0)
+    rubocop-ast (1.38.0)
       parser (>= 3.3.1.0)
     ruby-progressbar (1.13.0)
     ruby-xxHash (0.4.0.2)
     ruby2_keywords (0.0.5)
     rubyzip (2.4.1)
-    rufus-scheduler (2.0.24)
-      tzinfo (>= 0.3.22)
+    rufus-scheduler (3.9.2)
+      fugit (~> 1.1, >= 1.11.1)
+    securerandom (0.4.1)
     signet (0.19.0)
       addressable (~> 2.8)
       faraday (>= 0.17.5, < 3.a)
@@ -375,19 +454,13 @@ GEM
       simplecov (~> 0.19)
     simplecov-html (0.13.1)
     simplecov_json_formatter (0.1.4)
-    sinatra (1.4.8)
-      rack (~> 1.5)
-      rack-protection (~> 1.4)
-      tilt (>= 1.3, < 3)
-    sinatra-advanced-routes (0.5.3)
-      sinatra (~> 1.0)
-    sinatra-contrib (1.4.7)
-      backports (>= 2.0)
-      multi_json
-      rack-protection
-      rack-test
-      sinatra (~> 1.4.0)
-      tilt (>= 1.3, < 3)
+    sinatra (4.1.1)
+      logger (>= 1.6.0)
+      mustermann (~> 3.0)
+      rack (>= 3.0.0, < 4)
+      rack-protection (= 4.1.1)
+      rack-session (>= 2.0.0, < 3)
+      tilt (~> 2.0)
     sshkit (1.23.2)
       base64
       net-scp (>= 1.1.2)
@@ -396,12 +469,14 @@ GEM
       ostruct
     systemu (2.6.5)
     temple (0.10.3)
-    thread_safe (0.3.6)
+    thor (1.3.2)
     tilt (2.6.0)
+    time (0.4.1)
+      date
     timeout (0.4.3)
     trailblazer-option (0.1.2)
-    tzinfo (1.2.11)
-      thread_safe (~> 0.1)
+    tzinfo (2.0.6)
+      concurrent-ruby (~> 1.0)
     uber (0.1.0)
     unicode-display_width (3.1.4)
       unicode-emoji (~> 4.0, >= 4.0.4)
@@ -412,19 +487,21 @@ GEM
     unicorn-worker-killer (0.4.5)
       get_process_mem (~> 0)
       unicorn (>= 4, < 7)
+    uri (1.0.2)
     uuid (2.3.9)
       macaddr (~> 1.0)
-    webmock (3.19.1)
+    webmock (3.25.0)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
     webrick (1.9.1)
 
 PLATFORMS
+  arm64-darwin-24
   x86_64-linux
 
 DEPENDENCIES
-  activesupport (~> 5)
+  activesupport
   bcrypt_pbkdf (>= 1.0, < 2.0)
   bigdecimal
   capistrano (~> 3)
@@ -432,54 +509,57 @@ DEPENDENCIES
   capistrano-locally
   capistrano-rbenv
   crack (= 0.4.5)
-  cube-ruby
   ed25519 (>= 1.2, < 2.0)
-  ffi (~> 1.16.3)
+  ffi
   goo!
-  google-protobuf (= 3.25.3)
-  haml (~> 5.2.2)
-  json-ld
-  json-schema (~> 2.0)
-  minitest (~> 5.0)
-  minitest-hooks (~> 1.5)
+  google-protobuf
+  haml
+  json-ld (~> 3.2.0)
+  json-schema
+  minitest
+  minitest-fail-fast
+  minitest-hooks
+  minitest-reporters
   minitest-stub_any_instance
   multi_json
   ncbo_annotator!
   ncbo_cron!
   ncbo_ontology_recommender!
+  net-ftp
   newrelic_rpm
   oj
   ontologies_linked_data!
   parallel
   parseconfig
   rack
-  rack-accept (~> 0.4)
-  rack-attack (~> 6.6.1)
-  rack-cache (~> 1.13.0)
+  rack-accept
+  rack-attack
+  rack-cache
   rack-cors
   rack-mini-profiler
   rack-post-body-to-params!
   rack-test
   rack-timeout
-  rake (~> 10.0)
+  rackup
+  rake
+  rdf-raptor!
   redcarpet
   redis
-  redis-rack-cache (~> 2.0)
-  redis-store (~> 1.10)
+  redis-rack-cache
+  redis-store
   request_store
   rexml
   rubocop
   shotgun!
   simplecov
   simplecov-cobertura
-  sinatra (~> 1.0)
-  sinatra-advanced-routes
-  sinatra-contrib (~> 1.0)
+  sinatra
+  sinatra-contrib!
   sparql-client!
   unicorn
   unicorn-worker-killer
-  webmock (~> 3.19.1)
+  webmock
   webrick
 
 BUNDLED WITH
-   2.4.22
+   2.6.3
diff --git a/app.rb b/app.rb
index e09178bd..338b60b7 100644
--- a/app.rb
+++ b/app.rb
@@ -1,10 +1,11 @@
+$VERBOSE = false
+
 # sinatra-base
 require 'sinatra'
 
 # sinatra-contrib
 require 'sinatra/respond_with'
 require 'sinatra/namespace'
-require 'sinatra/advanced_routes'
 require 'sinatra/multi_route'
 
 # Other gem dependencies
@@ -24,7 +25,6 @@
 require 'rack-timeout'
 require 'rack/cors'
 require_relative 'lib/rack/slow_requests'
-require_relative 'lib/rack/cube_reporter'
 require_relative 'lib/rack/param_translator'
 require_relative 'lib/rack/slice_detection'
 require_relative 'lib/rack/request_lang'
@@ -86,25 +86,6 @@
   set :show_exceptions, false
 end
 
-# mini-profiler sets the etag header to nil, so don't use when caching is enabled
-if [:development].include?(settings.environment) && !LinkedData.settings.enable_http_cache && LinkedData::OntologiesAPI.settings.enable_miniprofiler
-  begin
-    require 'rack-mini-profiler'
-    Rack::MiniProfiler.config.storage = Rack::MiniProfiler::FileStore
-    Rack::MiniProfiler.config.position = 'right'
-    c = ::Rack::MiniProfiler.config
-    c.pre_authorize_cb = lambda { |env|
-      true
-    }
-    tmp = File.expand_path("../tmp/miniprofiler", __FILE__)
-    FileUtils.mkdir_p(tmp) unless File.exists?(tmp)
-    c.storage_options = {path: tmp}
-    use Rack::MiniProfiler
-    puts ">> rack-mini-profiler is enabled"
-  rescue LoadError
-    # profiler isn't there
-  end
-end
 
 use Rack::Cors do
   allow do
@@ -113,32 +94,14 @@
   end
 end
 
-# Use middleware (ORDER IS IMPORTANT)
-use Rack::Cors do
-  allow do
-    origins '*'
-    resource '*', :headers => :any, :methods => [:get, :post, :put, :patch, :delete, :options]
-  end
-end
 
-if Goo.queries_debug?
-  use Goo::Debug
-end
 
-# Monitoring middleware
-if LinkedData::OntologiesAPI.settings.enable_monitoring
-  cube_settings = {
-    cube_host: LinkedData::OntologiesAPI.settings.cube_host,
-    cube_port: LinkedData::OntologiesAPI.settings.cube_port
-  }
-  use Rack::CubeReporter, cube_settings
-  use Rack::SlowRequests, log_path: LinkedData::OntologiesAPI.settings.slow_request_log
-end
 
 # Show exceptions after timeout
 if LinkedData::OntologiesAPI.settings.enable_req_timeout
   use Rack::Timeout; Rack::Timeout.timeout = LinkedData::OntologiesAPI.settings.req_timeout # seconds, shorter than unicorn timeout
 end
+
 use Rack::SliceDetection
 use Rack::Accept
 use Rack::PostBodyToParams
diff --git a/config/logging.rb b/config/logging.rb
index e37ba4aa..66c323a5 100644
--- a/config/logging.rb
+++ b/config/logging.rb
@@ -1,23 +1,9 @@
 require 'logger'
-class CustomLogger < Logger
-  alias write <<
 
-  def flush
-    ((self.instance_variable_get :@logdev).instance_variable_get :@dev).flush
-  end
-end
-
-# Setup global logging
-require 'rack/logger'
-# if [:development, :console, :test].include?(settings.environment)
-if [:development, :console].include?(settings.environment)
-  LOGGER = CustomLogger.new(STDOUT)
-  LOGGER.level = Logger::DEBUG
-else
-  Dir.mkdir('log') unless File.exist?('log')
-  log = File.new("log/#{settings.environment}.log", "a+")
-  log.sync = true
-  LOGGER = CustomLogger.new(log)
-  LOGGER.level = Logger::INFO
-  use Rack::CommonLogger, log
+configure do
+  log_file = File.new("log/#{settings.environment}.log", 'a+')
+  log_file.sync = true
+  LOGGER = Logger.new(log_file)
+  LOGGER.level = settings.development? ? Logger::DEBUG : Logger::INFO
+  set :logger, LOGGER
 end
diff --git a/controllers/batch_controller.rb b/controllers/batch_controller.rb
index 2ee9b88c..33276cc8 100644
--- a/controllers/batch_controller.rb
+++ b/controllers/batch_controller.rb
@@ -15,7 +15,7 @@ class BatchController < ApplicationController
       goo_include = LinkedData::Models::Class.goo_attrs_to_load(incl)
       class_id_by_ontology = {}
       collection.each do |class_input|
-        unless class_input.instance_of?(Hash)
+        unless class_input.is_a?(Hash)
           error 422, "The collection param needs to be { 'class' : CLS_ID, 'ontology' : ont_id }"
         end
         unless class_input.include?("ontology") and class_input.include?("class")
diff --git a/controllers/notes_controller.rb b/controllers/notes_controller.rb
index d0ca83f8..cecca1f6 100644
--- a/controllers/notes_controller.rb
+++ b/controllers/notes_controller.rb
@@ -1,7 +1,7 @@
 class NotesController < ApplicationController
   ##
   # Ontology notes
-  get "/ontologies/:ontology/notes?:include_threads?" do
+  get '/ontologies/:ontology/notes' do
     ont = Ontology.find(params["ontology"]).include(:acronym).first
     error 404, "You must provide a valid id to retrieve notes for an ontology" if ont.nil?
     check_last_modified_segment(LinkedData::Models::Note, [ont.acronym])
@@ -13,7 +13,7 @@ class NotesController < ApplicationController
 
