Notification system

.env.sample

@@ -4,9 +4,20 @@ GOO_PATH=
 SPARQL_CLIENT_PATH=
 NCBO_PATH=
 
+REDIS_GOO_CACHE_HOST=redis-ut
+REDIS_HTTP_CACHE_HOST=redis-ut
+REDIS_PERSISTENT_HOST=redis-ut
+
 ## An ontology that will be imported in the starting of the API server
 STARTER_ONTOLOGY=STY
 ## API key of a remote API used to download the starter ontology
 OP_API_KEY=1de0a270-29c5-4dda-b043-7c3580628cd5
 ## API url of the remote API used to download the starter ontology
 OP_API_URL="https://data.agroportal.lirmm.fr"
+
+## PostgreSQL Database
+DATABASE_HOST=postgres-ut
+DATABASE_PORT=5432
+DATABASE_NAME=ontologies_api_development
+DATABASE_USER=ontoportal
+DATABASE_PASSWORD=ontoportal

.github/workflows/ruby-unit-tests.yml

@@ -30,6 +30,8 @@ jobs:
       - name: Run unit tests
         run: |
           cp .env.sample .env
+          # Create test database in the postgres container
+          docker compose exec -T postgres-ut psql -U ontoportal -d ontologies_api_development -c "CREATE DATABASE ontologies_api_test;" 2>/dev/null || true
           ci_env=`bash <(curl -s https://codecov.io/env)`
           GOO_SLICES=${{ matrix.goo-slice }} bundle exec rake test:docker:${{ matrix.triplestore }}
 

Gemfile

@@ -10,6 +10,7 @@ gem 'rake'
 gem 'rexml' # Investigate why unicorn fails to start under ruby 3 without adding rexml gem to the Gemfile
 gem 'sinatra'
 gem 'rackup'
+gem 'pony'
 
 github 'sinatra/sinatra' do
   gem 'sinatra-contrib'
@@ -38,6 +39,11 @@ gem 'redis-rack-cache'
 gem 'redis'
 gem 'redis-store'
 
+# Relational database
+gem 'activerecord', '~> 7.1'
+gem 'pg', '~> 1.5'
+gem 'sinatra-activerecord', '~> 2.0'
+
 # Monitoring
 gem "sentry-ruby", "~> 5.24"
 
@@ -50,11 +56,14 @@ gem 'haml', '~> 5.2.2'
 gem 'rack-contrib'
 gem 'pandoc-ruby'
 
+# Sidekiq
+gem 'sidekiq', '~> 7.3.9'
+
 # 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_ontology_recommender', git: 'https://github.com/ontoportal-lirmm/ncbo_ontology_recommender.git', branch: 'development'
-gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'development'
+gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'sidekiq'
 gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development'
 

Gemfile.lock

@@ -57,8 +57,8 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: e0e4547b49290ace0849b4d5bf294a7809196943
-  branch: development
+  revision: c05fefaffe91fac14cb3cd079d1e4dfa32dc3549
+  branch: sidekiq
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -103,7 +103,7 @@ GIT
 
