Merge branch 'pr/feature/update-resource-seetings' of github.com:onto…

…portal-lirmm/goo into ontoportal-lirmm-pr/feature/update-resource-seetings

goo.gemspec

@@ -6,7 +6,8 @@ Gem::Specification.new do |s|
   s.email = "manuelso@stanford.edu"
   s.files = Dir["lib/**/*.rb"]
   s.homepage = "http://github.com/ncbo/goo"
-    s.add_dependency("addressable", "~> 2.8")
+
+  s.add_dependency("addressable", "~> 2.8")
   s.add_dependency("pry")
   s.add_dependency("rdf", "= 1.0.8")
   s.add_dependency("redis")

lib/goo/base/resource.rb

@@ -42,9 +42,7 @@ def valid?
         self.class.attributes.each do |attr|
           inst_value = self.instance_variable_get("@#{attr}")
           attr_errors = Goo::Validators::Enforce.enforce(self,attr,inst_value)
-          unless attr_errors.nil?
-            validation_errors[attr] = attr_errors
-          end
+          validation_errors[attr] = attr_errors unless attr_errors.nil?
         end
 
         if !@persistent && validation_errors.length == 0
@@ -70,9 +68,7 @@ def valid?
       end
 
       def id=(new_id)
-        if !@id.nil? and @persistent
-          raise ArgumentError, "The id of a persistent object cannot be changed."
-        end
+        raise ArgumentError, "The id of a persistent object cannot be changed." if !@id.nil? and @persistent
         raise ArgumentError, "ID must be an RDF::URI" unless new_id.kind_of?(RDF::URI)
         @id = new_id
       end
@@ -133,6 +129,7 @@ def unmapped_get(attribute)
 
       def unmmaped_to_array
         cpy = {}
+
         @unmapped.each do |attr,v|
           cpy[attr] = v.to_a
         end
@@ -147,19 +144,15 @@ def unmapped(*args)
 
       def delete(*args)
         if self.kind_of?(Goo::Base::Enum)
-          unless args[0] && args[0][:init_enum]
-            raise ArgumentError, "Enums cannot be deleted"
-          end
+          raise ArgumentError, "Enums cannot be deleted" unless args[0] && args[0][:init_enum]
         end
 
         raise ArgumentError, "This object is not persistent and cannot be deleted" if !@persistent
 
         if !fully_loaded?
           missing = missing_load_attributes
           options_load = { models: [ self ], klass: self.class, :include => missing }
-          if self.class.collection_opts
-            options_load[:collection] = self.collection
-          end
+          options_load[:collection] = self.collection if self.class.collection_opts
           Goo::SPARQL::Queries.model_load(options_load)
         end
 
@@ -175,25 +168,19 @@ def delete(*args)
         end
         @persistent = false
         @modified = true
-        if self.class.inmutable? && self.class.inm_instances
-          self.class.load_inmutable_instances
-        end
+        self.class.load_inmutable_instances if self.class.inmutable? && self.class.inm_instances
         return nil
       end
 
       def bring(*opts)
         opts.each do |k|
           if k.kind_of?(Hash)
             k.each do |k2,v|
-              if self.class.handler?(k2)
-                raise ArgumentError, "Unable to bring a method based attr #{k2}"
-              end
+              raise ArgumentError, "Unable to bring a method based attr #{k2}" if self.class.handler?(k2)
               self.instance_variable_set("@#{k2}",nil)
             end
           else
-            if self.class.handler?(k)
-              raise ArgumentError, "Unable to bring a method based attr #{k}"
-            end
+            raise ArgumentError, "Unable to bring a method based attr #{k}" if self.class.handler?(k)
             self.instance_variable_set("@#{k}",nil)
           end
         end
@@ -208,9 +195,7 @@ def bring(*opts)
 
       def graph
         opts = self.class.collection_opts
-        if opts.nil?
-          return self.class.uri_type
-        end
+        return self.class.uri_type if opts.nil?
         col = collection
         if col.is_a?Array
           if col.length == 1
@@ -290,9 +275,7 @@ def collection
         if opts.instance_of?(Symbol)
           if self.class.attributes.include?(opts)
             value = self.send("#{opts}")
-            if value.nil?
-              raise ArgumentError, "Collection `#{opts}` is nil"
-            end
+            raise ArgumentError, "Collection `#{opts}` is nil" if value.nil?
             return value
           else
             raise ArgumentError, "Collection `#{opts}` is not an attribute"
@@ -307,26 +290,45 @@ def add_aggregate(attribute,aggregate,value)
       def save(*opts)
 