   ##
   # Class notes
-  get "/ontologies/:ontology/classes/:cls/notes?:include_threads?" do
+  get "/ontologies/:ontology/classes/:cls/notes" do
     ont = Ontology.find(params["ontology"]).include(:submissions, :acronym).first
     error 404, "You must provide a valid id to retrieve notes for an ontology" if ont.nil?
     check_last_modified_segment(LinkedData::Models::Note, [ont.acronym])
@@ -27,7 +27,7 @@ class NotesController < ApplicationController
 
   namespace "/notes" do
     # Display all notes
-    get "?:include_threads?" do
+    get '' do
       check_last_modified_collection(LinkedData::Models::Note)
       notes = LinkedData::Models::Note.where.include(LinkedData::Models::Note.goo_attrs_to_load(includes_param)).to_a
       recurse_replies(notes) if params["include_threads"]
@@ -35,7 +35,7 @@ class NotesController < ApplicationController
     end
 
     # Display a single note
-    get '/:noteid?:include_threads?' do
+    get '/:noteid' do
       noteid = params["noteid"]
       note = LinkedData::Models::Note.find(noteid).include(relatedOntology: [:acronym]).first
       error 404, "Note #{noteid} not found" if note.nil?
@@ -121,4 +121,4 @@ def clean_notes_hash(hash)
       hash
     end
   end
-end
\ No newline at end of file
+end
diff --git a/controllers/ontology_analytics_controller.rb b/controllers/ontology_analytics_controller.rb
index 8ecd77d5..81218b84 100644
--- a/controllers/ontology_analytics_controller.rb
+++ b/controllers/ontology_analytics_controller.rb
@@ -4,14 +4,14 @@ class OntologyAnalyticsController < ApplicationController
 
   ##
   # get all ontology analytics for a given year/month combination
-  namespace "/analytics" do
+  namespace '/analytics' do
 
     get do
       expires 86400, :public
       year = year_param(params)
-      error 400, "The year you supplied is invalid. Valid years start with 2 and contain 4 digits." if params["year"] && !year
+      error 400, 'The year you supplied is invalid. Valid years start with 2 and contain 4 digits.' if params['year'] && !year
       month = month_param(params)
-      error 400, "The month you supplied is invalid. Valid months are 1-12." if params["month"] && !month
+      error 400, 'The month you supplied is invalid. Valid months are 1-12.' if params['month'] && !month
       acronyms = restricted_ontologies_to_acronyms(params)
       analytics = Ontology.analytics(year, month, acronyms)
 
@@ -22,32 +22,31 @@ class OntologyAnalyticsController < ApplicationController
 
   ##
   # get all analytics for a given ontology
-  namespace "/ontologies/:acronym/analytics" do
+  namespace '/ontologies/:acronym/analytics' do
 
     get do
       expires 86400, :public
-      ont = Ontology.find(params["acronym"]).first
+      ont = Ontology.find(params['acronym']).first
       error 404, "No ontology exists with the acronym: #{params["acronym"]}" if ont.nil?
       analytics = ont.analytics
 
-      if params["format"].to_s.downcase.eql?("csv")
+      if params['format'].to_s.downcase.eql?('csv')
         tf = Tempfile.new("analytics-#{params['acronym']}")
         csv = CSV.new(tf, headers: true, return_headers: true, write_headers: true)
         csv << [:month, :visits]
-        years = analytics[params["acronym"]].keys.sort
+        years = analytics[params['acronym']].keys.sort
         now = Time.now
         years.each do |year|
-          months = analytics[params["acronym"]][year].keys.sort
+          months = analytics[params['acronym']][year].keys.sort
           months.each do |month|
             next if now.year == year && now.month <= month || (year == 2013 && month < 10) # we don't have good data going back past Oct 2013
-            visits = analytics[params["acronym"]][year][month]
-            month = DateTime.parse("#{year}/#{month}").strftime("%b %Y")
+            visits = analytics[params['acronym']][year][month]
+            month = DateTime.parse("#{year}/#{month}").strftime('%b %Y')
             csv << [month, visits]
           end
         end
         csv.close
-        content_type "text/csv"
-        send_file tf.path, filename: "analytics-#{params['acronym']}.csv"
+        send_file tf.path, filename: "analytics-#{params['acronym']}.csv", type: 'text/csv', status: 200
       else
         reply analytics
       end
diff --git a/controllers/replies_controller.rb b/controllers/replies_controller.rb
index 081238a1..9ee0fbd6 100644
--- a/controllers/replies_controller.rb
+++ b/controllers/replies_controller.rb
@@ -12,7 +12,7 @@ class RepliesController < ApplicationController
   namespace "/replies" do
 
     # Display all replies
-    get "?:include_threads?" do
+    get "" do
       check_last_modified_collection(LinkedData::Models::Notes::Reply)
       replies = LinkedData::Models::Notes::Reply.where.include(LinkedData::Models::Notes::Reply.goo_attrs_to_load(includes_param)).to_a
       reply replies
@@ -82,4 +82,4 @@ class RepliesController < ApplicationController
       halt 204
     end
   end
-end
\ No newline at end of file
+end
diff --git a/controllers/search_controller.rb b/controllers/search_controller.rb
index ce34d51d..682bd7bf 100644
--- a/controllers/search_controller.rb
+++ b/controllers/search_controller.rb
@@ -184,7 +184,7 @@ class SearchController < ApplicationController
     def search(model, query, params = {})
       query = query.blank? ? "*" : query
 
-      resp = model.search(query, search_params(params))
+      resp = model.search(query, search_params(**params))
 
       total_found = resp["response"]["numFound"]
       docs = resp["response"]["docs"]
diff --git a/helpers/application_helper.rb b/helpers/application_helper.rb
index 51bd4f08..c6554141 100644
--- a/helpers/application_helper.rb
+++ b/helpers/application_helper.rb
@@ -8,13 +8,13 @@ module ApplicationHelper
       ##
       # Escape text for use in html
       def h(text)
-        Rack::Utils.escape_html(text)
+        Rack::Utils.escape_html(text).gsub('/', '&#x2F;')
       end
 
       ##
       # Populate +obj+ using values from +params+
       # Will also try to find related objects using a Goo lookup.
-      # TODO: Currerntly, this allows for mass-assignment of everything, which will permit
+      # TODO: Currently, this allows for mass-assignment of everything, which will permit
       # users to overwrite any attribute, including things like passwords.
       def populate_from_params(obj, params)
         return if obj.nil?
@@ -23,7 +23,7 @@ def populate_from_params(obj, params)
         if obj.is_a?(LinkedData::Models::Base)
           obj.bring_remaining if obj.exist?
           no_writable_attributes = obj.class.attributes(:all) - obj.class.attributes
-          params = params.reject  {|k,v| no_writable_attributes.include? k.to_sym}
+          params = params.reject { |k, v| no_writable_attributes.include? k.to_sym }
         end
         params.each do |attribute, value|
           next if value.nil?
@@ -63,7 +63,7 @@ def populate_from_params(obj, params)
           elsif attr_cls && not_hash_or_array || (attr_cls && not_array_of_hashes)
             # Replace the initial value with the object, handling Arrays as appropriate
             if value.is_a?(Array)
-              value = value.map {|e| attr_cls.find(uri_as_needed(e)).include(attr_cls.attributes).first}
+              value = value.map { |e| attr_cls.find(uri_as_needed(e)).include(attr_cls.attributes).first }
             elsif !value.nil?
               value = attr_cls.find(uri_as_needed(value)).include(attr_cls.attributes).first
             end
@@ -72,6 +72,7 @@ def populate_from_params(obj, params)
             if value.is_a?(Array)
               retrieved_values = []
               value.each do |e|
+                e = e.to_h
                 retrieved_value = attr_cls.where(e.symbolize_keys).first
                 if retrieved_value
                   retrieved_values << retrieved_value
@@ -80,7 +81,7 @@ def populate_from_params(obj, params)
                 end
               end
             else
-              retrieved_values = attr_cls.where(value.symbolize_keys).to_a
+              retrieved_values = attr_cls.where(value.to_h.symbolize_keys).to_a
               unless retrieved_values
                 retrieved_values = populate_from_params(attr_cls.new, e.symbolize_keys).save
               end
@@ -89,7 +90,7 @@ def populate_from_params(obj, params)
           elsif attribute_settings && attribute_settings[:enforce] && attribute_settings[:enforce].include?(:date_time)
             # TODO: Remove this awful hack when obj.class.model_settings[:range][attribute] contains DateTime class
             is_array = value.is_a?(Array)
-            value = Array(value).map{ |v| DateTime.parse(v) }
+            value = Array(value).map { |v| DateTime.parse(v) }
             value = value.first unless is_array
             value
           elsif attribute_settings && attribute_settings[:enforce] && attribute_settings[:enforce].include?(:uri) && attribute_settings[:enforce].include?(:list)
@@ -157,9 +158,19 @@ def halt(*response)
           status = obj
           obj = nil
         end
-        status, obj = response.first, response.last if response.length == 2
-        status, headers, obj = response.first, response[1], response.last if response.length == 3
-        if obj.is_a?(Rack::File) # Avoid the serializer when returning files
+
+        if response.length == 2
+          status = response.first
+          obj = response.last
+        end
+
+        if response.length == 3
+          status = response.first
+          headers = response[1]
+          obj = response.last
+        end
+
+        if obj.is_a?(Rack::Files) || obj.is_a?(Rack::Files::Iterator) # Avoid the serializer when returning files
           super(response)
         else
           super(LinkedData::Serializer.build_response(@env, status: status, headers: headers, ld_object: obj))
@@ -184,7 +195,7 @@ def error(*message)
       # Look for the includes parameter and provide a formatted list of attributes
       def includes_param
         if @params["display"]
-          return @params["display"].split(",").map {|e| e.to_sym}
+          return @params["display"].split(",").map { |e| e.to_sym }
         end
         Array.new
       end
@@ -192,14 +203,14 @@ def includes_param
       ##
       # Look for the ontologies acronym and give back a formatted list of ontolody id uris
       # This can be called without passing an argument and it will use the values from the current request
-      def ontologies_param(params=nil)
+      def ontologies_param(params = nil)
         params ||= @params
 
         if params["ontologies"]
           # Get list
-          ontologies = params["ontologies"].split(",").map {|o| o.strip}
+          ontologies = params["ontologies"].split(",").map { |o| o.strip }
           # When they aren't URIs, make them URIs
-          ontologies.map! {|o| o.start_with?("http://") ? replace_url_prefix(o) : ontology_uri_from_acronym(o)}
+          ontologies.map! { |o| o.start_with?("http://") ? replace_url_prefix(o) : ontology_uri_from_acronym(o) }
           if ontologies.include? nil
             error 404, "The ontologies parameter `[#{params["ontologies"]}]` includes non-existent acronyms. Notice that acronyms are case sensitive."
           end
@@ -208,7 +219,7 @@ def ontologies_param(params=nil)
         Array.new
       end
 
