Merge to staging

Gemfile

@@ -13,6 +13,7 @@ gem 'rake', '~> 10.0'
 gem 'sinatra', '~> 1.0'
 gem 'sinatra-advanced-routes'
 gem 'sinatra-contrib', '~> 1.0'
+gem 'request_store'
 
 # Rack middleware
 gem 'ffi'
@@ -26,7 +27,7 @@ gem 'rack-timeout'
 gem 'redis-rack-cache', '~> 2.0'
 
 # Data access (caching)
-gem 'redis'
+gem 'redis', '~> 4.8.1'
 gem 'redis-activesupport'
 
 # Monitoring
@@ -42,12 +43,12 @@ gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107
 gem 'redcarpet'
 
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', git: 'https://github.com/ontoportal-lirmm/goo.git', branch: 'master'
+gem 'goo', git: 'https://github.com/ontoportal-lirmm/goo.git', branch: 'development'
 gem 'ncbo_annotator', git: 'https://github.com/ontoportal-lirmm/ncbo_annotator.git', branch: 'master'
 gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'master'
 gem 'ncbo_ontology_recommender', git: 'https://github.com/ncbo/ncbo_ontology_recommender.git', branch: 'master'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'master'
-gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'master'
+gem 'ontologies_linked_data', git: 'https://github.com/ontoportal-lirmm/ontologies_linked_data.git', branch: 'development'
 
