Merge branch 'development' into stage

Gemfile

@@ -30,9 +30,8 @@ gem 'rack-timeout'
 gem 'redis-rack-cache', '~> 2.0'
 
 # Data access (caching)
-gem 'redis', '~> 4.8.1'
-gem 'redis-activesupport'
-gem 'redis-store', '1.9.1'
+gem 'redis'
+gem 'redis-store', '~>1.10'
 
 # Monitoring
 gem 'cube-ruby', require: 'cube'
@@ -48,10 +47,10 @@ 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: 'master'
+gem 'ncbo_cron', git: 'https://github.com/ontoportal-lirmm/ncbo_cron.git', branch: 'development'
 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 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
+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

Gemfile.lock

@@ -11,7 +11,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: 0e554fce49713ce4d5a742a06c2fb59a547caf47
+  revision: b2a635fb1e8206e6e3010be4dbe033b47eb58481
   branch: development
   specs:
     goo (0.0.2)
@@ -40,8 +40,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ncbo_cron.git
-  revision: 9ec0147203007cc368a5119ffe1a019fa8701c14
-  branch: master
+  revision: 865f00adf94a5bd471eb9b35adc90812a3b854a9
+  branch: development
   specs:
     ncbo_cron (0.0.1)
       dante
@@ -57,7 +57,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 135b0df0d6394f69162f496674c5b2f2a3dcba4c
+  revision: 1278507e6ae8224edca746c7c150775ec2210195
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -77,13 +77,12 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/sparql-client.git
-  revision: 180c818f7715baac64b2699bb452ef5c756f62c5
-  branch: master
+  revision: 59251e59346c9a69a67c88552ba55a1244eec602
+  branch: development
   specs:
-    sparql-client (1.0.1)
-      json_pure (>= 1.4)
-      net-http-persistent (= 2.9.4)
-      rdf (>= 1.0)
+    sparql-client (3.2.2)
+      net-http-persistent (~> 4.0, >= 4.0.2)
+      rdf (~> 3.2, >= 3.2.11)
 
 GIT
   remote: https://github.com/palexander/rack-post-body-to-params.git
@@ -114,7 +113,8 @@ GEM
     backports (3.25.0)
     base64 (0.2.0)
     bcrypt (3.1.20)
-    bcrypt_pbkdf (1.1.0)
+    bcrypt_pbkdf (1.1.1)
+    bcrypt_pbkdf (1.1.1-x86_64-darwin)
     bigdecimal (1.4.2)
     builder (3.2.4)
     capistrano (3.18.1)
@@ -131,6 +131,7 @@ GEM
       sshkit (~> 1.3)
     coderay (1.1.3)
     concurrent-ruby (1.2.3)
+    connection_pool (2.4.1)
     crack (1.0.0)
       bigdecimal
       rexml
@@ -181,9 +182,9 @@ GEM
     google-analytics-data-v1beta (0.12.0)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
-    google-apis-analytics_v3 (0.15.0)
-      google-apis-core (>= 0.14.0, < 2.a)
-    google-apis-core (0.14.1)
+    google-apis-analytics_v3 (0.16.0)
+      google-apis-core (>= 0.15.0, < 2.a)
+    google-apis-core (0.15.0)
       addressable (~> 2.5, >= 2.5.1)
       googleauth (~> 1.9)
       httpclient (>= 2.8.1, < 3.a)
@@ -197,6 +198,7 @@ GEM
     google-cloud-env (2.1.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.4.0)
+    google-protobuf (3.25.3-x86_64-darwin)
     google-protobuf (3.25.3-x86_64-linux)
     googleapis-common-protos (1.5.0)
       google-protobuf (~> 3.18)
@@ -211,7 +213,10 @@ GEM
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.62.0-x86_64-linux)
+    grpc (1.63.0-x86_64-darwin)
+      google-protobuf (~> 3.25)
+      googleapis-common-protos-types (~> 1.0)
+    grpc (1.63.0-x86_64-linux)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
     haml (5.2.2)
@@ -231,7 +236,6 @@ GEM
       rdf (>= 2.2.8, < 4.0)
     json-schema (2.8.1)
       addressable (>= 2.4)
-    json_pure (2.7.2)
     jwt (2.8.1)
       base64
     kgio (2.11.4)
@@ -248,17 +252,18 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0305)
+    mime-types-data (3.2024.0507)
     mini_mime (1.1.5)
     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 (2.4.0)
+    multipart-post (2.4.1)
     mutex_m (0.2.0)
-    net-http-persistent (2.9.4)
-    net-imap (0.4.10)
+    net-http-persistent (4.0.2)
+      connection_pool (~> 2.2)
+    net-imap (0.4.11)
       date
       net-protocol
     net-pop (0.1.2)
@@ -301,7 +306,7 @@ GEM
       rack
     rack-test (2.1.0)
       rack (>= 1.3)
-    rack-timeout (0.6.3)
+    rack-timeout (0.7.0)
     raindrops (0.20.1)
     rake (10.5.0)
     rdf (3.2.11)
@@ -320,28 +325,29 @@ GEM
       rdf (~> 3.2)
       rexml (~> 3.2)
     redcarpet (3.6.0)
-    redis (4.8.1)
-    redis-activesupport (5.3.0)
-      activesupport (>= 3, < 8)
-      redis-store (>= 1.3, < 2)
+    redis (5.2.0)
+      redis-client (>= 0.22.0)
+    redis-client (0.22.1)
+      connection_pool
     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 (1.10.0)
+      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 (1.6.0)
+    request_store (1.7.0)
       rack (>= 1.4)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     retriable (3.1.2)
-    rexml (3.2.6)
+    rexml (3.2.8)
+      strscan (>= 3.0.9)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -377,12 +383,13 @@ GEM
       rack-test
       sinatra (~> 1.4.0)
       tilt (>= 1.3, < 3)
-    sshkit (1.22.1)
+    sshkit (1.22.2)
       base64
       mutex_m
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)
       net-ssh (>= 2.8.0)
+    strscan (3.1.0)
     systemu (2.6.5)
     temple (0.10.3)
     tilt (2.3.0)
@@ -405,6 +412,7 @@ GEM
       hashdiff (>= 0.4.0, < 2.0.0)
 