-      def restricted_ontologies(params=nil)
+      def restricted_ontologies(params = nil)
         params ||= @params
 
         found_onts = false
@@ -237,23 +248,23 @@ def restricted_ontologies(params=nil)
         return onts
       end
 
-      def restricted_ontologies_to_acronyms(params=nil, onts=nil)
+      def restricted_ontologies_to_acronyms(params = nil, onts = nil)
         onts ||= restricted_ontologies(params)
-        return onts.map {|o| o.acronym }
+        return onts.map { |o| o.acronym }
       end
 
-      def ontologies_param_to_acronyms(params=nil)
+      def ontologies_param_to_acronyms(params = nil)
         ontResourceIds = ontologies_param(params)
-        return ontResourceIds.map { |ontResourceId| ontResourceId.to_s.split('/')[-1]}
+        return ontResourceIds.map { |ontResourceId| ontResourceId.to_s.split('/')[-1] }
       end
 
       ##
       # Get semantic types parameter in the form [semantic_types=T099,T085,T345]
-      def semantic_types_param(params=nil)
+      def semantic_types_param(params = nil)
         params ||= @params
 
         if params["semantic_types"]
-          semanticTypes = params["semantic_types"].split(",").map {|o| o.strip}
+          semanticTypes = params["semantic_types"].split(",").map { |o| o.strip }
           return semanticTypes
         end
         Array.new
@@ -261,21 +272,21 @@ def semantic_types_param(params=nil)
 
       ##
       # Get cui parameter in the form [cui=C0302369,C0522224,C0176617]
-      def cui_param(params=nil)
+      def cui_param(params = nil)
         params ||= @params
         if params["cui"]
-          cui = params["cui"].split(",").map {|o| o.strip}
+          cui = params["cui"].split(",").map { |o| o.strip }
           return cui
         end
         Array.new
       end
 
       # validates month for 1-12 or 01-09
-      def month_param(params=nil)
+      def month_param(params = nil)
         params ||= @params
         if params["month"]
           month = params["month"].strip
-          if %r{(?<month>^(0[1-9]|[1-9]|1[0-2])$)}x === month
+          if /(?<month>^(0[1-9]|[1-9]|1[0-2])$)/x === month
             return month.to_i.to_s
           end
         end
@@ -283,11 +294,11 @@ def month_param(params=nil)
       end
 
       # validates year for starting with 1 or 2 and containing 4 digits
-      def year_param(params=nil)
+      def year_param(params = nil)
         params ||= @params
         if params["year"]
           year = params["year"].strip
-          if %r{(?<year>^([1-2]\d{3})$)}x === year
+          if /(?<year>^([1-2]\d{3})$)/x === year
             return year.to_i.to_s
           end
         end
@@ -327,14 +338,14 @@ def ontology_from_acronym(acronym)
       def ontology_objects_from_params(params = nil)
         ontologies = Set.new(ontologies_param(params))
         all_onts = LinkedData::Models::Ontology.where.include(LinkedData::Models::Ontology.goo_attrs_to_load).to_a
-        all_onts.select {|o| ontologies.include?(o.id.to_s)}
+        all_onts.select { |o| ontologies.include?(o.id.to_s) }
       end
 
       def ontology_uri_acronym_map
         cached_map = naive_expiring_cache_read(__method__)
         return cached_map if cached_map
         map = {}
-        LinkedData::Models::Ontology.where.include(:acronym).all.each {|o| map[o.acronym] = o.id.to_s}
+        LinkedData::Models::Ontology.where.include(:acronym).all.each { |o| map[o.acronym] = o.id.to_s }
         naive_expiring_cache_write(__method__, map)
         map
       end
@@ -343,7 +354,7 @@ def acronym_ontology_uri_map
         cached_map = naive_expiring_cache_read(__method__)
         return cached_map if cached_map
         map = {}
-        LinkedData::Models::Ontology.where.include(:acronym).all.each {|o| map[o.id.to_s] = o.acronym}
+        LinkedData::Models::Ontology.where.include(:acronym).all.each { |o| map[o.id.to_s] = o.acronym }
         naive_expiring_cache_write(__method__, map)
         map
       end
@@ -381,10 +392,10 @@ def retrieve_latest_submissions(options = {})
 
       def get_ontology_and_submission
         ont = Ontology.find(@params["ontology"])
-              .include(:acronym, :administeredBy, :acl, :viewingRestriction)
-              .include(submissions:
-                       [:submissionId, submissionStatus: [:code], ontology: [:acronym], metrics: :classes])
-                .first
+                      .include(:acronym, :administeredBy, :acl, :viewingRestriction)
+                      .include(submissions:
+                                 [:submissionId, submissionStatus: [:code], ontology: [:acronym], metrics: :classes])
+                      .first
         error(404, "Ontology '#{@params["ontology"]}' not found.") if ont.nil?
         check_access(ont) if LinkedData.settings.enable_security # Security check
         submission = nil
@@ -392,7 +403,7 @@ def get_ontology_and_submission
           submission = ont.submission(@params[:ontology_submission_id])
           if submission.nil?
             error 404,
-               "You must provide an existing submission ID for the #{@params["acronym"]} ontology"
+                  "You must provide an existing submission ID for the #{@params["acronym"]} ontology"
           end
         else
           submission = ont.latest_submission(status: [:RDF])
@@ -418,28 +429,29 @@ def include_param_contains?(str)
         return class_params_include || params_include
       end
 
-
       ##
       # Checks to see if the request has a file attached
       def request_has_file?
-        @params.any? {|p,v| v.instance_of?(Hash) && v.key?(:tempfile) && v[:tempfile].instance_of?(Tempfile)}
+        @params.any? { |p, v| v.instance_of?(Hash) && v.key?(:tempfile) && v[:tempfile].instance_of?(Tempfile) }
       end
 
       ##
       # Looks for a file that was included as a multipart in a request
       def file_from_request
-        @params.each do |param, value|
-          if value.instance_of?(Hash) && value.has_key?(:tempfile) && value[:tempfile].instance_of?(Tempfile)
+        @params.each_value do |value|
+          if value.is_a?(Hash) && value.key?(:tempfile) && value[:tempfile].instance_of?(Tempfile)
             return value[:filename], value[:tempfile]
           end
         end
-        return nil, nil
+
+        [nil, nil]
       end
+
       private
 
       def naive_expiring_cache_write(key, object, timeout = 60)
         @naive_expiring_cache ||= {}
-        @naive_expiring_cache[key] = {timeout: Time.now + timeout, object: object}
+        @naive_expiring_cache[key] = { timeout: Time.now + timeout, object: object }
       end
 
       def naive_expiring_cache_read(key)
@@ -450,7 +462,6 @@ def naive_expiring_cache_read(key)
         return object[:object]
       end
 
-
       def save_submission_language(submission, language_property = :naturalLanguage)
         request_lang = RequestStore.store[:requested_lang]
 
@@ -463,7 +474,7 @@ def save_submission_language(submission, language_property = :naturalLanguage)
         collection_natural_language = collection_natural_language.values.flatten if collection_natural_language.is_a?(Hash)
         submissions_language = collection_natural_language.map { |natural_language| natural_language.to_s.split('/').last[0..1] }.compact.first
 
-        RequestStore.store[:requested_lang] =  submissions_language if submissions_language
+        RequestStore.store[:requested_lang] = submissions_language if submissions_language
       end
 
     end
diff --git a/init.rb b/init.rb
index 44a1eef5..8ab393b3 100644
--- a/init.rb
+++ b/init.rb
@@ -1,34 +1,29 @@
-# Recursively require files from directories and their sub-directories
+# Recursively require files from directories
 def require_dir(dir)
-  Dir.glob("#{dir}/*.rb").each {|f| require_relative f }
-  Dir.glob("#{dir}/*/").each {|d| require_dir(d.gsub(/\/+$/, '')) }
+  Dir.glob("#{dir}/**/*.rb").sort.each { |f| require_relative f }
 end
 
-# Require controller base files
-require_relative "controllers/application_controller"
+# Require core files
+require_relative 'controllers/application_controller'
+require_dir('lib')
+require_dir('helpers')
+require_dir('models')
+require_dir('controllers')
 
-# Require known directories
-require_dir("lib")
-require_dir("helpers")
-require_dir("models")
-require_dir("controllers")
+# Add optional trailing slash to routes
+Sinatra.register do
+  def self.registered(app)
+    app.routes.each do |verb, routes|
+      routes.each do |route|
+        pattern = route[0]
+        next if pattern.to_s.end_with?('/')
 
