Merge branch 'development'

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

@@ -11,7 +11,7 @@ jobs:
         backend: ['ruby'] # ruby runs tests with 4store backend and ruby-agraph runs with AllegroGraph backend
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up solr configsets
       run: ./test/solr/generate_ncbo_configsets.sh
     - name: create config.rb file

Gemfile

@@ -1,7 +1,7 @@
 source 'https://rubygems.org'
 
 gem 'activesupport', '~> 4'
-gem 'addressable', '= 2.3.5'
+gem 'addressable', '~> 2.8'
 gem 'bcrypt', '~> 3.0'
 gem 'cube-ruby', require: 'cube'
 gem 'faraday', '~> 1.9'

Gemfile.lock

@@ -1,17 +1,16 @@
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: 835aefa458186485eef60d3845315c478a95ff23
+  revision: 3d5bbe1db4a6aca2ff621ccfcdb85a32dbe9704e
   branch: development
   specs:
     goo (0.0.2)
-      addressable (= 2.3.5)
+      addressable (~> 2.8)
       pry
       rdf (= 1.0.8)
       redis
       rest-client
       rsolr
       sparql-client
-      systemu
       uuid
 
 GIT
@@ -33,7 +32,8 @@ GEM
       multi_json (~> 1.3)
       thread_safe (~> 0.1)
       tzinfo (~> 0.3.37)
-    addressable (2.3.5)
+    addressable (2.8.1)
+      public_suffix (>= 2.0.2, < 6.0)
     ansi (1.5.0)
     ast (2.4.2)
     bcrypt (3.1.18)
@@ -43,6 +43,7 @@ GEM
     connection_pool (2.3.0)
     cube-ruby (0.0.3)
     daemons (1.4.1)
+    date (3.3.2)
     docile (1.4.0)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
@@ -82,16 +83,19 @@ GEM
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.6.2)
-    json_pure (2.6.2)
-    launchy (2.4.3)
-      addressable (~> 2.3)
+    json (2.6.3)
+    json_pure (2.6.3)
+    launchy (2.5.0)
+      addressable (~> 2.7)
     libxml-ruby (2.9.0)
-    logger (1.5.1)
+    logger (1.5.3)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
-    mail (2.7.1)
+    mail (2.8.0)
       mini_mime (>= 0.1.1)
+      net-imap
+      net-pop
+      net-smtp
     method_source (1.0.0)
     mime-types (3.4.1)
       mime-types-data (~> 3.2015)
@@ -106,12 +110,21 @@ GEM
     multi_json (1.15.0)
     multipart-post (2.2.3)
     net-http-persistent (2.9.4)
+    net-imap (0.3.2)
+      date
+      net-protocol
+    net-pop (0.1.2)
+      net-protocol
+    net-protocol (0.2.1)
+      timeout
+    net-smtp (0.3.3)
+      net-protocol
     netrc (0.11.0)
     oj (2.18.5)
     omni_logger (0.1.4)
       logger
     parallel (1.22.1)
-    parser (3.1.2.1)
+    parser (3.1.3.0)
       ast (~> 2.4.1)
     pony (1.13.1)
       mail (>= 2.0)
@@ -120,6 +133,7 @@ GEM
     pry (0.14.1)
       coderay (~> 1.1)
       method_source (~> 1.0)
+    public_suffix (5.0.1)
     rack (1.6.13)
     rack-test (0.8.3)
       rack (>= 1.0, < 3)
@@ -129,9 +143,9 @@ GEM
       addressable (>= 2.2)
     redis (5.0.5)
       redis-client (>= 0.9.0)
-    redis-client (0.9.0)
+    redis-client (0.11.2)
       connection_pool
-    regexp_parser (2.5.0)
+    regexp_parser (2.6.1)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
@@ -140,17 +154,17 @@ GEM
     rexml (3.2.5)
     rsolr (1.1.2)
       builder (>= 2.1.2)
-    rubocop (1.36.0)
+    rubocop (1.40.0)
       json (~> 2.3)
       parallel (~> 1.10)
       parser (>= 3.1.2.1)
       rainbow (>= 2.2.2, < 4.0)
       regexp_parser (>= 1.8, < 3.0)
       rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.20.1, < 2.0)
+      rubocop-ast (>= 1.23.0, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 1.4.0, < 3.0)
-    rubocop-ast (1.21.0)
+    rubocop-ast (1.24.0)
       parser (>= 3.1.1.0)
     ruby-progressbar (1.11.0)
     ruby2_keywords (0.0.5)
@@ -172,6 +186,7 @@ GEM
       eventmachine (~> 1.0, >= 1.0.4)
       rack (>= 1, < 3)
     thread_safe (0.3.6)
+    timeout (0.3.1)
     tzinfo (0.3.61)
     unf (0.1.4)
       unf_ext
@@ -185,7 +200,7 @@ PLATFORMS
 
