Merge pull request #159 from ncbo/develop

Develop -> Master merge, Release v5.33.0

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

@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        ruby-version: ['2.7', '3.0']
+        ruby-version: ['3.0', '3.1']
         triplestore: ['fs', 'ag']
 
     steps:

.ruby-version

@@ -1 +1 @@
-2.7.8
+3.0.6

Gemfile.lock

@@ -31,45 +31,50 @@ GEM
       multi_json (~> 1.3)
       thread_safe (~> 0.1)
       tzinfo (~> 0.3.37)
-    addressable (2.8.6)
-      public_suffix (>= 2.0.2, < 6.0)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
     base64 (0.2.0)
-    builder (3.2.4)
+    builder (3.3.0)
     coderay (1.1.3)
-    concurrent-ruby (1.2.3)
+    concurrent-ruby (1.3.4)
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
     daemons (1.4.1)
-    docile (1.4.0)
+    docile (1.4.1)
     domain_name (0.6.20240107)
     eventmachine (1.2.7)
-    faraday (2.8.1)
-      base64
-      faraday-net_http (>= 2.0, < 3.1)
-      ruby2_keywords (>= 0.0.4)
-    faraday-net_http (3.0.2)
+    faraday (2.12.0)
+      faraday-net_http (>= 2.0, < 3.4)
+      json
+      logger
+    faraday-net_http (3.3.0)
+      net-http
     http-accept (1.7.0)
-    http-cookie (1.0.5)
+    http-cookie (1.0.7)
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
+    json (2.7.2)
     json_pure (2.7.2)
+    logger (1.6.1)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0305)
+    mime-types-data (3.2024.0903)
     minitest (4.7.5)
     multi_json (1.15.0)
-    mustermann (3.0.0)
+    mustermann (3.0.3)
       ruby2_keywords (~> 0.0.1)
+    net-http (0.4.1)
+      uri
     net-http-persistent (2.9.4)
     netrc (0.11.0)
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.5)
+    public_suffix (6.0.1)
     rack (2.2.9)
     rack-accept (0.4.5)
       rack (>= 0.4)
@@ -81,9 +86,9 @@ GEM
     rake (13.2.1)
     rdf (1.0.8)
       addressable (>= 2.2)
-    redis (5.2.0)
+    redis (5.3.0)
       redis-client (>= 0.22.0)
-    redis-client (0.22.1)
+    redis-client (0.22.2)
       connection_pool
     request_store (1.7.0)
       rack (>= 1.4)
@@ -92,7 +97,7 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.2.6)
+    rexml (3.3.7)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -104,7 +109,7 @@ GEM
     simplecov-cobertura (2.1.0)
       rexml
       simplecov (~> 0.19)
-    simplecov-html (0.12.3)
+    simplecov-html (0.13.1)
     simplecov_json_formatter (0.1.4)
     sinatra (3.2.0)
       mustermann (~> 3.0)
@@ -117,8 +122,9 @@ GEM
       eventmachine (~> 1.0, >= 1.0.4)
       rack (>= 1, < 3)
     thread_safe (0.3.6)
-    tilt (2.3.0)
+    tilt (2.4.0)
     tzinfo (0.3.62)
+    uri (0.13.1)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
@@ -145,4 +151,4 @@ DEPENDENCIES
   uuid
 
 BUNDLED WITH
-   2.4.22
+   2.5.20

docker-compose.yml

@@ -21,7 +21,7 @@ services:
       retries: 5
 
   agraph-ut:
-    image: franzinc/agraph:v8.1.0
+    image: franzinc/agraph:v8.2.1
     platform: linux/amd64
     environment:
       - AGRAPH_SUPER_USER=test

goo.gemspec

@@ -6,7 +6,8 @@ Gem::Specification.new do |s|
   s.email = "[email protected]"
   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