-##
-# Look for routes without an optional trailing slash or existing trailing slash
-# and add the optional trailing slash so both /ontologies/ and /ontologies works
-def rewrite_routes_trailing_slash
-  trailing_slash = Regexp.new(/.*\/\?\\z/)
-  no_trailing_slash = Regexp.new(/(.*)\\z\//)
-  Sinatra::Application.routes.each do |method, routes|
-    routes.each do |r|
-      route_regexp_str = r[0].inspect
-      if trailing_slash.match(route_regexp_str)
-        next
-      else
-        new_route = route_regexp_str.gsub(no_trailing_slash, "\\1\\/?\\z/")
-        r[0] = eval(new_route)
+        http_verb = verb.to_s.downcase
+        app.public_send(http_verb, "#{pattern}/") do
+          pass unless request.path_info.end_with?('/')
+          redirect "#{request.path_info}/", 301
+        end
       end
     end
   end
 end
-rewrite_routes_trailing_slash()
\ No newline at end of file
diff --git a/lib/rack/cube_reporter.rb b/lib/rack/cube_reporter.rb
deleted file mode 100644
index d6694b87..00000000
--- a/lib/rack/cube_reporter.rb
+++ /dev/null
@@ -1,41 +0,0 @@
-require 'cube'
-
-##
-# This enables collection of request statistics for anaylsis via cube.
-# A cube server is required. See http://square.github.io/cube/ for more info.
-module Rack
-  class CubeReporter
-
-    def initialize(app = nil, options = {})
-      host = options[:cube_host] || "localhost"
-      port = options[:cube_port] || 1180
-      @app = app
-      @cube = ::Cube::Client.new(host, port)
-    end
-
-    def call(env)
-      start = Time.now
-      data = @app.call(env)
-      finish = Time.now
-      cache_hit = !data[1]["X-Rack-Cache"].nil? && data[1]["X-Rack-Cache"].eql?("fresh")
-      user = env["REMOTE_USER"]
-      apikey = user.apikey if user
-      username = user.username if user
-      req_data = {
-        duration_ms: ((finish - start)*1000).ceil,
-        path: env["REQUEST_PATH"],
-        cache_hit: cache_hit,
-        status: data[0],
-        user: {
-          apikey: apikey,
-          username: username,
-          ip: env["REMOTE_ADDR"],
-          user_agent: env["HTTP_USER_AGENT"]
-        }
-      }
-      @cube.send "ontologies_api_request", DateTime.now, req_data
-      data
-    end
-
-  end
-end
\ No newline at end of file
diff --git a/mise.toml b/mise.toml
index 83aa57a8..a050f48b 100644
--- a/mise.toml
+++ b/mise.toml
@@ -1,2 +1,2 @@
 [tools]
-ruby = "2.7.8"
+ruby = "3.1.0"
diff --git a/test/controllers/test_batch_controller.rb b/test/controllers/test_batch_controller.rb
index ca37b156..72d0a98c 100644
--- a/test/controllers/test_batch_controller.rb
+++ b/test/controllers/test_batch_controller.rb
@@ -22,7 +22,7 @@ def test_class_batch_one_ontology
         "display" => "prefLabel,synonym"
       }
     }
-    post "/batch/", call_params
+    post "/batch", call_params
     assert last_response.ok?
     data = MultiJson.load(last_response.body)
     classes = data["http://www.w3.org/2002/07/owl#Class"]
@@ -48,7 +48,7 @@ def test_class_wrong_params
         "display" => "prefLabel,synonym"
       }
     }
-    post "/batch/", call_params
+    post "/batch", call_params
     assert last_response.status = 422
   end
 
@@ -72,7 +72,7 @@ def test_class_batch_multiple
         "display" => "prefLabel"
       }
     }
-    post "/batch/", call_params
+    post "/batch", call_params
     assert last_response.ok?
     data = MultiJson.load(last_response.body)
     classes = data["http://www.w3.org/2002/07/owl#Class"]
@@ -101,7 +101,7 @@ def test_class_all_bro
         "display" => "prefLabel"
       }
     }
-    post "/batch/", call_params
+    post "/batch", call_params
     assert last_response.ok?
 #    refute last_response.ok?
     data = MultiJson.load(last_response.body)
diff --git a/test/controllers/test_classes_controller.rb b/test/controllers/test_classes_controller.rb
index 323d241d..2def5e89 100644
--- a/test/controllers/test_classes_controller.rb
+++ b/test/controllers/test_classes_controller.rb
@@ -420,7 +420,7 @@ def test_calls_not_found
     escaped_cls= CGI.escape("http://my.bogus.inexistent.class/that/this/is")
 
     #404 on ontology
-    get "/ontologies/NO-ONT-ZZZZZZ/classes/"
+    get "/ontologies/NO-ONT-ZZZZZZ/classes"
     assert last_response.status == 404
     get "/ontologies/NO-ONT-ZZZZZZ/classes/#{escaped_cls}/children"
     assert last_response.status == 404
diff --git a/test/controllers/test_external_mappings_controller.rb b/test/controllers/test_external_mappings_controller.rb
index 0a18bf63..1bd0eaf5 100644
--- a/test/controllers/test_external_mappings_controller.rb
+++ b/test/controllers/test_external_mappings_controller.rb
@@ -65,7 +65,7 @@ def delete_external_mappings
                 creator: "tim"
     }
 
-    post "/mappings/", MultiJson.dump(mapping), "CONTENT_TYPE" => "application/json"
+    post "/mappings", MultiJson.dump(mapping), "CONTENT_TYPE" => "application/json"
     assert last_response.status == 201, "Error creating the external mapping: #{last_response.body}"
 
     response = MultiJson.load(last_response.body)
diff --git a/test/controllers/test_mappings_controller.rb b/test/controllers/test_mappings_controller.rb
index 2ab61261..9aa76b23 100644
--- a/test/controllers/test_mappings_controller.rb
+++ b/test/controllers/test_mappings_controller.rb
@@ -124,7 +124,7 @@ def commun_created_mappings_test(created, mapping_term_a, mapping_term_b, relati
     end
     assert rest_count == 3
 
-    get "/mappings/recent/"
+    get "/mappings/recent"
     assert last_response.status == 200
     response = MultiJson.load(last_response.body)
     assert (response.length == 5)
@@ -191,7 +191,7 @@ def mappings_between_ontologies
     ]
     ontologies_params.each do |ontologies|
       ont1, ont2 = ontologies.split(",")
-      get "/mappings/?ontologies=#{ontologies}"
+      get "/mappings?ontologies=#{ontologies}"
       assert last_response.ok?
       mappings = MultiJson.load(last_response.body)
       #pages
@@ -284,7 +284,7 @@ def create_mapping
     created = []
 
     mappings.each_with_index do |mapping, i|
-      post '/mappings/',
+      post '/mappings',
            MultiJson.dump(mapping),
            "CONTENT_TYPE" => "application/json"
 
@@ -315,7 +315,7 @@ def delete_mapping
     created = []
     mappings.each do |mapping|
 
-      post "/mappings/",
+      post "/mappings",
            MultiJson.dump(mapping),
            "CONTENT_TYPE" => "application/json"
 
@@ -351,7 +351,7 @@ def mappings_statistics
     end
     NcboCron::Models::QueryWarmer.new(Logger.new(TestLogFile.new)).run
     assert LinkedData::Models::MappingCount.where.all.length > 2
-    get "/mappings/statistics/ontologies/"
+    get "/mappings/statistics/ontologies"
     assert last_response.ok?
     stats = MultiJson.load(last_response.body)
     data = {"CNO-TEST-MAP-0"=>19,
diff --git a/test/controllers/test_ontologies_controller.rb b/test/controllers/test_ontologies_controller.rb
index d05959e8..97005339 100644
--- a/test/controllers/test_ontologies_controller.rb
+++ b/test/controllers/test_ontologies_controller.rb
@@ -97,7 +97,7 @@ def test_create_ontology
     assert last_response.status == 201
 
     delete "/ontologies/#{@@acronym}"
-    post "/ontologies/", @@file_params.merge(acronym: @@acronym)
+    post "/ontologies", @@file_params.merge(acronym: @@acronym)
     assert last_response.status == 201
   end
 
diff --git a/test/controllers/test_ontology_submissions_controller.rb b/test/controllers/test_ontology_submissions_controller.rb
index 670658a7..f9130c85 100644
--- a/test/controllers/test_ontology_submissions_controller.rb
+++ b/test/controllers/test_ontology_submissions_controller.rb
@@ -10,27 +10,27 @@ def before_suite
   end
 
   def self._set_vars
-    @@acronym = "TST"
-    @@name = "Test Ontology"
-    @@test_file = File.expand_path("../../data/ontology_files/BRO_v3.1.owl", __FILE__)
+    @@acronym = 'TST'
+    @@name = 'Test Ontology'
+    @@test_file = File.expand_path('../../data/ontology_files/BRO_v3.1.owl', __FILE__)
     @@file_params = {
       name: @@name,
-      hasOntologyLanguage: "OWL",
-      administeredBy: "tim",
-      "file" => Rack::Test::UploadedFile.new(@@test_file, ""),
+      hasOntologyLanguage: 'OWL',
+      administeredBy: 'tim',
+      'file' => Rack::Test::UploadedFile.new(@@test_file, ''),
       released: DateTime.now.to_s,
-      contact: [{name: "test_name", email: "test3@example.org"}],
+      contact: [{name: 'test_name', email: 'test3@example.org'}],
       URI: 'https://test.com/test',
       status: 'production',
       description: 'ontology description'
     }
-    @@status_uploaded = "UPLOADED"
-    @@status_rdf = "RDF"
+    @@status_uploaded = 'UPLOADED'
+    @@status_rdf = 'RDF'
   end
 
   def self._create_user
-    username = "tim"
-    test_user = User.new(username: username, email: "#{username}@example.org", password: "password")
+    username = 'tim'
+    test_user = User.new(username: username, email: "#{username}@example.org", password: 'password')
     test_user.save if test_user.valid?
     @@user = test_user.valid? ? test_user : User.find(username).first
   end
@@ -47,7 +47,7 @@ def setup
   end
 
   def test_submissions_for_given_ontology
-    num_onts_created, created_ont_acronyms = create_ontologies_and_submissions(ont_count: 1)
+    _, created_ont_acronyms = create_ontologies_and_submissions(ont_count: 1)
     ontology = created_ont_acronyms.first
     get "/ontologies/#{ontology}/submissions"
     assert last_response.ok?
@@ -59,104 +59,104 @@ def test_submissions_for_given_ontology
   end
 