 DEPENDENCIES
   activesupport (~> 4)
-  addressable (= 2.3.5)
+  addressable (~> 2.8)
   bcrypt (~> 3.0)
   cube-ruby
   email_spec
@@ -214,4 +229,4 @@ DEPENDENCIES
   thin
 
 BUNDLED WITH
-   2.3.14
+   2.3.15

bin/owlapi-wrapper.jar

@@ -1 +1 @@
-./owlapi-wrapper-1.4.1.jar
+./owlapi-wrapper-1.4.2.jar

config/config.rb.sample

@@ -15,6 +15,9 @@ LinkedData.config do |config|
   config.purl_password          = ""
   config.purl_maintainers       = ""
   config.purl_target_url_prefix = "http://bioportal.bioontology.org"
+  Goo.configure do |conf|
+      conf.main_languages = ['en']
+  end
 end
 
 #sometimes tmp by default cannot allocate large files

config/config.test.rb

@@ -31,5 +31,5 @@
   config.ontology_analytics_redis_port = REDIS_PORT.to_i
   config.search_server_url             = SOLR_TERM_SEARCH_URL.to_s
   config.property_search_server_url    = SOLR_PROP_SEARCH_URL.to_s
-#  config.enable_notifications          = false
-end
+  #  config.enable_notifications          = false
+end

lib/ontologies_linked_data/concerns/concepts/concept_in_collection.rb

@@ -0,0 +1,25 @@
+module LinkedData
+  module Concerns
+    module Concept
+      module InCollection
+        def self.included(base)
+          base.serialize_methods :isInActiveCollection
+        end
+
+        def isInActiveCollection
+          @isInActiveCollection
+        end
+
+        def inCollection?(collection)
+          self.memberOf.include?(collection)
+        end
+
+        def load_is_in_collection(collections = [])
+          included = collections.select { |s| inCollection?(s) }
+          @isInActiveCollection = included
+        end
+
+      end
+    end
+  end
+end

lib/ontologies_linked_data/concerns/concepts/concept_in_scheme.rb

@@ -0,0 +1,26 @@
+module LinkedData
+  module Concerns
+    module Concept
+      module InScheme
+        def self.included(base)
+          base.serialize_methods :isInActiveScheme
+        end
+
+        def isInActiveScheme
+          @isInActiveScheme
+        end
+
+        def inScheme?(scheme)
+          self.inScheme.include?(scheme)
+        end
+
+        def load_is_in_scheme(schemes = [])
+          included = schemes.select { |s| inScheme?(s) }
+          included = [self.submission.get_main_concept_scheme] if included.empty? && schemes&.empty?
+          @isInActiveScheme = included
+        end
+
+      end
+    end
+  end
+end

lib/ontologies_linked_data/concerns/concepts/concept_sort.rb

@@ -0,0 +1,55 @@
+module LinkedData
+  module Concerns
+    module Concept
+      module Sort
+        module ClassMethods
+          def compare_classes(class_a, class_b)
+            label_a = ""
+            label_b = ""
+            class_a.bring(:prefLabel) if class_a.bring?(:prefLabel)
+            class_b.bring(:prefLabel) if class_b.bring?(:prefLabel)
+
+            begin
+              label_a = class_a.prefLabel unless (class_a.prefLabel.nil? || class_a.prefLabel.empty?)
+            rescue Goo::Base::AttributeNotLoaded
+              label_a = ""
+            end
+
+            begin
+              label_b = class_b.prefLabel unless (class_b.prefLabel.nil? || class_b.prefLabel.empty?)
+            rescue Goo::Base::AttributeNotLoaded
+              label_b = ""
+            end
+
+            label_a = class_a.id if label_a.empty?
+            label_b = class_b.id if label_b.empty?
+
+            [label_a.downcase] <=> [label_b.downcase]
+          end
+
+          def sort_classes(classes)
+            classes.sort { |class_a, class_b| compare_classes(class_a, class_b) }
+          end
+
+          def sort_tree_children(root_node)
+            sort_classes!(root_node.children)
+            root_node.children.each { |ch| sort_tree_children(ch) }
+          end
+
+          private
+
+
+
+          def sort_classes!(classes)
+            classes.sort! { |class_a, class_b| LinkedData::Models::Class.compare_classes(class_a, class_b) }
+            classes
+          end
+        end
+
+        def self.included(base)
+          base.extend(ClassMethods)
+        end
+      end
+    end
+  end
+end