Feature: Align to AgroPortal 3.0

Gemfile

@@ -23,13 +23,14 @@ gem 'request_store'
 gem 'parallel'
 gem 'json-ld'
 gem 'ffi', '~> 1.16.3'
+gem 'activesupport', '~> 3.2.22.5'
 
 # Monitoring
 gem 'cube-ruby', require: 'cube'
 
-gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'master'
+gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'development'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'development'
-gem 'ontologies_linked_data', github: 'BiodivPortal/ontologies_linked_data', branch: 'master'
+gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'development'
 gem 'ncbo_annotator', github: 'ontoportal-lirmm/ncbo_annotator', branch: 'development'
 # Testing
 group :test do

Gemfile.lock

@@ -1,27 +1,7 @@
-GIT
-  remote: https://github.com/BiodivPortal/ontologies_linked_data.git
-  revision: 4bd30687ba5800edd1d349267e1aacbd0cc6d0ca
-  branch: master
-  specs:
-    ontologies_linked_data (0.0.1)
-      activesupport
-      bcrypt
-      goo
-      json
-      libxml-ruby
-      multi_json
-      oj
-      omni_logger
-      pony
-      rack
-      rack-test
-      rsolr
-      rubyzip
-
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: c48a1e4dfe82a2e5c42614a30380f3bdb2044ba9
-  branch: master
+  revision: f8ac7b00e8d8b46d1eea04de014175525c1cdd83
+  branch: development
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -47,6 +27,26 @@ GIT
       redis
       ruby-xxHash
 