   def test_create_new_submission_missing_file_and_pull_location
-    post "/ontologies/#{@@acronym}/submissions", name: @@name, hasOntologyLanguage: "OWL"
-    assert_equal(400, last_response.status, msg=get_errors(last_response))
-    assert MultiJson.load(last_response.body)["errors"]
+    post "/ontologies/#{@@acronym}/submissions", name: @@name, hasOntologyLanguage: 'OWL'
+    assert_equal(400, last_response.status, get_errors(last_response))
+    assert MultiJson.load(last_response.body)['errors']
   end
 
   def test_create_new_submission_file
     post "/ontologies/#{@@acronym}/submissions", @@file_params
-    assert_equal(201, last_response.status, msg=get_errors(last_response))
+    assert_equal(201, last_response.status, get_errors(last_response))
     sub = MultiJson.load(last_response.body)
     get "/ontologies/#{@@acronym}"
     ont = MultiJson.load(last_response.body)
-    assert ont["acronym"].eql?(@@acronym)
+    assert ont['acronym'].eql?(@@acronym)
     # Cleanup
     delete "/ontologies/#{@@acronym}/submissions/#{sub['submissionId']}"
-    assert_equal(204, last_response.status, msg=get_errors(last_response))
+    assert_equal(204, last_response.status, get_errors(last_response))
   end
 
   def test_create_new_ontology_submission
     post "/ontologies/#{@@acronym}/submissions", @@file_params
-    assert_equal(201, last_response.status, msg=get_errors(last_response))
+    assert_equal(201, last_response.status, get_errors(last_response))
     # Cleanup
     sub = MultiJson.load(last_response.body)
     delete "/ontologies/#{@@acronym}/submissions/#{sub['submissionId']}"
-    assert_equal(204, last_response.status, msg=get_errors(last_response))
+    assert_equal(204, last_response.status, get_errors(last_response))
   end
 
   def test_patch_ontology_submission
-    num_onts_created, created_ont_acronyms = create_ontologies_and_submissions(ont_count: 1)
+    _, created_ont_acronyms = create_ontologies_and_submissions(ont_count: 1)
     ont = Ontology.find(created_ont_acronyms.first).include(submissions: [:submissionId, ontology: :acronym]).first
     assert(ont.submissions.length > 0)
     submission = ont.submissions[0]
-    new_values = {description: "Testing new description changes"}
-    patch "/ontologies/#{submission.ontology.acronym}/submissions/#{submission.submissionId}", MultiJson.dump(new_values), "CONTENT_TYPE" => "application/json"
-    assert_equal(204, last_response.status, msg=get_errors(last_response))
+    new_values = {description: 'Testing new description changes'}
+    patch "/ontologies/#{submission.ontology.acronym}/submissions/#{submission.submissionId}", MultiJson.dump(new_values), 'CONTENT_TYPE' => 'application/json'
+    assert_equal(204, last_response.status, get_errors(last_response))
     get "/ontologies/#{submission.ontology.acronym}/submissions/#{submission.submissionId}"
     submission = MultiJson.load(last_response.body)
-    assert submission["description"].eql?("Testing new description changes")
+    assert submission['description'].eql?('Testing new description changes')
   end
 
   def test_delete_ontology_submission
-    num_onts_created, created_ont_acronyms = create_ontologies_and_submissions(ont_count: 1, random_submission_count: false, submission_count: 5)
+    _, created_ont_acronyms = create_ontologies_and_submissions(ont_count: 1, random_submission_count: false, submission_count: 5)
     acronym = created_ont_acronyms.first
     submission_to_delete = (1..5).to_a.shuffle.first
     delete "/ontologies/#{acronym}/submissions/#{submission_to_delete}"
-    assert_equal(204, last_response.status, msg=get_errors(last_response))
+    assert_equal(204, last_response.status, get_errors(last_response))
 
     get "/ontologies/#{acronym}/submissions/#{submission_to_delete}"
-    assert_equal(404, last_response.status, msg=get_errors(last_response))
+    assert_equal(404, last_response.status, get_errors(last_response))
   end
 
   def test_download_submission
     num_onts_created, created_ont_acronyms, onts = create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: false)
-    assert_equal(1, num_onts_created, msg="Failed to create 1 ontology?")
-    assert_equal(1, onts.length, msg="Failed to create 1 ontology?")
+    assert_equal(1, num_onts_created, 'Failed to create 1 ontology?')
+    assert_equal(1, onts.length, 'Failed to create 1 ontology?')
     ont = onts.first
     ont.bring(:submissions, :acronym)
-    assert_instance_of(Ontology, ont, msg="ont is not a #{Ontology.class}")
-    assert_equal(1, ont.submissions.length, msg="Failed to create 1 ontology submission?")
+    assert_instance_of(Ontology, ont, "ont is not a #{Ontology.class}")
+    assert_equal(1, ont.submissions.length, 'Failed to create 1 ontology submission?')
     sub = ont.submissions.first
     sub.bring(:submissionId)
-    assert_instance_of(OntologySubmission, sub, msg="sub is not a #{OntologySubmission.class}")
+    assert_instance_of(OntologySubmission, sub, "sub is not a #{OntologySubmission.class}")
     # Clear restrictions on downloads
     LinkedData::OntologiesAPI.settings.restrict_download = []
     # Download the specific submission
     get "/ontologies/#{ont.acronym}/submissions/#{sub.submissionId}/download"
-    assert_equal(200, last_response.status, msg='failed download for specific submission : ' + get_errors(last_response))
+    assert_equal(200, last_response.status, 'failed download for specific submission : ' + get_errors(last_response))
     # Add restriction on download
     acronym = created_ont_acronyms.first
     LinkedData::OntologiesAPI.settings.restrict_download = [acronym]
     # Try download
     get "/ontologies/#{ont.acronym}/submissions/#{sub.submissionId}/download"
     # download should fail with a 403 status
-    assert_equal(403, last_response.status, msg='failed to restrict download for ontology : ' + get_errors(last_response))
+    assert_equal(403, last_response.status, 'failed to restrict download for ontology : ' + get_errors(last_response))
     # Clear restrictions on downloads
     LinkedData::OntologiesAPI.settings.restrict_download = []
     # see also test_ontologies_controller::test_download_ontology
 
     # Test downloads of nonexistent ontology
-    get "/ontologies/BOGUS66/submissions/55/download"
-    assert_equal(422, last_response.status, "failed to handle downloads of nonexistent ontology" + get_errors(last_response))
+    get '/ontologies/BOGUS66/submissions/55/download'
+    assert_equal(422, last_response.status, 'failed to handle downloads of nonexistent ontology' + get_errors(last_response))
   end
 
   def test_download_ontology_submission_rdf
-    count, created_ont_acronyms, onts = create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: true)
+    _, created_ont_acronyms, onts = create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: true)
     acronym = created_ont_acronyms.first
     ont = onts.first
     sub = ont.submissions.first
 
     get "/ontologies/#{acronym}/submissions/#{sub.submissionId}/download?download_format=rdf"
-    assert_equal(200, last_response.status, msg="Download failure for '#{acronym}' ontology: " + get_errors(last_response))
+    assert_equal(200, last_response.status, "Download failure for '#{acronym}' ontology: " + get_errors(last_response))
 
     # Download should fail with a 400 status.
     get "/ontologies/#{acronym}/submissions/#{sub.submissionId}/download?download_format=csr"
-    assert_equal(400, last_response.status, msg="Download failure for '#{acronym}' ontology: " + get_errors(last_response))
+    assert_equal(400, last_response.status, "Download failure for '#{acronym}' ontology: " + get_errors(last_response))
   end
 
   def test_download_acl_only
-    count, created_ont_acronyms, onts = create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: false)
+    _, created_ont_acronyms, onts = create_ontologies_and_submissions(ont_count: 1, submission_count: 1, process_submission: false)
     acronym = created_ont_acronyms.first
     ont = onts.first.bring_remaining
     ont.bring(:submissions)
@@ -165,65 +165,65 @@ def test_download_acl_only
 
     begin
       allowed_user = User.new({
-        username: "allowed",
-        email: "test4@example.org",
-        password: "12345"
+        username: 'allowed',
+        email: 'test4@example.org',
+        password: '12345'
       })
       allowed_user.save
       blocked_user = User.new({
-        username: "blocked",
-        email: "test5@example.org",
-        password: "12345"
+        username: 'blocked',
+        email: 'test5@example.org',
+        password: '12345'
       })
       blocked_user.save
 
       ont.acl = [allowed_user]
-      ont.viewingRestriction = "private"
+      ont.viewingRestriction = 'private'
       ont.save
 
       LinkedData.settings.enable_security = true
 
       get "/ontologies/#{acronym}/submissions/#{sub.submissionId}/download?apikey=#{allowed_user.apikey}"
-      assert_equal(200, last_response.status, msg="User who is in ACL couldn't download ontology")
+      assert_equal(200, last_response.status, "User who is in ACL couldn't download ontology")
 
       get "/ontologies/#{acronym}/submissions/#{sub.submissionId}/download?apikey=#{blocked_user.apikey}"
-      assert_equal(403, last_response.status, msg="User who isn't in ACL could download ontology")
+      assert_equal(403, last_response.status, "User who isn't in ACL could download ontology")
 
       admin = ont.administeredBy.first
       admin.bring(:apikey)
       get "/ontologies/#{acronym}/submissions/#{sub.submissionId}/download?apikey=#{admin.apikey}"
-      assert_equal(200, last_response.status, msg="Admin couldn't download ontology")
+      assert_equal(200, last_response.status, "Admin couldn't download ontology")
     ensure
       LinkedData.settings.enable_security = false
-      del = User.find("allowed").first
+      del = User.find('allowed').first
       del.delete if del
-      del = User.find("blocked").first
+      del = User.find('blocked').first
       del.delete if del
     end
   end
 
   def test_ontology_submissions_access_controller
-    count, created_ont_acronyms, onts = create_ontologies_and_submissions(ont_count: 2, submission_count: 1, process_submission: false)
+    _, created_ont_acronyms, onts = create_ontologies_and_submissions(ont_count: 2, submission_count: 1, process_submission: false)
     # case first submission is private
-    acronym = created_ont_acronyms.first
+    created_ont_acronyms.first
     ont = onts.first.bring_remaining
 
     begin
       allowed_user = User.new({
-                                username: "allowed",
-                                email: "test@example.org",
-                                password: "12345"
+                                username: 'allowed',
+                                email: 'test@example.org',
+                                password: '12345'
                               })
       allowed_user.save
       blocked_user = User.new({
-                                username: "blocked",
-                                email: "test1254@example.org",
-                                password: "12345"
+                                username: 'blocked',
+                                email: 'test1254@example.org',
+                                password: '12345'
                               })
       blocked_user.save
 
       ont.acl = [allowed_user]
-      ont.viewingRestriction = "private"
+      ont.viewingRestriction = 'private'
       ont.save
 