 GIT
   remote: https://github.com/sinatra/sinatra.git
-  revision: 4062e3669c7dff0f59ca1d0b0bfa67f7eef444af
+  revision: 9e5c4ec8ade92c7375f44acf4c6e1103d32d6c12
   specs:
     rack-protection (4.2.1)
       base64 (>= 0.1.0)
@@ -128,6 +128,12 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
+    activemodel (7.2.3)
+      activesupport (= 7.2.3)
+    activerecord (7.2.3)
+      activemodel (= 7.2.3)
+      activesupport (= 7.2.3)
+      timeout (>= 0.4.0)
     activesupport (7.2.3)
       base64
       benchmark (>= 0.3)
@@ -153,7 +159,7 @@ GEM
     bcrypt_pbkdf (1.1.2-arm64-darwin)
     bcrypt_pbkdf (1.1.2-x86_64-darwin)
     benchmark (0.5.0)
-    bigdecimal (3.3.1)
+    bigdecimal (4.0.1)
     builder (3.3.0)
     capistrano (3.20.0)
       airbrussh (>= 1.0.0)
@@ -185,11 +191,11 @@ GEM
       faraday-net_http (>= 2.0, < 3.5)
       json
       logger
-    faraday-follow_redirects (0.4.0)
+    faraday-follow_redirects (0.5.0)
       faraday (>= 1, < 3)
     faraday-net_http (3.4.2)
       net-http (~> 0.5)
-    faraday-retry (2.3.2)
+    faraday-retry (2.4.0)
       faraday (~> 2.0)
     ffi (1.15.0)
     fugit (1.12.1)
@@ -232,7 +238,9 @@ GEM
     google-cloud-errors (1.5.0)
     google-logging-utils (0.2.0)
     google-protobuf (3.25.3)
+    google-protobuf (3.25.3-aarch64-linux)
     google-protobuf (3.25.3-arm64-darwin)
+    google-protobuf (3.25.3-x86-linux)
     google-protobuf (3.25.3-x86_64-darwin)
     google-protobuf (3.25.3-x86_64-linux)
     googleapis-common-protos (1.8.0)
@@ -241,7 +249,7 @@ GEM
       grpc (~> 1.41)
     googleapis-common-protos-types (1.20.0)
       google-protobuf (>= 3.18, < 5.a)
-    googleauth (1.16.0)
+    googleauth (1.16.1)
       faraday (>= 1.0, < 3.a)
       google-cloud-env (~> 2.2)
       google-logging-utils (~> 0.1)
@@ -252,9 +260,15 @@ GEM
     grpc (1.70.1)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
+    grpc (1.70.1-aarch64-linux)
+      google-protobuf (>= 3.25, < 5.0)
+      googleapis-common-protos-types (~> 1.0)
     grpc (1.70.1-arm64-darwin)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
+    grpc (1.70.1-x86-linux)
+      google-protobuf (>= 3.25, < 5.0)
+      googleapis-common-protos-types (~> 1.0)
     grpc (1.70.1-x86_64-darwin)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
@@ -272,7 +286,7 @@ GEM
     i18n (1.14.8)
       concurrent-ruby (~> 1.0)
     io-console (0.8.2)
-    json (2.18.0)
+    json (2.18.1)
     json-canonicalization (0.4.0)
     json-ld (3.2.5)
       htmlentities (~> 4.3)
@@ -281,9 +295,8 @@ GEM
       multi_json (~> 1.15)
       rack (>= 2.2, < 4)
       rdf (~> 3.2, >= 3.2.10)
-    json-schema (5.2.2)
+    json-schema (5.1.0)
       addressable (~> 2.8)
-      bigdecimal (~> 3.1)
     jwt (3.1.2)
       base64
     kgio (2.11.4)
@@ -304,11 +317,11 @@ GEM
     mime-types (3.7.0)
       logger
       mime-types-data (~> 3.2025, >= 3.2025.0507)
-    mime-types-data (3.2026.0113)
+    mime-types-data (3.2026.0203)
     mini_mime (1.1.5)
     minitest (5.27.0)
-    minitest-fail-fast (0.1.0)
-      minitest (~> 5)
+    minitest-fail-fast (0.2.0)
+      minitest (>= 5.0, < 7)
     minitest-hooks (1.5.3)
       minitest (> 5.3)
     minitest-reporters (1.7.1)
@@ -354,12 +367,19 @@ GEM
     pandoc-ruby (2.1.10)
     parallel (1.27.0)
     parseconfig (1.1.2)
-    parser (3.3.10.0)
+    parser (3.3.10.1)
       ast (~> 2.4.1)
       racc
+    pg (1.6.3)
+    pg (1.6.3-aarch64-linux)
+    pg (1.6.3-aarch64-linux-musl)
+    pg (1.6.3-arm64-darwin)
+    pg (1.6.3-x86_64-darwin)
+    pg (1.6.3-x86_64-linux)
+    pg (1.6.3-x86_64-linux-musl)
     pony (1.13.1)
       mail (>= 2.0)
-    prism (1.7.0)
+    prism (1.9.0)
     pry (0.16.0)
       coderay (~> 1.1)
       method_source (~> 1.0)
@@ -392,13 +412,9 @@ GEM
     rainbow (3.1.1)
     raindrops (0.20.1)
     rake (13.3.1)
-    rdf (3.3.4)
+    rdf (3.3.1)
       bcp47_spec (~> 0.2)
-      bigdecimal (~> 3.1, >= 3.1.5)
       link_header (~> 0.0, >= 0.0.8)
-      logger (~> 1.5)
-      ostruct (~> 0.6)
-      readline (~> 0.0)
     rdf-rdfxml (3.3.0)
       builder (~> 3.2, >= 3.2.4)
       htmlentities (~> 4.3)
@@ -409,11 +425,9 @@ GEM
     rdf-xsd (3.3.0)
       rdf (~> 3.3)
       rexml (~> 3.2)
-    readline (0.0.4)
-      reline
     redis (5.4.1)
       redis-client (>= 0.22.0)
-    redis-client (0.26.3)
+    redis-client (0.26.4)
       connection_pool
     redis-rack-cache (2.2.1)
       rack-cache (>= 1.10, < 2)
@@ -439,20 +453,20 @@ GEM
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.82.0)
+    rubocop (1.84.1)
       json (~> 2.3)
       language_server-protocol (~> 3.17.0.2)
       lint_roller (~> 1.1.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 2.9.3, < 3.0)
-      rubocop-ast (>= 1.48.0, < 2.0)
+      rubocop-ast (>= 1.49.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 4.0)
-    rubocop-ast (1.48.0)
+    rubocop-ast (1.49.0)
       parser (>= 3.3.7.2)
-      prism (~> 1.4)
+      prism (~> 1.7)
     ruby-progressbar (1.13.0)
     ruby-xxHash (0.4.0.2)
     ruby2_keywords (0.0.5)
@@ -463,6 +477,12 @@ GEM
     sentry-ruby (5.28.1)
       bigdecimal
       concurrent-ruby (~> 1.0, >= 1.0.2)
+    sidekiq (7.3.10)
+      base64
+      connection_pool (>= 2.3.0, < 3)
+      logger
+      rack (>= 2.2.4, < 3.3)
+      redis-client (>= 0.23.0, < 1)
     signet (0.21.0)
       addressable (~> 2.8)
       faraday (>= 0.17.5, < 3.a)
@@ -484,6 +504,9 @@ GEM
       rack-protection (= 4.2.1)
       rack-session (>= 2.0.0, < 3)
       tilt (~> 2.0)
+    sinatra-activerecord (2.0.28)
+      activerecord (>= 4.1)
+      sinatra (>= 1.0)
     sshkit (1.25.0)
       base64
       logger
@@ -493,7 +516,7 @@ GEM
       ostruct
     systemu (2.6.5)
     temple (0.10.4)
-    tilt (2.6.1)
+    tilt (2.7.0)
     time (0.4.2)
       date
     timeout (0.6.0)
@@ -520,12 +543,17 @@ GEM
     webrick (1.9.2)
 
