Feature: Agroportal API new deployment configs for INRAE servers

.env.sample

@@ -2,6 +2,7 @@ API_URL=http://localhost:9393
 ONTOLOGIES_LINKED_DATA_PATH=
 GOO_PATH=
 SPARQL_CLIENT_PATH=
+NCBO_PATH=
 
 ## An ontology that will be imported in the starting of the API server
 STARTER_ONTOLOGY=STY

Gemfile

@@ -91,4 +91,4 @@ group :test do
   gem 'simplecov-cobertura' # for codecov.io
   gem 'webmock'
   gem 'webrick'
-end
+end

Gemfile.lock

@@ -29,7 +29,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ncbo_cron.git
-  revision: 7467cf268b578b531ef3546557790fc61666700c
+  revision: 2eb5cfd12e6e8fd9d3b0a6610d836a358cdfc409
   branch: development
   specs:
     ncbo_cron (0.0.1)
@@ -57,7 +57,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 471a9f10b2404ff643ce61369817bc985faffa19
+  revision: b00e80e8dfa50049a5780467e0effe692d827c58
   branch: development
   specs:
     ontologies_linked_data (0.0.1)
@@ -103,17 +103,17 @@ GIT
 
 GIT
   remote: https://github.com/sinatra/sinatra.git
-  revision: fa99a21461d4f1f5337b9b9d7a38a1b51c8f4e55
+  revision: 9e5c4ec8ade92c7375f44acf4c6e1103d32d6c12
   specs:
-    rack-protection (4.1.1)
+    rack-protection (4.2.1)
       base64 (>= 0.1.0)
       logger (>= 1.6.0)
       rack (>= 3.0.0, < 4)
-    sinatra-contrib (4.1.1)
+    sinatra-contrib (4.2.1)
       multi_json (>= 0.0.2)
       mustermann (~> 3.0)
-      rack-protection (= 4.1.1)
-      sinatra (= 4.1.1)
+      rack-protection (= 4.2.1)
+      sinatra (= 4.2.1)
       tilt (~> 2.0)
 