       LinkedData.settings.enable_security = true
@@ -239,34 +239,34 @@ def test_ontology_submissions_access_controller
       assert_equal 1, submissions.size
     ensure
       LinkedData.settings.enable_security = false
-      del = User.find("allowed").first
+      del = User.find('allowed').first
       del.delete if del
-      del = User.find("blocked").first
+      del = User.find('blocked').first
       del.delete if del
     end
   end
   def test_submissions_pagination
-    num_onts_created, created_ont_acronyms, ontologies = create_ontologies_and_submissions(ont_count: 2, submission_count: 2)
+    create_ontologies_and_submissions(ont_count: 2, submission_count: 2)
 
-    get "/submissions"
+    get '/submissions'
     assert last_response.ok?
     submissions = MultiJson.load(last_response.body)
 
     assert_equal 2, submissions.length
 
 
-    get "/submissions?page=1&pagesize=1"
+    get '/submissions?page=1&pagesize=1'
     assert last_response.ok?
     submissions = MultiJson.load(last_response.body)
-    assert_equal 1, submissions["collection"].length
+    assert_equal 1, submissions['collection'].length
   end
 
   def test_submissions_pagination_filter
     num_onts_created, created_ont_acronyms, ontologies = create_ontologies_and_submissions(ont_count: 10, submission_count: 1)
-    group1 = LinkedData::Models::Group.new(acronym: 'group-1', name: "Test Group 1").save
-    group2 = LinkedData::Models::Group.new(acronym: 'group-2', name: "Test Group 2").save
-    category1 = LinkedData::Models::Category.new(acronym: 'category-1', name: "Test Category 1").save
-    category2 = LinkedData::Models::Category.new(acronym: 'category-2', name: "Test Category 2").save
+    group1 = LinkedData::Models::Group.new(acronym: 'group-1', name: 'Test Group 1').save
+    group2 = LinkedData::Models::Group.new(acronym: 'group-2', name: 'Test Group 2').save
+    category1 = LinkedData::Models::Category.new(acronym: 'category-1', name: 'Test Category 1').save
+    category2 = LinkedData::Models::Category.new(acronym: 'category-2', name: 'Test Category 2').save
 
     ontologies1 = ontologies[0..5].each do |o|
       o.bring_remaining
@@ -287,28 +287,28 @@ def test_submissions_pagination_filter
     # test filter by group and category
     get "/submissions?page=1&pagesize=100&group=#{group1.acronym}"
     assert last_response.ok?
-    assert_equal ontologies1.size, MultiJson.load(last_response.body)["collection"].length
+    assert_equal ontologies1.size, MultiJson.load(last_response.body)['collection'].length
     get "/submissions?page=1&pagesize=100&group=#{group2.acronym}"
     assert last_response.ok?
-    assert_equal ontologies2.size, MultiJson.load(last_response.body)["collection"].length
+    assert_equal ontologies2.size, MultiJson.load(last_response.body)['collection'].length
     get "/submissions?page=1&pagesize=100&hasDomain=#{category1.acronym}"
     assert last_response.ok?
-    assert_equal ontologies1.size, MultiJson.load(last_response.body)["collection"].length
+    assert_equal ontologies1.size, MultiJson.load(last_response.body)['collection'].length
     get "/submissions?page=1&pagesize=100&hasDomain=#{category2.acronym}"
     assert last_response.ok?
-    assert_equal ontologies2.size, MultiJson.load(last_response.body)["collection"].length
+    assert_equal ontologies2.size, MultiJson.load(last_response.body)['collection'].length
     get "/submissions?page=1&pagesize=100&hasDomain=#{category2.acronym}&group=#{group1.acronym}"
     assert last_response.ok?
-    assert_equal 0, MultiJson.load(last_response.body)["collection"].length
+    assert_equal 0, MultiJson.load(last_response.body)['collection'].length
     get "/submissions?page=1&pagesize=100&hasDomain=#{category2.acronym}&group=#{group2.acronym}"
     assert last_response.ok?
-    assert_equal ontologies2.size, MultiJson.load(last_response.body)["collection"].length
+    assert_equal ontologies2.size, MultiJson.load(last_response.body)['collection'].length
 
     ontologies3 = ontologies[9]
     ontologies3.bring_remaining
     ontologies3.group = [group1, group2]
     ontologies3.hasDomain = [category1, category2]
-    ontologies3.name = "name search test"
+    ontologies3.name = 'name search test'
     ontologies3.save
 
     # test search with acronym
@@ -320,7 +320,7 @@ def test_submissions_pagination_filter
       get "/submissions?page=1&pagesize=100&acronym=#{acronym_search}"
       assert last_response.ok?
       submissions = MultiJson.load(last_response.body)
-      assert_equal count, submissions["collection"].length
+      assert_equal count, submissions['collection'].length
     end
 
 
@@ -333,94 +333,94 @@ def test_submissions_pagination_filter
       get "/submissions?page=1&pagesize=100&name=#{name_search}"
       assert last_response.ok?
       submissions = MultiJson.load(last_response.body)
-      binding.pry unless submissions["collection"].length.eql?(count)
-      assert_equal count, submissions["collection"].length
+      binding.pry unless submissions['collection'].length.eql?(count)
+      assert_equal count, submissions['collection'].length
     end
 
     # test search with name and acronym
     # search by name
-    get "/submissions?page=1&pagesize=100&name=search&acronym=search"
+    get '/submissions?page=1&pagesize=100&name=search&acronym=search'
     assert last_response.ok?
     submissions = MultiJson.load(last_response.body)
-    assert_equal 1, submissions["collection"].length
+    assert_equal 1, submissions['collection'].length
     # search by acronym
-    get "/submissions?page=1&pagesize=100&name=9&acronym=9"
+    get '/submissions?page=1&pagesize=100&name=9&acronym=9'
     assert last_response.ok?
     submissions = MultiJson.load(last_response.body)
-    assert_equal 1, submissions["collection"].length
+    assert_equal 1, submissions['collection'].length
     # search by acronym or name
-    get "/submissions?page=1&pagesize=100&name=search&acronym=8"
+    get '/submissions?page=1&pagesize=100&name=search&acronym=8'
     assert last_response.ok?
     submissions = MultiJson.load(last_response.body)
-    assert_equal 2, submissions["collection"].length
+    assert_equal 2, submissions['collection'].length
 
-    ontologies.first.name = "sort by test"
+    ontologies.first.name = 'sort by test'
     ontologies.first.save
     sub = ontologies.first.latest_submission(status: :any).bring_remaining
     sub.status = 'retired'
-    sub.description = "234"
+    sub.description = '234'
     sub.creationDate = DateTime.yesterday.to_datetime
     sub.hasOntologyLanguage = LinkedData::Models::OntologyFormat.find('SKOS').first
     sub.save
 
     #test search with sort
-    get "/submissions?page=1&pagesize=100&acronym=tes&name=tes&order_by=ontology_name"
+    get '/submissions?page=1&pagesize=100&acronym=tes&name=tes&order_by=ontology_name'
     assert last_response.ok?
     submissions = MultiJson.load(last_response.body)
-    refute_empty submissions["collection"]
-    assert_equal ontologies.map{|x| x.name}.sort, submissions["collection"].map{|x| x["ontology"]["name"]}
+    refute_empty submissions['collection']
+    assert_equal ontologies.map{|x| x.name}.sort, submissions['collection'].map{|x| x['ontology']['name']}
 
-    get "/submissions?page=1&pagesize=100&acronym=tes&name=tes&order_by=creationDate"
+    get '/submissions?page=1&pagesize=100&acronym=tes&name=tes&order_by=creationDate'
     assert last_response.ok?
     submissions = MultiJson.load(last_response.body)
-    refute_empty submissions["collection"]
-    assert_equal ontologies.map{|x| x.latest_submission(status: :any).bring(:creationDate).creationDate}.sort, submissions["collection"].map{|x| DateTime.parse(x["creationDate"])}.reverse
+    refute_empty submissions['collection']
+    assert_equal ontologies.map{|x| x.latest_submission(status: :any).bring(:creationDate).creationDate}.sort, submissions['collection'].map{|x| DateTime.parse(x['creationDate'])}.reverse
 
     # test search with format
-    get "/submissions?page=1&pagesize=100&acronym=tes&name=tes&hasOntologyLanguage=SKOS"
+    get '/submissions?page=1&pagesize=100&acronym=tes&name=tes&hasOntologyLanguage=SKOS'
     assert last_response.ok?
     submissions = MultiJson.load(last_response.body)
-    refute_empty submissions["collection"]
-    assert_equal 1, submissions["collection"].size
+    refute_empty submissions['collection']
+    assert_equal 1, submissions['collection'].size
 
-    get "/submissions?page=1&pagesize=100&acronym=tes&name=tes&hasOntologyLanguage=OWL"
+    get '/submissions?page=1&pagesize=100&acronym=tes&name=tes&hasOntologyLanguage=OWL'
     assert last_response.ok?
     submissions = MultiJson.load(last_response.body)
-    refute_empty submissions["collection"]
-    assert_equal ontologies.size-1 , submissions["collection"].size
+    refute_empty submissions['collection']
+    assert_equal ontologies.size-1 , submissions['collection'].size
 