         if self.kind_of?(Goo::Base::Enum)
-          unless opts[0] && opts[0][:init_enum]
-            raise ArgumentError, "Enums can only be created on initialization"
-          end
+          raise ArgumentError, "Enums can only be created on initialization" unless opts[0] && opts[0][:init_enum]
         end
         batch_file = nil
-        if opts && opts.length > 0
-          if opts.first.is_a?(Hash) && opts.first[:batch] && opts.first[:batch].is_a?(File)
+        callbacks = true
+        if opts && opts.length > 0 && opts.first.is_a?(Hash)
+          if opts.first[:batch] && opts.first[:batch].is_a?(File)
             batch_file = opts.first[:batch]
           end
+
+          callbacks = opts.first[:callbacks]
         end
 
         if !batch_file
-          if not modified?
-            return self
-          end
+          return self if not modified?
           raise Goo::Base::NotValidException, "Object is not valid. Check errors." unless valid?
         end
 
+        #set default values before saving
+        unless self.persistent?
+          self.class.attributes_with_defaults.each do |attr|
+            value = self.send("#{attr}")
+            if value.nil?
+              value = self.class.default(attr).call(self)
+              self.send("#{attr}=", value)
+            end
+          end
+        end
+
+        #call update callback before saving
+        if callbacks
+          self.class.attributes_with_update_callbacks.each do |attr|
+            Goo::Validators::Enforce.enforce_callbacks(self, attr)
+          end
+        end
+
         graph_insert, graph_delete = Goo::SPARQL::Triples.model_update_triples(self)
-        graph = self.graph()
+        graph = self.graph
+
+
         if graph_delete and graph_delete.size > 0
           begin
             Goo.sparql_update_client.delete_data(graph_delete, graph: graph)
@@ -360,9 +362,7 @@ def save(*opts)
 
         @modified_attributes = Set.new
         @persistent = true
-        if self.class.inmutable? && self.class.inm_instances
-          self.class.load_inmutable_instances
-        end
+        self.class.load_inmutable_instances if self.class.inmutable? && self.class.inm_instances
         return self
       end
 
@@ -400,9 +400,7 @@ def to_hash
             end
           end
           @unmapped.each do |attr,values|
-            unless all_attr_uris.include?(attr)
-              attr_hash[attr] = values.map { |v| v.to_s }
-            end
+            attr_hash[attr] = values.map { |v| v.to_s } unless all_attr_uris.include?(attr)
           end
         end
         attr_hash[:id] = @id

lib/goo/base/settings/settings.rb

@@ -1,4 +1,5 @@
 require 'active_support/core_ext/string'
+require_relative 'yaml_settings'
 
 module Goo
   module Base
@@ -12,8 +13,10 @@ module ClassMethods
         attr_reader :model_name
         attr_reader :attribute_uris
 
+        include YAMLScheme
+
         def default_model_options
-          return {}
+           {}
         end
 
         def model(*args)
@@ -34,7 +37,9 @@ def model(*args)
 
           @model_settings = default_model_options.merge(options || {})
 
-          unless options.include?:name_with
+          init_yaml_scheme_settings
+
+          unless options.include? :name_with
             raise ArgumentError, "The model `#{model_name}` definition should include the :name_with option"
           end
           Goo.add_model(@model_name,self)
@@ -91,6 +96,16 @@ def attributes_with_defaults
                   select{ |attr,opts| opts[:default] }).keys()
         end
 
+        def attributes_with_update_callbacks
+           (@model_settings[:attributes].
+            select{ |attr,opts| opts[:onUpdate] }).keys
+        end
+
+
+        def update_callbacks(attr)
+          @model_settings[:attributes][attr][:onUpdate]
+        end
+
         def default(attr)
           return @model_settings[:attributes][attr][:default]
         end
@@ -185,10 +200,14 @@ def attribute(*args)
           attr_name = attr_name.to_sym
           options = options.pop
           options = {} if options.nil?
-          if options[:enforce].nil? or !options[:enforce].include?(:list)
-            options[:enforce] = options[:enforce] ? (options[:enforce] << :no_list) : [:no_list]
-          end
+
+          options[:enforce] ||= []
+
+          set_data_type(options)
+          set_no_list_by_default(options)
+
           @model_settings[:attributes][attr_name] = options
+          load_yaml_scheme_options(attr_name)
           shape_attribute(attr_name)
           namespace = attribute_namespace(attr_name)
           namespace = namespace || @model_settings[:namespace]
@@ -232,15 +251,13 @@ def shape_attribute(attr)
               raise ArgumentError, "Method based attributes cannot be set"
             end
             if self.class.inverse?(attr) && !(args && args.last.instance_of?(Hash) && args.last[:on_load])
-              raise ArgumentError,
-                "`#{attr}` is an inverse attribute. Values cannot be assigned."
+              raise ArgumentError, "`#{attr}` is an inverse attribute. Values cannot be assigned."
             end
             @loaded_attributes.add(attr)
             value = args[0]
             unless args.last.instance_of?(Hash) and args.last[:on_load]
               if self.persistent? and self.class.name_with == attr
-                raise ArgumentError, 
-                    "`#{attr}` attribute is used to name this resource and cannot be modified."
+                raise ArgumentError, "`#{attr}` attribute is used to name this resource and cannot be modified."
               end
               prev = self.instance_variable_get("@#{attr}")
               if !prev.nil? and !@modified_attributes.include?(attr)
@@ -391,6 +408,20 @@ def not_show_all_languages?(values, args)
           values.is_a?(Hash) && !show_all_languages?(args)
         end
 
