Merge pull request #153 from ncbo/develop

Merge develop to master, release v5.30.0

.ruby-version

@@ -0,0 +1 @@
+2.7.8

Gemfile

@@ -6,6 +6,8 @@ gem "activesupport"
 gem "cube-ruby", require: "cube"
 gem "rake"
 gem "uuid"
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
+
 
 group :test do
   gem "minitest", '< 5.0'
@@ -21,4 +23,3 @@ group :profiling do
   gem "thin"
 end
 
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: 55e7dbf858eb571c767bc67868f9af61663859cb
+  revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc
   branch: develop
   specs:
     sparql-client (1.0.1)
@@ -16,6 +16,7 @@ PATH
       pry
       rdf (= 1.0.8)
       redis
+      request_store
       rest-client
       rsolr
       sparql-client
@@ -52,10 +53,10 @@ GEM
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json_pure (2.7.1)
+    json_pure (2.7.2)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
-    method_source (1.0.0)
+    method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
     mime-types-data (3.2024.0305)
@@ -68,29 +69,31 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.4)
-    rack (2.2.8.1)
+    public_suffix (5.0.5)
+    rack (2.2.9)
     rack-accept (0.4.5)
       rack (>= 0.4)
     rack-post-body-to-params (0.1.8)
       activesupport (>= 2.3)
     rack-protection (3.2.0)
       base64 (>= 0.1.0)
       rack (~> 2.2, >= 2.2.4)
-    rake (13.1.0)
+    rake (13.2.1)
     rdf (1.0.8)
       addressable (>= 2.2)
-    redis (5.1.0)
-      redis-client (>= 0.17.0)
-    redis-client (0.21.0)
+    redis (5.2.0)
+      redis-client (>= 0.22.0)
+    redis-client (0.22.1)
       connection_pool
+    request_store (1.6.0)
+      rack (>= 1.4)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     rexml (3.2.6)
-    rsolr (2.5.0)
+    rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
     ruby2_keywords (0.0.5)
@@ -120,7 +123,8 @@ GEM
       macaddr (~> 1.0)
 
 PLATFORMS
-  ruby
+  x86_64-darwin-21
+  x86_64-darwin-23
   x86_64-linux
 
 DEPENDENCIES

docker-compose.yml

@@ -39,11 +39,11 @@ services:
         ; agtool users grant anonymous root:ontoportal_test:rw
         ; tail -f /agraph/data/agraph.log"
     healthcheck:
-      test: ["CMD-SHELL", "curl -m 1 -sf http://127.0.0.1:10035/repositories/ontoportal_test/status | grep -iqE '(^running|^lingering)' || exit 1"]
-      start_period: 60s
+      test: ["CMD-SHELL", "agtool storage-report ontoportal_test || exit 1"]
+      start_period: 30s
       interval: 10s
-      timeout: 5s
-      retries: 5
+      timeout: 10s
+      retries: 10
     profiles:
       - ag
 

goo.gemspec

@@ -14,4 +14,5 @@ Gem::Specification.new do |s|
   s.add_dependency("rsolr")
   s.add_dependency("sparql-client")
   s.add_dependency("uuid")
+  s.add_dependency("request_store")
 end

lib/goo.rb

@@ -30,6 +30,11 @@ module Goo
 
   @@resource_options = Set.new([:persistent]).freeze
 
+  # Define the languages from which the properties values will be taken
+  # It choose the first language that match otherwise return all the values
+  @@main_languages = %w[en]
+  @@requested_language = nil
+
   @@configure_flag = false
   @@sparql_backends = {}
   @@model_by_name = {}
@@ -47,6 +52,27 @@ module Goo
 