     # test ontology filter with submission filter attributes
-    get "/submissions?page=1&pagesize=100&acronym=tes&name=tes&group=group-2&category=category-2&hasOntologyLanguage=OWL"
+    get '/submissions?page=1&pagesize=100&acronym=tes&name=tes&group=group-2&category=category-2&hasOntologyLanguage=OWL'
     assert last_response.ok?
     submissions = MultiJson.load(last_response.body)
-    refute_empty submissions["collection"]
-    assert_equal ontologies2.size + 1 , submissions["collection"].size
+    refute_empty submissions['collection']
+    assert_equal ontologies2.size + 1 , submissions['collection'].size
 
     # test ontology filter with status
-    get "/submissions?page=1&pagesize=100&status=retired"
+    get '/submissions?page=1&pagesize=100&status=retired'
     assert last_response.ok?
     submissions = MultiJson.load(last_response.body)
-    refute_empty submissions["collection"]
-    assert_equal 1 , submissions["collection"].size
+    refute_empty submissions['collection']
+    assert_equal 1 , submissions['collection'].size
 
-    get "/submissions?page=1&pagesize=100&status=alpha,beta,production"
+    get '/submissions?page=1&pagesize=100&status=alpha,beta,production'
     assert last_response.ok?
     submissions = MultiJson.load(last_response.body)
-    refute_empty submissions["collection"]
-    assert_equal ontologies.size - 1 , submissions["collection"].size
-    get "/submissions?page=1&pagesize=100&description=234&acronym=234&name=234"
+    refute_empty submissions['collection']
+    assert_equal ontologies.size - 1 , submissions['collection'].size
+    get '/submissions?page=1&pagesize=100&description=234&acronym=234&name=234'
     assert last_response.ok?
     submissions = MultiJson.load(last_response.body)
-    assert_equal 1 , submissions["collection"].size
+    assert_equal 1 , submissions['collection'].size
   end
 
   def test_submissions_default_includes
     ontology_count = 5
-    num_onts_created, created_ont_acronyms, ontologies = create_ontologies_and_submissions(ont_count: ontology_count, submission_count: 1, submissions_to_process: [])
+    _, created_ont_acronyms, = create_ontologies_and_submissions(ont_count: ontology_count, submission_count: 1, submissions_to_process: [])
 
     submission_default_attributes = LinkedData::Models::OntologySubmission.hypermedia_settings[:serialize_default].map(&:to_s)
 
-    get("/submissions?display_links=false&display_context=false&include_status=ANY")
+    get('/submissions?display_links=false&display_context=false&include_status=ANY')
     assert last_response.ok?
     submissions = MultiJson.load(last_response.body)
 
@@ -435,80 +435,59 @@ def test_submissions_default_includes
     assert(submissions.all? { |sub| submission_default_attributes.eql?(submission_keys(sub)) })
   end
 
+
   def test_submissions_all_includes
     ontology_count = 5
-    num_onts_created, created_ont_acronyms, ontologies = create_ontologies_and_submissions(ont_count: ontology_count, submission_count: 1, submissions_to_process: [])
-    def submission_all_attributes
-      attrs = OntologySubmission.goo_attrs_to_load([:all])
-      embed_attrs = attrs.select { |x| x.is_a?(Hash) }.first
-
-      attrs.delete_if { |x| x.is_a?(Hash) }.map(&:to_s) + embed_attrs.keys.map(&:to_s)
-    end
-    get("/submissions?include=all&display_links=false&display_context=false")
-
-    assert last_response.ok?
-    submissions = MultiJson.load(last_response.body)
-    assert_equal ontology_count, submissions.size
+    _, created_ont_acronyms, = create_ontologies_and_submissions(ont_count: ontology_count, submission_count: 1, submissions_to_process: [])
 
-    assert(submissions.all? { |sub| submission_all_attributes.sort.eql?(submission_keys(sub).sort) })
-    assert(submissions.all? { |sub| sub["contact"] && (sub["contact"].first.nil? || sub["contact"].first.keys.eql?(%w[name email id])) })
+    submission_all_attributes = begin
+                                  attrs = OntologySubmission.goo_attrs_to_load([:all])
+                                  embed_attrs = attrs.select { |x| x.is_a?(Hash) }.first || {}
+                                  attrs.reject { |x| x.is_a?(Hash) }.map(&:to_s) + embed_attrs.keys.map(&:to_s)
+                                end.sort
 
-    get("/ontologies/#{created_ont_acronyms.first}/submissions?include=all&display_links=false&display_context=false")
+    params = '?include=all&display_links=false&display_context=false'
 
-    assert last_response.ok?
-    submissions = MultiJson.load(last_response.body)
-    assert_equal 1, submissions.size
-
-    assert(submissions.all? { |sub| submission_all_attributes.sort.eql?(submission_keys(sub).sort) })
-    assert(submissions.all? { |sub| sub["contact"] && (sub["contact"].first.nil? || sub["contact"].first.keys.eql?(%w[name email id])) })
-
-    get("/ontologies/#{created_ont_acronyms.first}/latest_submission?include=all&display_links=false&display_context=false")
-    assert last_response.ok?
-    sub = MultiJson.load(last_response.body)
+    [
+      "/submissions#{params}",
+      "/ontologies/#{created_ont_acronyms.first}/submissions#{params}",
+      "/ontologies/#{created_ont_acronyms.first}/latest_submission#{params}",
+      "/ontologies/#{created_ont_acronyms.first}/submissions/1#{params}"
+    ].each do |url|
+      get(url)
+      assert last_response.ok?
 
-    assert(submission_all_attributes.sort.eql?(submission_keys(sub).sort))
-    assert(sub["contact"] && (sub["contact"].first.nil? || sub["contact"].first.keys.eql?(%w[name email id])))
+      response_body = MultiJson.load(last_response.body)
+      submissions = response_body.is_a?(Array) ? response_body : [response_body]
 
-    get("/ontologies/#{created_ont_acronyms.first}/submissions/1?include=all&display_links=false&display_context=false")
-    assert last_response.ok?
-    sub = MultiJson.load(last_response.body)
-
-    assert(submission_all_attributes.sort.eql?(submission_keys(sub).sort))
-    assert(sub["contact"] && (sub["contact"].first.nil? || sub["contact"].first.keys.eql?(%w[name email id])))
+      assert_equal(ontology_count, submissions.size) if url == "/submissions#{params}"
+      assert(submissions.all? { |sub| submission_all_attributes.eql?(submission_keys(sub).sort) })
+      assert(submissions.all? { |sub| sub['contact']&.first&.keys.to_a.sort.eql?(%w[name email id].sort) })
+    end
   end
 
   def test_submissions_custom_includes
     ontology_count = 5
-    num_onts_created, created_ont_acronyms, ontologies = create_ontologies_and_submissions(ont_count: ontology_count, submission_count: 1, submissions_to_process: [])
-    include = 'ontology,contact,submissionId'
-
-    get("/submissions?include=#{include}&display_links=false&display_context=false")
+    _, created_ont_acronyms, _ = create_ontologies_and_submissions(ont_count: ontology_count, submission_count: 1, submissions_to_process: [])
+    include_keys = %w[ontology contact submissionId]
+    params = "?include=#{include_keys.join(',')}&display_links=false&display_context=false"
 
-    assert last_response.ok?
-    submissions = MultiJson.load(last_response.body)
-    assert_equal ontology_count, submissions.size
-    assert(submissions.all? { |sub| include.split(',').eql?(submission_keys(sub)) })
-    assert(submissions.all? { |sub| sub["contact"] && (sub["contact"].first.nil? || sub["contact"].first.keys.eql?(%w[name email id])) })
-
-    get("/ontologies/#{created_ont_acronyms.first}/submissions?include=#{include}&display_links=false&display_context=false")
-
-    assert last_response.ok?
-    submissions = MultiJson.load(last_response.body)
-    assert_equal 1, submissions.size
-    assert(submissions.all? { |sub| include.split(',').eql?(submission_keys(sub)) })
-    assert(submissions.all? { |sub| sub["contact"] && (sub["contact"].first.nil? || sub["contact"].first.keys.eql?(%w[name email id])) })
+    [
+      "/submissions#{params}",
+      "/ontologies/#{created_ont_acronyms.first}/submissions#{params}",
+      "/ontologies/#{created_ont_acronyms.first}/latest_submission#{params}",
+      "/ontologies/#{created_ont_acronyms.first}/submissions/1#{params}"
+    ].each do |url|
+      get(url)
+      assert last_response.ok?
 
