Merge remote-tracking branch 'ecoportal/master' into ecoportal-ontopo…

…rtal-reset

Gemfile

@@ -19,7 +19,7 @@ gem 'json-ld'
 
 
 # Rack middleware
-gem 'ffi'
+gem 'ffi', '~> 1.15.5'
 gem 'rack-accept', '~> 0.4'
 gem 'rack-attack', '~> 6.6.1', require: 'rack/attack'
 gem 'rack-cache', '~> 1.13.0'
@@ -52,6 +52,7 @@ 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/lifewatch-eric/ontologies_linked_data.git', branch: 'master'
 gem 'ncbo_cron', git: 'https://github.com/lifewatch-eric/ncbo_cron.git', branch: 'master'
+gem 'request_store'
 
 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

@@ -426,7 +426,7 @@ DEPENDENCIES
   cube-ruby
   ed25519 (>= 1.2, < 2.0)
   faraday (~> 1.9)
-  ffi
+  ffi (~> 1.15.5)
   goo!
   haml (~> 5.2.2)
   json-ld

config/deploy/production.rb

@@ -1,39 +1,13 @@
-# Simple Role Syntax
-# ==================
-# Supports bulk-adding hosts to roles, the primary
-# server in each group is considered to be the first
-# unless any hosts have the primary property set.
-# Don't declare `role :all`, it's a meta role
-role :app, %w{[email protected]}
-role :web, %w{[email protected]}
-role :db,  %w{[email protected]}
+set :branch, 'master'
+set :server, 'ecoportal.lifewatch.eu'
 
-# Extended Server Syntax
-# ======================
-# This can be used to drop a more detailed server
-# definition into the server list. The second argument
-# something that quacks like a hash can be used to set
-# extended properties on the server.
-server 'example.com', user: 'deploy', roles: %w{web app}, my_property: :my_value
+server fetch(:server), user: fetch(:user), roles: %w{web app}
 
-# you can set custom ssh options
-# it's possible to pass any option but you need to keep in mind that net/ssh understand limited list of options
-# you can see them in [net/ssh documentation](http://net-ssh.github.io/net-ssh/classes/Net/SSH.html#method-c-start)
-# set it globally
-#  set :ssh_options, {
-#    keys: %w(/home/rlisowski/.ssh/id_rsa),
-#    forward_agent: false,
-#    auth_methods: %w(password)
-#  }
-# and/or per server
-# server 'example.com',
-#   user: 'user_name',
-#   roles: %w{web app},
-#   ssh_options: {
-#     user: 'user_name', # overrides user setting above
-#     keys: %w(/home/user_name/.ssh/id_rsa),
-#     forward_agent: false,
-#     auth_methods: %w(publickey password)
-#     # password: 'please use keys'
-#   }
-# setting per server overrides global ssh_options
+set :ssh_options, {
+  user: 'ontoportal',
+  forward_agent: 'true',
+  #keys: %w(config/deploy_id_rsa),
+  #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')
+}

controllers/users_controller.rb

@@ -135,7 +135,7 @@ def sso_auth
         }
 
         user = instance_from_params(User, user_creation_params)
-        save_user(user)
+        save_user(user, send_notifications: true)
       end
       user
     end
@@ -153,11 +153,11 @@ def create_user(send_notifications: true)
       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)
-      save_user(user)
+      save_user(user, send_notifications: send_notifications)
       reply 201, user
     end
 
-    def save_user(user)
+    def save_user(user, send_notifications: true)
       if user.valid?
         user.save(send_notifications: send_notifications)
       else

test/controllers/test_identifier_request_controller.rb

@@ -21,7 +21,7 @@ def setup
                                           hasOntologyLanguage: LinkedData::Models::OntologyFormat.find('OWL').first,
                                           contact: [LinkedData::Models::Contact.new(email: '[email protected]', name: 'test').save],
                                            released: DateTime.now, uploadFilePath: '',
-                                           URI: 'https://test.com/test',
+                                           URI: RDF::URI.new('https://test.com/test'),
                                            status: 'production',
                                            description: 'ontology description' ).save
     end

test/controllers/test_users_controller.rb

@@ -112,6 +112,7 @@ def test_authentication
   end
 
   def test_oauth_authentication
+    skip
     fake_responses = {
       github: {
         id: 123456789,