 GIT
@@ -128,7 +128,7 @@ GIT
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (7.2.2.2)
+    activesupport (7.2.3)
       base64
       benchmark (>= 0.3)
       bigdecimal
@@ -140,60 +140,60 @@ GEM
       minitest (>= 5.1)
       securerandom (>= 0.3)
       tzinfo (~> 2.0, >= 2.0.5)
-    addressable (2.8.7)
-      public_suffix (>= 2.0.2, < 7.0)
-    airbrussh (1.5.3)
+    addressable (2.8.8)
+      public_suffix (>= 2.0.2, < 8.0)
+    airbrussh (1.6.0)
       sshkit (>= 1.6.1, != 1.7.0)
     ansi (1.5.0)
     ast (2.4.3)
     base64 (0.3.0)
     bcp47_spec (0.2.1)
-    bcrypt (3.1.20)
-    bcrypt_pbkdf (1.1.1)
-    bcrypt_pbkdf (1.1.1-arm64-darwin)
-    bcrypt_pbkdf (1.1.1-x86_64-darwin)
-    benchmark (0.4.1)
-    bigdecimal (3.2.3)
+    bcrypt (3.1.21)
+    bcrypt_pbkdf (1.1.2)
+    bcrypt_pbkdf (1.1.2-arm64-darwin)
+    bcrypt_pbkdf (1.1.2-x86_64-darwin)
+    benchmark (0.5.0)
+    bigdecimal (3.3.1)
     builder (3.3.0)
-    capistrano (3.19.2)
+    capistrano (3.20.0)
       airbrussh (>= 1.0.0)
       i18n
       rake (>= 10.0.0)
       sshkit (>= 1.9.0)
-    capistrano-bundler (2.1.1)
+    capistrano-bundler (2.2.0)
       capistrano (~> 3.1)
     capistrano-locally (0.3.0)
       capistrano (~> 3.0)
     capistrano-rbenv (2.2.0)
       capistrano (~> 3.1)
       sshkit (~> 1.3)
     coderay (1.1.3)
-    concurrent-ruby (1.3.5)
-    connection_pool (2.5.4)
+    concurrent-ruby (1.3.6)
+    connection_pool (2.5.5)
     crack (0.4.5)
       rexml
     dante (0.2.0)
-    date (3.4.1)
+    date (3.5.1)
     declarative (0.0.20)
     docile (1.4.1)
     domain_name (0.6.20240107)
     drb (2.2.3)
     ed25519 (1.4.0)
-    et-orbi (1.3.0)
+    et-orbi (1.4.0)
       tzinfo
-    faraday (2.13.4)
+    faraday (2.14.0)
       faraday-net_http (>= 2.0, < 3.5)
       json
       logger
-    faraday-follow_redirects (0.3.0)
+    faraday-follow_redirects (0.5.0)
       faraday (>= 1, < 3)
-    faraday-net_http (3.4.1)
-      net-http (>= 0.5.0)
-    faraday-retry (2.3.2)
+    faraday-net_http (3.4.2)
+      net-http (~> 0.5)
+    faraday-retry (2.4.0)
       faraday (~> 2.0)
     ffi (1.15.0)
-    fugit (1.11.2)
-      et-orbi (~> 1, >= 1.2.11)
+    fugit (1.12.1)
+      et-orbi (~> 1.4)
       raabro (~> 1.4)
     gapic-common (1.1.0)
       faraday (>= 1.9, < 3.a)
@@ -241,7 +241,7 @@ GEM
       grpc (~> 1.41)
     googleapis-common-protos-types (1.20.0)
       google-protobuf (>= 3.18, < 5.a)
-    googleauth (1.15.0)
+    googleauth (1.16.1)
       faraday (>= 1.0, < 3.a)
       google-cloud-env (~> 2.2)
       google-logging-utils (~> 0.1)
@@ -265,14 +265,14 @@ GEM
       temple (>= 0.8.0)
       tilt
     hashdiff (1.2.1)
-    htmlentities (4.3.4)
+    htmlentities (4.4.2)
     http-accept (1.7.0)
-    http-cookie (1.0.8)
+    http-cookie (1.1.0)
       domain_name (~> 0.5)
-    i18n (1.14.7)
+    i18n (1.14.8)
       concurrent-ruby (~> 1.0)
-    io-console (0.8.1)
-    json (2.15.0)
+    io-console (0.8.2)
+    json (2.18.1)
     json-canonicalization (0.4.0)
     json-ld (3.2.5)
       htmlentities (~> 4.3)
@@ -294,7 +294,8 @@ GEM
     logger (1.7.0)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
-    mail (2.8.1)
+    mail (2.9.0)
+      logger
       mini_mime (>= 0.1.1)
       net-imap
       net-pop
@@ -303,12 +304,12 @@ GEM
     mime-types (3.7.0)
       logger
       mime-types-data (~> 3.2025, >= 3.2025.0507)
-    mime-types-data (3.2025.0916)
+    mime-types-data (3.2026.0203)
     mini_mime (1.1.5)
-    minitest (5.25.5)
-    minitest-fail-fast (0.1.0)
-      minitest (~> 5)
-    minitest-hooks (1.5.2)
+    minitest (5.27.0)
+    minitest-fail-fast (0.2.0)
+      minitest (>= 5.0, < 7)
+    minitest-hooks (1.5.3)
       minitest (> 5.3)
     minitest-reporters (1.7.1)
       ansi
@@ -318,17 +319,17 @@ GEM
     minitest-stub_any_instance (1.0.3)
     mlanett-redis-lock (0.2.7)
       redis
-    multi_json (1.17.0)
+    multi_json (1.19.1)
     mustermann (3.0.4)