-    get("/ontologies/#{created_ont_acronyms.first}/latest_submission?include=#{include}&display_links=false&display_context=false")
-    assert last_response.ok?
-    sub = MultiJson.load(last_response.body)
-    assert(include.split(',').eql?(submission_keys(sub)))
-    assert(sub["contact"] && (sub["contact"].first.nil? || sub["contact"].first.keys.eql?(%w[name email id])))
+      response_body = MultiJson.load(last_response.body)
+      submissions = response_body.is_a?(Array) ? response_body : [response_body]
 
-    get("/ontologies/#{created_ont_acronyms.first}/submissions/1?include=#{include}&display_links=false&display_context=false")
-    assert last_response.ok?
-    sub = MultiJson.load(last_response.body)
-    assert(include.split(',').eql?(submission_keys(sub)))
-    assert(sub["contact"] && (sub["contact"].first.nil? || sub["contact"].first.keys.eql?(%w[name email id])))
+      assert_equal(ontology_count, submissions.size) if url == "/submissions#{params}"
+      assert(submissions.all? { |sub| include_keys.eql?(submission_keys(sub)) })
+      assert(submissions.all? { |sub| sub['contact']&.first&.keys&.sort.eql?(%w[name email id].sort) })
+    end
   end
 
   def test_submissions_param_include
@@ -519,7 +498,7 @@ def test_submissions_param_include
   end
 
   def test_submission_diff
-    num_onts_created, created_ont_acronyms, onts = create_ontologies_and_submissions(ont_count: 1, submission_count: 2,
+    _, _, onts = create_ontologies_and_submissions(ont_count: 1, submission_count: 2,
                                                                                      process_submission: true,
                                                                                      process_options: { process_rdf: true, extract_metadata: false, diff: true} )
 
diff --git a/test/helpers/test_application_helper.rb b/test/helpers/test_application_helper.rb
index 2315a677..f1557243 100644
--- a/test/helpers/test_application_helper.rb
+++ b/test/helpers/test_application_helper.rb
@@ -9,22 +9,22 @@ def before_suite
 
   def test_it_escapes_html
     escaped_html = helper.h("<a>http://testlink.com</a>")
-    assert escaped_html.eql?("&lt;a&gt;http:&#x2F;&#x2F;testlink.com&lt;&#x2F;a&gt;")
+    assert_equal "&lt;a&gt;http:&#x2F;&#x2F;testlink.com&lt;&#x2F;a&gt;", escaped_html
   end
 
   def test_ontologies_param
-    ids = @@ontologies.map {|o| o.id.to_s}
-    acronyms = @@ontologies.map {|o| o.id.to_s.split("/").last}
-    params = {"ontologies" => acronyms.join(",")}
+    ids = @@ontologies.map { |o| o.id.to_s }
+    acronyms = @@ontologies.map { |o| o.id.to_s.split("/").last }
+    params = { "ontologies" => acronyms.join(",") }
     ontologies = ontologies_param(params)
     assert ontologies == ids
 
-    params = {"ontologies" => ids.join(",")}
+    params = { "ontologies" => ids.join(",") }
     ontologies = ontologies_param(params)
     assert ontologies == ids
 
     id_acronym = ids + acronyms
-    params = {"ontologies" => id_acronym.join(",")}
+    params = { "ontologies" => id_acronym.join(",") }
     ontologies = ontologies_param(params)
     assert ontologies == (ids + ids)
   end
@@ -48,16 +48,16 @@ def test_acronym_from_ontology_uri
   def test_bad_accept_header_handling
     # This accept header contains '*; q=.2', which isn't valid according to the spec, should be '*/*; q=.2'
     bad_accept_header = "text/html, image/gif, image/jpeg, *; q=.2, */*; q=.2"
-    get "/ontologies", {}, {"HTTP_ACCEPT" => bad_accept_header}
+    get "/ontologies", {}, { "HTTP_ACCEPT" => bad_accept_header }
     assert last_response.status == 400
     assert last_response.body.include?("Accept header `#{bad_accept_header}` is invalid")
   end
 
   def test_http_method_override
-    post "/ontologies", {}, {"HTTP_X_HTTP_METHOD_OVERRIDE" => "GET"}
+    post "/ontologies", {}, { "HTTP_X_HTTP_METHOD_OVERRIDE" => "GET" }
     assert last_response.ok?
-    acronyms = @@ontologies.map {|o| o.bring(:acronym).acronym}.sort
-    resp_acronyms = MultiJson.load(last_response.body).map {|o| o["acronym"]}.sort
+    acronyms = @@ontologies.map { |o| o.bring(:acronym).acronym }.sort
+    resp_acronyms = MultiJson.load(last_response.body).map { |o| o["acronym"] }.sort
     assert_equal acronyms, resp_acronyms
   end
 end
diff --git a/test/helpers/test_slices_helper.rb b/test/helpers/test_slices_helper.rb
index ae01aae7..7e8cfdac 100644
--- a/test/helpers/test_slices_helper.rb
+++ b/test/helpers/test_slices_helper.rb
@@ -79,7 +79,7 @@ def test_search_slices
   def test_mappings_slices
     LinkedData::Mappings.create_mapping_counts(Logger.new(TestLogFile.new))
 
-    get "/mappings/statistics/ontologies/"
+    get "/mappings/statistics/ontologies"
     
     expected_result_without_slice = ["PARSED-0",
       "PARSED-1",
@@ -90,7 +90,7 @@ def test_mappings_slices
 
     assert_equal expected_result_without_slice, MultiJson.load(last_response.body).keys.sort
 
-    get "http://#{@@group_acronym}/mappings/statistics/ontologies/"
+    get "http://#{@@group_acronym}/mappings/statistics/ontologies"
 
     expected_result_with_slice = ["PARSED-0",
       "http://data.bioontology.org/metadata/ExternalMappings",
diff --git a/test/middleware/test_rack_attack.rb b/test/middleware/test_rack_attack.rb
index 92b4d636..937c1bf0 100644
--- a/test/middleware/test_rack_attack.rb
+++ b/test/middleware/test_rack_attack.rb
@@ -40,7 +40,7 @@ def before_suite
     # Fork the process to create two servers. This isolates the Rack::Attack configuration, which makes other tests fail if included.
     @@pid1 = fork do
       require_relative '../../config/rack_attack'
-      Rack::Server.start(
+      Rackup::Server.start(
         config: RACK_CONFIG,
         Port: @@port1
       )
@@ -50,7 +50,7 @@ def before_suite
     @@port2 = unused_port
     @@pid2 = fork do
       require_relative '../../config/rack_attack'
-      Rack::Server.start(
+      Rackup::Server.start(
         config: RACK_CONFIG,
         Port: @@port2
       )
diff --git a/test/test_case.rb b/test/test_case.rb
index e9b8956d..b1de654c 100644
--- a/test/test_case.rb
+++ b/test/test_case.rb
@@ -28,21 +28,24 @@
 require 'multi_json'
 require 'oj'
 require 'json-schema'
-
+require 'minitest/reporters'
+Minitest::Reporters.use! [Minitest::Reporters::SpecReporter.new(:color => true), Minitest::Reporters::MeanTimeReporter.new]
 MAX_TEST_REDIS_SIZE = 10_000
 
 # Check to make sure you want to run if not pointed at localhost
 safe_hosts = Regexp.new(/localhost|-ut|ncbo-dev*|ncbo-unittest*/)
+
 def safe_redis_hosts?(sh)
   return [LinkedData.settings.http_redis_host,
-   Annotator.settings.annotator_redis_host,
-   LinkedData.settings.goo_redis_host].select { |x|
+          Annotator.settings.annotator_redis_host,
+          LinkedData.settings.goo_redis_host].select { |x|
     x.match(sh)
   }.length == 3
 end
+
 unless LinkedData.settings.goo_host.match(safe_hosts) &&
-        safe_redis_hosts?(safe_hosts) &&
-        LinkedData.settings.search_server_url.match(safe_hosts)
+  safe_redis_hosts?(safe_hosts) &&
+  LinkedData.settings.search_server_url.match(safe_hosts)
   print "\n\n================================== WARNING ==================================\n"
   print "** TESTS CAN BE DESTRUCTIVE -- YOU ARE POINTING TO A POTENTIAL PRODUCTION/STAGE SERVER **\n"
   print "Servers:\n"
@@ -77,8 +80,7 @@ def count_pattern(pattern)
   def backend_4s_delete
     if count_pattern("?s ?p ?o") < 400000
       puts 'clear backend & index'
-      raise StandardError, 'Too many triples in KB, does not seem right to run tests' unless
-        count_pattern('?s ?p ?o') < 400000
+      raise StandardError, 'Too many triples in KB, does not seem right to run tests' unless count_pattern('?s ?p ?o') < 400000
 
       graphs = Goo.sparql_query_client.query("SELECT DISTINCT  ?g WHERE  { GRAPH ?g { ?s ?p ?o . } }")
       graphs.each_solution do |sol|
@@ -114,8 +116,6 @@ def after_all
     super
   end
 
-
-
   def _run_suite(suite, type)
     begin
       backend_4s_delete
@@ -160,12 +160,11 @@ def app
   # @option options [TrueClass, FalseClass] :process_submission Parse the test ontology file
   def create_ontologies_and_submissions(options = {})
     if options[:process_submission] && options[:process_options].nil?
-      options[:process_options] =  { process_rdf: true, extract_metadata: false, generate_missing_labels: false }
+      options[:process_options] = { process_rdf: true, extract_metadata: false, generate_missing_labels: false }
     end
     LinkedData::SampleData::Ontology.create_ontologies_and_submissions(options)
   end
 
-
   def agent_data(type: 'organization')
     schema_agencies = LinkedData::Models::AgentIdentifier::IDENTIFIER_SCHEMES.keys
     users = LinkedData::Models::User.all
@@ -206,13 +205,13 @@ def delete_goo_models(gooModelArray)
   # @param [String] jsonData a json string that will be parsed by MultiJson.load
   # @param [String] jsonSchemaString a json schema string that will be parsed by MultiJson.load
   # @param [boolean] list set it true for jsonObj array of items to validate against jsonSchemaString
-  def validate_json(jsonData, jsonSchemaString, list=false)
+  def validate_json(jsonData, jsonSchemaString, list = false)
     schemaVer = :draft3
     jsonObj = MultiJson.load(jsonData)
     jsonSchema = MultiJson.load(jsonSchemaString)
     assert(
-        JSON::Validator.validate(jsonSchema, jsonObj, :list => list, :version => schemaVer),
-        JSON::Validator.fully_validate(jsonSchema, jsonObj, :list => list, :version => schemaVer, :validate_schema => true).to_s
+      JSON::Validator.validate(jsonSchema, jsonObj, list: list, version: schemaVer),
+      JSON::Validator.fully_validate(jsonSchema, jsonObj, list: list, version: schemaVer, validate_schema: true).to_s
     )
   end
 
@@ -236,11 +235,10 @@ def self.enable_security
     LinkedData.settings.enable_security = true
   end
 
-  def self.reset_security(old_security =  @@old_security_setting)
+  def self.reset_security(old_security = @@old_security_setting)
     LinkedData.settings.enable_security = old_security
   end
 
-
   def self.make_admin(user)
     user.bring_remaining
     user.role = [LinkedData::Models::Users::Role.find(LinkedData::Models::Users::Role::ADMIN).first]
@@ -261,6 +259,7 @@ def unused_port
   end
 
   private
+
   def port_in_use?(port)
     server = TCPServer.new(port)
     server.close