   @@slice_loading_size = 500
 
+
+  def self.main_languages
+    @@main_languages
+  end
+  def self.main_languages=(lang)
+    @@main_languages = lang
+  end
+
+  def self.requested_language
+    @@requested_language
+  end
+
+  def self.requested_language=(lang)
+    @@requested_language = lang
+  end
+
+  def self.language_includes(lang)
+    lang_str = lang.to_s
+    main_languages.index { |l| lang_str.downcase.eql?(l) || lang_str.upcase.eql?(l)}
+  end
+
   def self.add_namespace(shortcut, namespace,default=false)
     if !(namespace.instance_of? RDF::Vocabulary)
       raise ArgumentError, "Namespace must be a RDF::Vocabulary object"
@@ -84,7 +110,7 @@ def self.add_sparql_backend(name, *opts)
     @@sparql_backends[name][:backend_name] = opts[:backend_name]
     @@sparql_backends.freeze
   end
-
+  
   def self.use_cache=(value)
     @@use_cache = value
     set_sparql_cache

lib/goo/base/resource.rb

@@ -15,7 +15,7 @@ class Resource
       attr_reader :modified_attributes
       attr_reader :errors
       attr_reader :aggregates
-      attr_reader :unmapped
+      attr_writer :unmapped
 
       attr_reader :id
 
@@ -123,7 +123,12 @@ def missing_load_attributes
 
       def unmapped_set(attribute,value)
         @unmapped ||= {}
-        (@unmapped[attribute] ||= Set.new) << value
+        @unmapped[attribute] ||= Set.new
+        @unmapped[attribute].merge(Array(value)) unless value.nil?
+      end
+
+      def unmapped_get(attribute)
+        @unmapped[attribute]
       end
 
       def unmmaped_to_array
@@ -134,6 +139,12 @@ def unmmaped_to_array
         @unmapped = cpy
       end
 
+      def unmapped(*args)
+        @unmapped&.transform_values do  |language_values|
+          self.class.not_show_all_languages?(language_values, args) ?  language_values.values.flatten: language_values
+        end
+      end
+
       def delete(*args)
         if self.kind_of?(Goo::Base::Enum)
           unless args[0] && args[0][:init_enum]
@@ -211,13 +222,13 @@ def graph
         return col ? col.id : nil
       end
 
-      def self.map_attributes(inst,equivalent_predicates=nil)
+      def self.map_attributes(inst,equivalent_predicates=nil, include_languages: false)
         if (inst.kind_of?(Goo::Base::Resource) && inst.unmapped.nil?) ||
-            (!inst.respond_to?(:unmapped) && inst[:unmapped].nil?)
+          (!inst.respond_to?(:unmapped) && inst[:unmapped].nil?)
           raise ArgumentError, "Resource.map_attributes only works for :unmapped instances"
         end
         klass = inst.respond_to?(:klass) ? inst[:klass] : inst.class
-        unmapped = inst.respond_to?(:klass) ? inst[:unmapped] : inst.unmapped
+        unmapped = inst.respond_to?(:klass) ? inst[:unmapped] : inst.unmapped(include_languages: include_languages)
         list_attrs = klass.attributes(:list)
         unmapped_string_keys = Hash.new
         unmapped.each do |k,v|
@@ -228,36 +239,38 @@ def self.map_attributes(inst,equivalent_predicates=nil)
           next unless inst.respond_to?(attr)
           attr_uri = klass.attribute_uri(attr,inst.collection).to_s
           if unmapped_string_keys.include?(attr_uri.to_s) ||
-              (equivalent_predicates && equivalent_predicates.include?(attr_uri))
-            object = nil
+            (equivalent_predicates && equivalent_predicates.include?(attr_uri))
             if !unmapped_string_keys.include?(attr_uri)
-              equivalent_predicates[attr_uri].each do |eq_attr|
-                if object.nil? and !unmapped_string_keys[eq_attr].nil?
-                  object = unmapped_string_keys[eq_attr].dup
-                else
-                  if object.is_a?Array
-                    if !unmapped_string_keys[eq_attr].nil?
-                      object.concat(unmapped_string_keys[eq_attr])
-                    end
-                  end
+              object = Array(equivalent_predicates[attr_uri].map { |eq_attr| unmapped_string_keys[eq_attr] }).flatten.compact
+              if include_languages && [RDF::URI, Hash].all?{|c| object.map(&:class).include?(c)}
+                object = object.reduce({})  do |all, new_v|
+                  new_v =  { none: [new_v] } if new_v.is_a?(RDF::URI)
+                  all.merge(new_v) {|_, a, b| a + b }
                 end
+              elsif include_languages
+                object = object.first
               end
+
               if object.nil?
-                inst.send("#{attr}=",
-                           list_attrs.include?(attr) ? [] : nil, on_load: true)
+                inst.send("#{attr}=", list_attrs.include?(attr) ? [] : nil, on_load: true)
                 next
               end
             else
               object = unmapped_string_keys[attr_uri]
             end
-            object = object.map { |o| o.is_a?(RDF::URI) ? o : o.object }
+
+            if object.is_a?(Hash)
+              object = object.transform_values{|values| Array(values).map{|o|o.is_a?(RDF::URI) ? o : o.object}}
+            else
+              object = object.map {|o| o.is_a?(RDF::URI) ? o : o.object}
+            end
+
             if klass.range(attr)
               object = object.map { |o|
                 o.is_a?(RDF::URI) ? klass.range_object(attr,o) : o }
             end
-            unless list_attrs.include?(attr)
-              object = object.first
-            end
+
+            object = object.first unless list_attrs.include?(attr) || include_languages
             if inst.respond_to?(:klass)
               inst[attr] = object
             else
@@ -266,16 +279,12 @@ def self.map_attributes(inst,equivalent_predicates=nil)
           else
             inst.send("#{attr}=",
                       list_attrs.include?(attr) ? [] : nil, on_load: true)
-            if inst.id.to_s == "http://purl.obolibrary.org/obo/IAO_0000415"
-              if attr == :definition
-               # binding.pry
-              end
-            end
           end
 