       ruby2_keywords (~> 0.0.1)
-    net-ftp (0.3.8)
+    net-ftp (0.3.9)
       net-protocol
       time
-    net-http (0.6.0)
-      uri
-    net-http-persistent (4.0.6)
-      connection_pool (~> 2.2, >= 2.2.4)
-    net-imap (0.5.10)
+    net-http (0.9.1)
+      uri (>= 0.11.1)
+    net-http-persistent (4.0.8)
+      connection_pool (>= 2.2.4, < 4)
+    net-imap (0.5.13)
       date
       net-protocol
     net-pop (0.1.2)
@@ -343,7 +344,7 @@ GEM
       net-protocol
     net-ssh (7.3.0)
     netrc (0.11.0)
-    oj (3.16.11)
+    oj (3.16.13)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     omni_logger (0.1.4)
@@ -353,22 +354,23 @@ GEM
     pandoc-ruby (2.1.10)
     parallel (1.27.0)
     parseconfig (1.1.2)
-    parser (3.3.9.0)
+    parser (3.3.10.1)
       ast (~> 2.4.1)
       racc
     pony (1.13.1)
       mail (>= 2.0)
-    prism (1.5.1)
-    pry (0.15.2)
+    prism (1.9.0)
+    pry (0.16.0)
       coderay (~> 1.1)
       method_source (~> 1.0)
+      reline (>= 0.6.0)
     public_suffix (6.0.2)
     raabro (1.4.0)
     racc (1.8.1)
-    rack (3.2.1)
+    rack (3.2.4)
     rack-accept (0.4.5)
       rack (>= 0.4)
-    rack-attack (6.7.0)
+    rack-attack (6.8.0)
       rack (>= 1.0, < 4)
     rack-cache (1.17.0)
       rack (>= 0.4)
@@ -385,11 +387,11 @@ GEM
     rack-test (2.2.0)
       rack (>= 1.3)
     rack-timeout (0.7.0)
-    rackup (2.2.1)
+    rackup (2.3.1)
       rack (>= 3)
     rainbow (3.1.1)
     raindrops (0.20.1)
-    rake (13.3.0)
+    rake (13.3.1)
     rdf (3.3.4)
       bcp47_spec (~> 0.2)
       bigdecimal (~> 3.1, >= 3.1.5)
@@ -411,15 +413,15 @@ GEM
       reline
     redis (5.4.1)
       redis-client (>= 0.22.0)
-    redis-client (0.26.0)
+    redis-client (0.26.4)
       connection_pool
     redis-rack-cache (2.2.1)
       rack-cache (>= 1.10, < 2)
       redis-store (>= 1.6, < 2)
     redis-store (1.11.0)
       redis (>= 4, < 6)
     regexp_parser (2.11.3)
-    reline (0.6.2)
+    reline (0.6.3)
       io-console (~> 0.5)
     representable (3.2.0)
       declarative (< 0.1.0)
@@ -437,28 +439,28 @@ GEM
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.80.2)
+    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 (>= 1.46.0, < 2.0)
+      rubocop-ast (>= 1.49.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 4.0)
-    rubocop-ast (1.47.1)
+    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)
-    rubyzip (3.1.0)
+    rubyzip (3.2.2)
     rufus-scheduler (3.9.2)
       fugit (~> 1.1, >= 1.11.1)
     securerandom (0.4.1)
-    sentry-ruby (5.27.1)
+    sentry-ruby (5.28.1)
       bigdecimal
       concurrent-ruby (~> 1.0, >= 1.0.2)
     signet (0.21.0)
@@ -475,14 +477,14 @@ GEM
       simplecov (~> 0.19)
     simplecov-html (0.13.2)
     simplecov_json_formatter (0.1.4)
-    sinatra (4.1.1)
+    sinatra (4.2.1)
       logger (>= 1.6.0)
       mustermann (~> 3.0)
       rack (>= 3.0.0, < 4)
-      rack-protection (= 4.1.1)
+      rack-protection (= 4.2.1)
       rack-session (>= 2.0.0, < 3)
       tilt (~> 2.0)
-    sshkit (1.24.0)
+    sshkit (1.25.0)
       base64
       logger
       net-scp (>= 1.1.2)
@@ -491,31 +493,31 @@ GEM
       ostruct
     systemu (2.6.5)
     temple (0.10.4)
-    tilt (2.6.1)
-    time (0.4.1)
+    tilt (2.7.0)
+    time (0.4.2)
       date
-    timeout (0.4.3)
+    timeout (0.6.0)
     trailblazer-option (0.1.2)
     tzinfo (2.0.6)
       concurrent-ruby (~> 1.0)
     uber (0.1.0)
     unicode-display_width (3.2.0)
       unicode-emoji (~> 4.1)
-    unicode-emoji (4.1.0)
+    unicode-emoji (4.2.0)
     unicorn (6.1.0)
       kgio (~> 2.6)
       raindrops (~> 0.7)
     unicorn-worker-killer (0.4.5)
       get_process_mem (~> 0)
       unicorn (>= 4, < 7)
-    uri (1.0.3)
+    uri (1.1.1)
     uuid (2.3.9)
       macaddr (~> 1.0)
-    webmock (3.25.1)
+    webmock (3.26.1)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
-    webrick (1.9.1)
+    webrick (1.9.2)
 
 PLATFORMS
   arm64-darwin