+        private
+
+        def set_no_list_by_default(options)
+          if options[:enforce].nil? or !options[:enforce].include?(:list)
+            options[:enforce] = options[:enforce] ? (options[:enforce] << :no_list) : [:no_list]
+          end
+        end
+        def set_data_type(options)
+          if options[:type]
+            options[:enforce] += Array(options[:type])
+            options[:enforce].uniq!
+            options.delete :type
+          end
+        end
       end
     end
   end

lib/goo/base/settings/yaml_settings.rb

@@ -0,0 +1,45 @@
+require 'yaml'
+
+module Goo
+  module Base
+    module Settings
+      module YAMLScheme
+        attr_reader :yaml_settings
+
+        def init_yaml_scheme_settings
+          scheme_file_path = @model_settings[:scheme]
+          @yaml_settings = read_yaml_settings_file(scheme_file_path)
+        end
+
+        def attribute_yaml_settings(attr)
+
+          return {} if yaml_settings.nil?
+
+          yaml_settings[attr.to_sym]
+        end
+
+
+
+        private
+
+        def load_yaml_scheme_options(attr)
+          settings = attribute_settings(attr)
+          yaml_settings = attribute_yaml_settings(attr)
+          settings.merge! yaml_settings unless yaml_settings.nil? || yaml_settings.empty?
+        end
+
+        def read_yaml_settings_file(scheme_file_path)
+          return  if scheme_file_path.nil?
+
+          yaml_contents = File.read(scheme_file_path) rescue return
+
+          YAML.safe_load(yaml_contents, symbolize_names: true)
+        end
+      end
+    end
+  end
+end
+
+
+
+

lib/goo/sparql/query_builder.rb

@@ -357,7 +357,9 @@ def query_filter_sparql(klass, filter, filter_patterns, filter_graphs,
                                 filter_graphs, filter_operations,
                                 internal_variables, inspected_patterns, collection)
           else
+        #??  if !filter_operation.value.instance_of?(Goo::Filter)
             case filter_operation.operator
+
             when  :unbound
               filter_operations << "!BOUND(?#{filter_var.to_s})"
               return :optional
@@ -369,7 +371,6 @@ def query_filter_sparql(klass, filter, filter_patterns, filter_graphs,
               if  filter_operation.value.is_a?(String)
                 filter_operations << "REGEX(STR(?#{filter_var.to_s}) , \"#{filter_operation.value.to_s}\", \"i\")"
               end
-
             else
               value = RDF::Literal.new(filter_operation.value)
               if filter_operation.value.is_a? String

lib/goo/validators/enforce.rb

@@ -66,6 +66,17 @@ def enforce(inst,attr,value)
           errors_by_opt.length > 0 ? errors_by_opt : nil
         end
 
+        def enforce_callback(inst, attr)
+          callbacks = Array(inst.class.update_callbacks(attr))
+          callbacks.each do |proc|
+            if instance_proc?(inst, proc)
+              call_proc(inst.method(proc), inst, attr)
+            elsif proc.is_a?(Proc)
+              call_proc(proc, inst, attr)
+            end
+          end
+        end
+
         private
 
         def object_type(opt)
@@ -117,6 +128,10 @@ def add_error(opt, err)
       def self.enforce(inst,attr,value)
         EnforceInstance.new.enforce(inst,attr,value)
       end
+
+      def self.enforce_callbacks(inst, attr)
+        EnforceInstance.new.enforce_callback(inst, attr)
+      end
     end
   end
 end

lib/goo/validators/validator.rb

@@ -91,7 +91,11 @@ def empty_string?(string)
         end
 
         def empty_to_s?(object)
-          object && object.to_s&.strip.empty?
+          begin
+            object && object.to_s&.strip.empty?
+          rescue
+            return false
+          end
         end
 
         def empty_array?(array)