+GIT
+  remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
+  revision: 312ef426eeaa461e88fa23124ea5fd531f4276ba
+  branch: development
+  specs:
+    ontologies_linked_data (0.0.1)
+      activesupport
+      bcrypt
+      goo
+      json
+      libxml-ruby
+      multi_json
+      oj
+      omni_logger
+      pony
+      rack
+      rack-test
+      rsolr
+      rubyzip
+
 GIT
   remote: https://github.com/ontoportal-lirmm/sparql-client.git
   revision: 59251e59346c9a69a67c88552ba55a1244eec602
@@ -79,13 +79,11 @@ GEM
       multi_json (~> 1.0)
     addressable (2.8.7)
       public_suffix (>= 2.0.2, < 7.0)
-    airbrussh (1.5.2)
+    airbrussh (1.5.3)
       sshkit (>= 1.6.1, != 1.7.0)
     base64 (0.2.0)
     bcrypt (3.1.20)
     bcrypt_pbkdf (1.1.1)
-    bcrypt_pbkdf (1.1.1-arm64-darwin)
-    bcrypt_pbkdf (1.1.1-x86_64-darwin)
     bigdecimal (3.1.8)
     binding_of_caller (1.0.1)
       debug_inspector (>= 1.2.0)
@@ -154,40 +152,20 @@ GEM
     google-cloud-env (2.1.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.4.0)
-    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 (1.6.0)
       google-protobuf (>= 3.18, < 5.a)
       googleapis-common-protos-types (~> 1.7)
       grpc (~> 1.41)
-    googleapis-common-protos-types (1.15.0)
+    googleapis-common-protos-types (1.16.0)
       google-protobuf (>= 3.18, < 5.a)
-    googleauth (1.11.0)
+    googleauth (1.11.2)
       faraday (>= 1.0, < 3.a)
       google-cloud-env (~> 2.1)
       jwt (>= 1.4, < 3.0)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.65.2)
-      google-protobuf (>= 3.25, < 5.0)
-      googleapis-common-protos-types (~> 1.0)
-    grpc (1.65.2-aarch64-linux)
-      google-protobuf (>= 3.25, < 5.0)
-      googleapis-common-protos-types (~> 1.0)
-    grpc (1.65.2-arm64-darwin)
-      google-protobuf (>= 3.25, < 5.0)
-      googleapis-common-protos-types (~> 1.0)
-    grpc (1.65.2-x86-linux)
-      google-protobuf (>= 3.25, < 5.0)
-      googleapis-common-protos-types (~> 1.0)
-    grpc (1.65.2-x86_64-darwin)
-      google-protobuf (>= 3.25, < 5.0)
-      googleapis-common-protos-types (~> 1.0)
     grpc (1.65.2-x86_64-linux)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
@@ -198,7 +176,7 @@ GEM
     httpclient (2.8.3)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.7.2)
+    json (2.8.1)
     json-canonicalization (0.4.0)
     json-ld (3.2.5)
       htmlentities (~> 4.3)
@@ -207,51 +185,52 @@ GEM
       multi_json (~> 1.15)
       rack (>= 2.2, < 4)
       rdf (~> 3.2, >= 3.2.10)
-    jwt (2.8.2)
+    jwt (2.9.3)
       base64
     launchy (2.5.2)
       addressable (~> 2.8)
     libxml-ruby (5.0.3)
     link_header (0.0.8)
-    logger (1.6.0)
+    logger (1.6.1)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.6.6)
       mime-types (>= 1.16, < 4)
     method_source (1.1.0)
-    mime-types (3.5.2)
+    mime-types (3.6.0)
+      logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0806)
+    mime-types-data (3.2024.1105)
     mini_mime (1.1.5)
     minitest (4.7.5)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
     mutex_m (0.2.0)
-    net-http-persistent (4.0.2)
+    net-http-persistent (4.0.4)
       connection_pool (~> 2.2)
     net-scp (4.0.0)
       net-ssh (>= 2.6.5, < 8.0.0)
     net-sftp (4.0.0)
       net-ssh (>= 5.0.0, < 8.0.0)
-    net-ssh (7.2.3)
+    net-ssh (7.3.0)
     netrc (0.11.0)
-    oj (3.16.5)
+    oj (3.16.7)
       bigdecimal (>= 3.0)
       ostruct (>= 0.2)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
     ostruct (0.6.0)
-    parallel (1.26.2)
+    parallel (1.26.3)
     parseconfig (1.1.2)
     pony (1.13.1)
       mail (>= 2.0)
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.1.1)
-    rack (3.1.7)
+    rack (3.1.8)
     rack-test (2.1.0)
       rack (>= 1.3)
     rake (13.2.1)
@@ -270,7 +249,7 @@ GEM
     rdf-xsd (3.2.1)
       rdf (~> 3.2)
       rexml (~> 3.2)
-    redis (5.2.0)
+    redis (5.3.0)
       redis-client (>= 0.22.0)
     redis-client (0.22.2)
       connection_pool
@@ -286,8 +265,7 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     retriable (3.1.2)
-    rexml (3.3.5)
-      strscan
+    rexml (3.3.9)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -308,14 +286,14 @@ GEM
     simplecov-cobertura (2.1.0)
       rexml
       simplecov (~> 0.19)
-    simplecov-html (0.12.3)
+    simplecov-html (0.13.1)
     simplecov_json_formatter (0.1.4)
-    sshkit (1.23.0)
+    sshkit (1.23.2)
       base64
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)
       net-ssh (>= 2.8.0)
-    strscan (3.1.0)
+      ostruct
     sys-proctable (1.3.0)
       ffi (~> 1.1)
     systemu (2.6.5)
@@ -329,14 +307,10 @@ GEM
       macaddr (~> 1.0)
 
 PLATFORMS
-  aarch64-linux
-  arm64-darwin
-  ruby
-  x86-linux
-  x86_64-darwin
   x86_64-linux
 
 DEPENDENCIES
+  activesupport (~> 3.2.22.5)
   bcrypt_pbkdf (>= 1.0, < 2.0)
   binding_of_caller (~> 1.0)
   capistrano (~> 3)

config/deploy/production.rb

@@ -1,13 +1,13 @@
 set :branch, 'master'
-set :server, 'biodivportal.gfbio.org'
+set :server, '192.168.0.22'
 
 server fetch(:server), user: fetch(:user), roles: %w{web app}
 
 set :ssh_options, {
   user: 'ontoportal',
   forward_agent: 'true',
   #keys: %w(config/deploy_id_rsa),
-  #auth_methods: %w(publickey),
+  auth_methods: %w(publickey),
   # use ssh proxy if UI servers are on a private network
-  #proxy: Net::SSH::Proxy::Command.new('ssh [email protected] -W %h:%p')
+  proxy: Net::SSH::Proxy::Command.new('ssh [email protected] -W %h:%p')
 }