 group :development do
   # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/ncbo_ontology_recommender.git
-  revision: 6010ff60b99dc1282822b8a1fb59bd59f453755f
+  revision: d0ac992c88bd417f2f2137ba62934c3c41b6db7c
   branch: master
   specs:
     ncbo_ontology_recommender (0.0.1)
@@ -11,8 +11,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: 92968978e5d2436c648bf7956e25aff05440b59d
-  branch: master
+  revision: c3456c45c12ed92d4a3ae43cac7c1d4cdbf290b6
+  branch: development
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -37,13 +37,13 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ncbo_cron.git
-  revision: d09999177235029ba30a00cd59d10f7ca1a1fa93
+  revision: 8db3481116c57d2a21dc8f32bcd1695d95442280
   branch: master
   specs:
     ncbo_cron (0.0.1)
       dante
       goo
-      google-api-client
+      google-apis-analytics_v3
       mlanett-redis-lock
       multi_json
       ncbo_annotator
@@ -53,8 +53,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 9c5c56cf7b4546ccc45431a82bbce9a33184e4cc
-  branch: master
+  revision: 4ac9873f3d016259196a17cfc9c6ab8149468ec9
+  branch: development
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -103,16 +103,16 @@ GEM
     activesupport (3.2.22.5)
       i18n (~> 0.6, >= 0.6.4)
       multi_json (~> 1.0)
-    addressable (2.8.1)
+    addressable (2.8.4)
       public_suffix (>= 2.0.2, < 6.0)
     airbrussh (1.4.1)
       sshkit (>= 1.6.1, != 1.7.0)
-    backports (3.23.0)
+    backports (3.24.1)
     bcrypt (3.1.18)
     bcrypt_pbkdf (1.1.0)
     bigdecimal (1.4.2)
     builder (3.2.4)
-    capistrano (3.17.1)
+    capistrano (3.17.2)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
@@ -125,16 +125,16 @@ GEM
       capistrano (~> 3.1)
       sshkit (~> 1.3)
     coderay (1.1.3)
-    concurrent-ruby (1.1.10)
+    concurrent-ruby (1.2.2)
     cube-ruby (0.0.3)
     dante (0.2.0)
-    date (3.3.2)
+    date (3.3.3)
     declarative (0.0.20)
     docile (1.4.0)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
     ed25519 (1.3.0)
-    faraday (1.10.2)
+    faraday (1.10.3)
       faraday-em_http (~> 1.0)
       faraday-em_synchrony (~> 1.0)
       faraday-excon (~> 1.1)
@@ -160,22 +160,24 @@ GEM
     ffi (1.15.5)
     get_process_mem (0.2.7)
       ffi (~> 1.0)
-    google-api-client (0.52.0)
+    google-apis-analytics_v3 (0.13.0)
+      google-apis-core (>= 0.11.0, < 2.a)
+    google-apis-core (0.11.0)
       addressable (~> 2.5, >= 2.5.1)
-      googleauth (~> 0.9)
-      httpclient (>= 2.8.1, < 3.0)
+      googleauth (>= 0.16.2, < 2.a)
+      httpclient (>= 2.8.1, < 3.a)
       mini_mime (~> 1.0)
       representable (~> 3.0)
-      retriable (>= 2.0, < 4.0)
+      retriable (>= 2.0, < 4.a)
       rexml
-      signet (~> 0.12)
-    googleauth (0.17.1)
-      faraday (>= 0.17.3, < 2.0)
+      webrick
+    googleauth (1.5.2)
+      faraday (>= 0.17.3, < 3.a)
       jwt (>= 1.4, < 3.0)
       memoist (~> 0.16)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
-      signet (~> 0.15)
+      signet (>= 0.16, < 2.a)
     haml (5.2.2)
       temple (>= 0.8.0)
       tilt
@@ -189,13 +191,13 @@ GEM
     json-schema (2.8.1)
       addressable (>= 2.4)
     json_pure (2.6.3)
-    jwt (2.5.0)
+    jwt (2.7.0)
     kgio (2.11.4)
-    libxml-ruby (3.2.4)
+    libxml-ruby (4.1.0)
     logger (1.5.3)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
-    mail (2.8.0)
+    mail (2.8.1)
       mini_mime (>= 0.1.1)
       net-imap
       net-pop
@@ -204,16 +206,16 @@ GEM
     method_source (1.0.0)
     mime-types (3.4.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2022.0105)
+    mime-types-data (3.2023.0218.1)
     mini_mime (1.1.2)
     minitest (4.7.5)
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
-    multipart-post (2.2.3)
+    multipart-post (2.3.0)
     net-http-persistent (2.9.4)
-    net-imap (0.3.2)
+    net-imap (0.3.4)
       date
       net-protocol
     net-pop (0.1.2)
@@ -224,17 +226,17 @@ GEM
       net-ssh (>= 2.6.5, < 8.0.0)
     net-smtp (0.3.3)
       net-protocol
-    net-ssh (7.0.1)
+    net-ssh (7.1.0)
     netrc (0.11.0)
-    newrelic_rpm (8.14.0)
+    newrelic_rpm (9.2.2)
     oj (2.18.5)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
     parseconfig (1.1.2)
     pony (1.13.1)
       mail (>= 2.0)
-    pry (0.14.1)
+    pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.0.1)
@@ -247,31 +249,33 @@ GEM
       rack (>= 0.4)
     rack-cors (1.0.6)
       rack (>= 1.6.0)
-    rack-mini-profiler (3.0.0)
+    rack-mini-profiler (3.1.0)
       rack (>= 1.2.0)
     rack-protection (1.5.5)
       rack
-    rack-test (2.0.2)
+    rack-test (2.1.0)
       rack (>= 1.3)
     rack-timeout (0.6.3)
-    raindrops (0.20.0)
+    raindrops (0.20.1)
     rake (10.5.0)
     rdf (1.0.8)
       addressable (>= 2.2)
-    redcarpet (3.5.1)
-    redis (4.8.0)
+    redcarpet (3.6.0)
+    redis (4.8.1)
     redis-activesupport (5.3.0)
       activesupport (>= 3, < 8)
       redis-store (>= 1.3, < 2)
     redis-rack-cache (2.2.1)
       rack-cache (>= 1.10, < 2)
       redis-store (>= 1.6, < 2)
-    redis-store (1.9.1)
-      redis (>= 4, < 5)
+    redis-store (1.9.2)
+      redis (>= 4, < 6)
     representable (3.2.0)
       declarative (< 0.1.0)
       trailblazer-option (>= 0.1.1, < 0.2.0)
       uber (< 0.2.0)
+    request_store (1.5.1)
+      rack (>= 1.4)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
@@ -292,7 +296,7 @@ GEM
       faraday (>= 0.17.5, < 3.a)
       jwt (>= 1.5, < 3.0)
       multi_json (~> 1.10)
-    simplecov (0.21.2)
+    simplecov (0.22.0)
       docile (~> 1.1)
       simplecov-html (~> 0.11)
       simplecov_json_formatter (~> 0.1)
@@ -314,15 +318,15 @@ GEM
       rack-test
       sinatra (~> 1.4.0)
       tilt (>= 1.3, < 3)
-    sshkit (1.21.3)
+    sshkit (1.21.4)
       net-scp (>= 1.1.2)
       net-ssh (>= 2.8.0)
     systemu (2.6.5)
-    temple (0.9.1)
-    tilt (2.0.11)
-    timeout (0.3.1)
+    temple (0.10.0)
+    tilt (2.1.0)
+    timeout (0.3.2)
     trailblazer-option (0.1.2)
-    tzinfo (2.0.5)
+    tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     uber (0.1.0)
     unf (0.1.4)
@@ -336,6 +340,7 @@ GEM
       unicorn (>= 4, < 7)
     uuid (2.3.9)
       macaddr (~> 1.0)
+    webrick (1.8.1)
 