 PLATFORMS
+  x86_64-darwin-23
   x86_64-linux
 
 DEPENDENCIES
@@ -446,10 +454,9 @@ DEPENDENCIES
   rack-timeout
   rake (~> 10.0)
   redcarpet
-  redis (~> 4.8.1)
-  redis-activesupport
+  redis
   redis-rack-cache (~> 2.0)
-  redis-store (= 1.9.1)
+  redis-store (~> 1.10)
   request_store
   shotgun!
   simplecov
@@ -463,4 +470,4 @@ DEPENDENCIES
   webmock (~> 3.19.1)
 
 BUNDLED WITH
-   2.3.15
+   2.4.22

config/rack_attack.rb

@@ -3,15 +3,14 @@
 puts "(API) >> Throttling enabled at #{LinkedData::OntologiesAPI.settings.req_per_second_per_ip} req/sec"
 
 require 'rack/attack'
-require 'redis-activesupport'
 use Rack::Attack
 
 attack_redis_host_port = {
   host: LinkedData::OntologiesAPI.settings.http_redis_host,
-  port: LinkedData::OntologiesAPI.settings.http_redis_port
+  port: LinkedData::OntologiesAPI.settings.http_redis_port,
+  db: 1
 }
-attack_store = ActiveSupport::Cache::RedisStore.new(attack_redis_host_port)
-Rack::Attack.cache.store = attack_store
+Rack::Attack.cache.store = Redis.new(attack_redis_host_port)
 
 safe_ips = LinkedData::OntologiesAPI.settings.safe_ips ||= Set.new
 safe_ips.each do |safe_ip|

controllers/users_controller.rb

@@ -99,14 +99,14 @@ class UsersController < ApplicationController
     private
 
 
-    def create_user
+    def create_user(send_notifications: true)
       params ||= @params
       user = User.find(params["username"]).first
       error 409, "User with username `#{params["username"]}` already exists" unless user.nil?
       params.delete("role") unless current_user.admin?
       user = instance_from_params(User, params)
       if user.valid?
-        user.save(send_notifications: false)
+        user.save(send_notifications: send_notifications)
       else
         error 422, user.errors
       end

test/controllers/test_search_models_controller.rb

@@ -18,7 +18,8 @@ def test_show_all_collection
     get '/admin/search/collections'
     assert last_response.ok?
     res = MultiJson.load(last_response.body)
-    assert_equal res["collections"].sort, Goo.search_connections.keys.map(&:to_s).sort
+    array = %w[agents_metadata ontology_data ontology_metadata prop_search_core1 term_search_core1]
+    assert_equal res["collections"].sort , array.sort
   end
 
   def test_collection_schema
@@ -81,7 +82,7 @@ def test_search_security
     subs = LinkedData::Models::OntologySubmission.all
     subs.each do |s|
       s.bring_remaining
-      s.index_all_data(Logger.new($stdout))
+      s.index_all(Logger.new($stdout))
     end
 
 
@@ -416,7 +417,7 @@ def test_agents_search
   def test_search_data
     count, acronyms, bro = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
                                                                                                 process_submission: true,
-                                                                                                process_options: { process_rdf: true, extract_metadata: false, generate_missing_labels: false},
+                                                                                                process_options: { process_rdf: true, extract_metadata: false,  index_all_data: true, generate_missing_labels: false},
                                                                                                 acronym: "BROSEARCHTEST",
                                                                                                 name: "BRO Search Test",
                                                                                                 file_path: "./test/data/ontology_files/BRO_v3.2.owl",
@@ -427,7 +428,7 @@ def test_search_data
 
     count, acronyms, mccl = LinkedData::SampleData::Ontology.create_ontologies_and_submissions({
                                                                                                  process_submission: true,
-                                                                                                 process_options: { process_rdf: true, extract_metadata: false, generate_missing_labels: false},
+                                                                                                 process_options: { process_rdf: true, extract_metadata: false, index_all_data: true, generate_missing_labels: false},
                                                                                                  acronym: "MCCLSEARCHTEST",
                                                                                                  name: "MCCL Search Test",
                                                                                                  file_path: "./test/data/ontology_files/CellLine_OWL_BioPortal_v1.0.owl",
@@ -439,8 +440,6 @@ def test_search_data
     subs = LinkedData::Models::OntologySubmission.all
     count = []
     subs.each do |s|
-      s.bring_remaining
-      s.index_all_data(Logger.new($stdout))
       count << Goo.sparql_query_client.query("SELECT  (COUNT( DISTINCT ?id) as ?c)  FROM <#{s.id}> WHERE {?id ?p ?v}")
                  .first[:c]
                  .to_i