Merge pull request #187 from ncbo/develop

Merge Develop to Master, release v5.28.0

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

@@ -26,7 +26,7 @@ jobs:
         ci_env=`bash <(curl -s https://codecov.io/env)`
         docker-compose run $ci_env -e CI --rm ${{ matrix.backend }} bundle exec rake test TESTOPTS='-v'
     - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         flags: unittests
         verbose: true

lib/ontologies_linked_data.rb

@@ -17,6 +17,7 @@
 require "ontologies_linked_data/utils/file"
 require "ontologies_linked_data/utils/triples"
 require "ontologies_linked_data/utils/notifications"
+require "ontologies_linked_data/utils/notifier"
 require "ontologies_linked_data/utils/ontology_csv_writer"
 require "ontologies_linked_data/utils/multi_logger"
 require "ontologies_linked_data/parser/parser"

lib/ontologies_linked_data/config/config.rb

@@ -24,22 +24,18 @@ def config(&block)
     @settings.search_server_url             ||= 'http://localhost:8983/solr/term_search_core1'
     @settings.property_search_server_url    ||= 'http://localhost:8983/solr/prop_search_core1'
     @settings.repository_folder             ||= './test/data/ontology_files/repo'
-    @settings.rest_url_prefix                ||= 'http://data.bioontology.org/'
+    @settings.rest_url_prefix               ||= 'http://data.bioontology.org/'
     @settings.enable_security               ||= false
     @settings.enable_slices                 ||= false
 
     # Java/JVM options
     @settings.java_max_heap_size            ||= '10240M'
-    ### these params should be not ussed any more
-    # removed so that dependencies shout
-    #
-    # @settings.redis_host                    ||= "localhost"
-    # @settings.redis_port                    ||= 6379
-    # ###
 
+    @settings.ui_name                       ||= 'Bioportal'
     @settings.ui_host                       ||= 'bioportal.bioontology.org'
     @settings.replace_url_prefix            ||= false
-    @settings.id_url_prefix                 ||= 'http://data.bioontology.org/'
+    @settings.id_url_prefix                 ||= "http://data.bioontology.org/"
+
     @settings.queries_debug                 ||= false
     @settings.enable_monitoring             ||= false
     @settings.cube_host                     ||= 'localhost'
@@ -50,11 +46,11 @@ def config(&block)
     @settings.http_redis_host               ||= 'localhost'
     @settings.http_redis_port               ||= 6379
 
-    #Caching goo
+    # Caching goo
     @settings.goo_redis_host                ||= 'localhost'
     @settings.goo_redis_port                ||= 6379
 
-    #Ontology Analytics Redis
+    # Ontology Analytics Redis
     @settings.ontology_analytics_redis_host ||= 'localhost'
     @settings.ontology_analytics_redis_port ||= 6379
 
@@ -69,7 +65,8 @@ def config(&block)
 
     # Email settings
     @settings.enable_notifications          ||= false
-    @settings.email_sender                  ||= '[email protected]' # Default sender for emails
+    # Default sender From email address
+    @settings.email_sender                  ||= '[email protected]'
     @settings.email_override                ||= '[email protected]' # By default, all email gets sent here. Disable with email_override_disable.
     @settings.email_disable_override        ||= false
     @settings.smtp_host                     ||= 'localhost'
@@ -79,6 +76,13 @@ def config(&block)
     @settings.smtp_auth_type                ||= :none # :none, :plain, :login, :cram_md5
     @settings.smtp_domain                   ||= 'localhost.localhost'
     @settings.enable_starttls_auto          ||= false # set to true for use with gmail
+    # Support contact email address used in email notification send to ontoportal users.
+    @settings.support_contact_email         ||= '[email protected]'
+    # List of contact emails for OntoPortal site administrators
+    @settings.ontoportal_admin_emails       ||= ['[email protected]']
+    # Send administrative notifications for events including new user and
+    # ontology creation to OntoPortal site admins
+    @settings.enable_administrative_notifications ||= true
 
     # number of times to retry a query when empty records are returned
     @settings.num_retries_4store            ||= 10
@@ -89,12 +93,6 @@ def config(&block)
     # Override defaults
     yield @settings, overide_connect_goo if block_given?
 
-    unless @settings.redis_host.nil?
-      puts "Error: 'redis_host' is not a valid conf parameter."
-      puts '        Redis databases were split into multiple hosts (09/22/13).'
-      raise Exception, 'redis_host is not a valid conf parameter.'
-    end
-
     # Check to make sure url prefix has trailing slash
     @settings.rest_url_prefix = @settings.rest_url_prefix + '/' unless @settings.rest_url_prefix[-1].eql?('/')
 

lib/ontologies_linked_data/models/users/user.rb

@@ -24,13 +24,14 @@ class User < LinkedData::Models::Base
       attribute :subscription, enforce: [:list, :subscription]
       attribute :customOntology, enforce: [:list, :ontology]
       attribute :resetToken
+      attribute :resetTokenExpireTime
       attribute :provisionalClasses, inverse: { on: :provisional_class, attribute: :creator }
 
       # Hypermedia settings
       embed :subscription
       embed_values :role => [:role]
       serialize_default :username, :email, :role, :apikey
-      serialize_never :passwordHash, :show_apikey, :resetToken
+      serialize_never :passwordHash, :show_apikey, :resetToken, :restTokenExpireTime
       serialize_filter lambda {|inst| show_apikey?(inst)}
 
       # Cache