 PLATFORMS
   x86_64-linux
@@ -377,9 +382,10 @@ DEPENDENCIES
   rack-timeout
   rake (~> 10.0)
   redcarpet
-  redis
+  redis (~> 4.8.1)
   redis-activesupport
   redis-rack-cache (~> 2.0)
+  request_store
   shotgun!
   simplecov
   simplecov-cobertura
@@ -391,4 +397,4 @@ DEPENDENCIES
   unicorn-worker-killer
 
 BUNDLED WITH
-   2.3.23
+   2.3.14

app.rb

@@ -29,13 +29,16 @@
 require_relative 'lib/rack/cube_reporter'
 require_relative 'lib/rack/param_translator'
 require_relative 'lib/rack/slice_detection'
+require_relative 'lib/rack/request_lang'
 
 # Logging setup
 require_relative "config/logging"
 
 # Inflector setup
 require_relative "config/inflections"
 
+require 'request_store'
+
 # Protection settings
 set :protection, :except => :path_traversal
 
@@ -143,6 +146,9 @@
 use Rack::PostBodyToParams
 use Rack::ParamTranslator
 
+use RequestStore::Middleware
+use Rack::RequestLang
+
 use LinkedData::Security::Authorization
 use LinkedData::Security::AccessDenied
 

controllers/classes_controller.rb

@@ -9,7 +9,7 @@ class ClassesController < ApplicationController
       cls_count = submission.class_count(LOGGER)
       error 403, "Unable to display classes due to missing metrics for #{submission.id.to_s}. Please contact the administrator." if cls_count < 0
 
-      attributes, page, size, filter_by_label, order_by_hash, bring_unmapped_needed  =  settings_params(LinkedData::Models::Class)
+      attributes, page, size, order_by_hash, bring_unmapped_needed  =  settings_params(LinkedData::Models::Class)
       check_last_modified_segment(LinkedData::Models::Class, [ont.acronym])
 
       index = LinkedData::Models::Class.in(submission)

controllers/collection_controller.rb

@@ -30,7 +30,7 @@ class CollectionsController < ApplicationController
 
       get '/members' do
         ont, submission = get_ontology_and_submission
-        attributes, page, size, filter_by_label, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::Class)
+        attributes, page, size, order_by, bring_unmapped_needed  =  settings_params(LinkedData::Models::Class)
         collection_uri = get_collection_uri(params)
         data = LinkedData::Models::Class.where(memberOf: collection_uri).in(submission).include(attributes).page(page,size).all
         reply data