         end
       end
 
+
       def collection
         opts = self.class.collection_opts
         if opts.instance_of?(Symbol)
@@ -414,12 +423,8 @@ def self.range_object(attr,id)
       end
 
       def self.find(id, *options)
-        if !id.instance_of?(RDF::URI) && self.name_with == :id
-          id = RDF::URI.new(id)
-        end
-        unless id.instance_of?(RDF::URI)
-          id = id_from_unique_attribute(name_with(),id)
-        end
+        id = RDF::URI.new(id) if !id.instance_of?(RDF::URI) && self.name_with == :id
+        id = id_from_unique_attribute(name_with(),id) unless id.instance_of?(RDF::URI)
         if self.inmutable? && self.inm_instances && self.inm_instances[id]
           w = Goo::Base::Where.new(self)
           w.instance_variable_set("@result", [self.inm_instances[id]])

lib/goo/base/settings/settings.rb

@@ -257,18 +257,29 @@ def shape_attribute(attr)
             self.instance_variable_set("@#{attr}",value)
           end
           define_method("#{attr}") do |*args|
+            attr_value = self.instance_variable_get("@#{attr}")
+
+            if self.class.not_show_all_languages?(attr_value, args)
+              is_array = attr_value.values.first.is_a?(Array)
+              attr_value = attr_value.values.flatten
+              attr_value = attr_value.first unless is_array
+            end
+
+
             if self.class.handler?(attr)
               if @loaded_attributes.include?(attr)
-                return self.instance_variable_get("@#{attr}")
+                return attr_value
               end
               value = self.send("#{self.class.handler(attr)}")
               self.instance_variable_set("@#{attr}",value)
               @loaded_attributes << attr
               return value
             end
+
             if (not @persistent) or @loaded_attributes.include?(attr)
-              return self.instance_variable_get("@#{attr}")
+                return attr_value
             else
+              # TODO: bug here when no labels from one of the main_lang available... (when it is called by ontologies_linked_data ontologies_submission)
               raise Goo::Base::AttributeNotLoaded, "Attribute `#{attr}` is not loaded for #{self.id}. Loaded attributes: #{@loaded_attributes.inspect}."
             end
           end
@@ -372,6 +383,14 @@ def read_only(attributes)
           instance
         end
 
+        def show_all_languages?(args)
+          args.first.is_a?(Hash) && args.first.keys.include?(:include_languages) && args.first[:include_languages]
+        end
+
+        def not_show_all_languages?(values, args)
+          values.is_a?(Hash) && !show_all_languages?(args)
+        end
+
       end
     end
   end

lib/goo/base/where.rb

@@ -209,6 +209,11 @@ def process_query_intl(count=false)
 
         options_load[:ids] = ids if ids
         models_by_id = {}
+        if @page_i && (options_load[:models].length > 0)
+          options_load.delete(:filters)
+          options_load.delete(:order_by)
+        end
+
         if (@page_i && options_load[:models].length > 0) ||
             (!@page_i && (@count.nil? || @count > 0))
           models_by_id = Goo::SPARQL::Queries.model_load(options_load)