 PLATFORMS
+  aarch64-linux
+  aarch64-linux-musl
   arm64-darwin
   ruby
+  x86-linux
   x86_64-darwin
   x86_64-linux
+  x86_64-linux-musl
 
 DEPENDENCIES
+  activerecord (~> 7.1)
   activesupport
   bcrypt_pbkdf (>= 1.0, < 2.0)
   bigdecimal
@@ -557,6 +585,8 @@ DEPENDENCIES
   pandoc-ruby
   parallel
   parseconfig
+  pg (~> 1.5)
+  pony
   rack
   rack-accept
   rack-attack
@@ -578,9 +608,11 @@ DEPENDENCIES
   rubocop
   sentry-ruby (~> 5.24)
   shotgun!
+  sidekiq (~> 7.3.9)
   simplecov
   simplecov-cobertura
   sinatra
+  sinatra-activerecord (~> 2.0)
   sinatra-contrib!
   sparql-client!
   unicorn
@@ -589,4 +621,4 @@ DEPENDENCIES
   webrick
 
 BUNDLED WITH
-   2.6.7
+   2.6.9

app.rb

@@ -29,6 +29,10 @@
 require_relative 'lib/rack/slice_detection'
 require_relative 'lib/rack/request_lang'
 
+# sidekiq requirements
+require 'sidekiq/web'
+require 'sidekiq'
+
 # Logging setup
 require_relative 'config/logging'
 
@@ -37,6 +41,9 @@
 
 require 'request_store'
 
+# Postgtres Database connection
+require_relative 'config/relationalDatabase'
+RelationalDatabase.connect!
 # Protection settings
 set :protection, except: :path_traversal
 

bin/ontoportal

@@ -113,7 +113,7 @@ build_docker_run_cmd() {
     fi
   done
 
-  bash_cmd+=" (bundle check || bundle install || bundle update) && $custom_command"
+  bash_cmd+=" (bundle check || bundle install || bundle update) && bundle exec rake db:migrate && $custom_command"
   docker_run_cmd+=" --service-ports api bash -c \"$bash_cmd\""
 
   echo "[+] Run docker command $docker_run_cmd"
@@ -370,4 +370,4 @@ case "$1" in
     show_help
     exit 1
     ;;
-esac
+esac

config.ru

@@ -1,2 +1,6 @@
 require './app.rb'
 run Sinatra::Application
+
+map '/sidekiq' do
+  run Sidekiq::Web
+end