Develop to master merge, release v5.31.0

.gitignore

@@ -1,3 +1,4 @@
+.bundle/
 *.swp
 *.gemtags
 .bundle

Gemfile

@@ -16,6 +16,8 @@ gem 'rest-client'
 gem 'rsolr'
 gem 'rubyzip', '~> 1.0'
 gem 'thin'
+gem 'request_store'
+
 
 # Testing
 group :test do
@@ -31,7 +33,6 @@ end
 group :development do
   gem 'rubocop', require: false
 end
-
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', github: 'ncbo/goo', branch: 'master'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
+gem 'goo', github: 'ncbo/goo', branch: 'develop'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'

Gemfile.lock

@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: ef2d816df2d263c905bd034efd449a964fa4890f
-  branch: master
+  revision: 70007faf43d0d96292809f89f15a27a757ccaa25
+  branch: develop
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -16,8 +16,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
-  branch: master
+  revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc
+  branch: develop
   specs:
     sparql-client (1.0.1)
       json_pure (>= 1.4)
@@ -39,7 +39,7 @@ GEM
     ast (2.4.2)
     base64 (0.2.0)
     bcrypt (3.1.20)
-    bigdecimal (3.1.7)
+    bigdecimal (3.1.8)
     builder (3.2.4)
     coderay (1.1.3)
     concurrent-ruby (1.2.3)
@@ -84,7 +84,7 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0305)
+    mime-types-data (3.2024.0507)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-reporters (0.14.24)
@@ -94,7 +94,7 @@ GEM
       powerbar
     multi_json (1.15.0)
     net-http-persistent (2.9.4)
-    net-imap (0.4.10)
+    net-imap (0.4.11)
       date
       net-protocol
     net-pop (0.1.2)
@@ -120,7 +120,7 @@ GEM
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.0.5)
-    racc (1.7.3)
+    racc (1.8.0)
     rack (2.2.9)
     rack-test (0.8.3)
       rack (>= 1.0, < 3)
@@ -132,19 +132,20 @@ GEM
       redis-client (>= 0.22.0)
     redis-client (0.22.1)
       connection_pool
-    regexp_parser (2.9.0)
+    regexp_parser (2.9.2)
     request_store (1.7.0)
       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)
+    rexml (3.2.8)
+      strscan (>= 3.0.9)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.63.4)
+    rubocop (1.63.5)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -169,6 +170,7 @@ GEM
       simplecov (~> 0.19)
     simplecov-html (0.12.3)
     simplecov_json_formatter (0.1.4)
+    strscan (3.1.0)
     systemu (2.6.5)
     thin (1.8.2)
       daemons (~> 1.0, >= 1.0.9)
@@ -182,8 +184,10 @@ GEM
       macaddr (~> 1.0)
 
 PLATFORMS
-  arm64-darwin-22
+  aarch64-linux
   x86_64-darwin-21
+  x86_64-darwin-23
+  x86_64-linux
 
 DEPENDENCIES
   activesupport (~> 4)
@@ -204,6 +208,7 @@ DEPENDENCIES
   rack
   rack-test (~> 0.6)
   rake (~> 10.0)
+  request_store
   rest-client
   rsolr
   rubocop

lib/ontologies_linked_data/config/config.rb

@@ -94,15 +94,13 @@ def config(&block)
     yield @settings, overide_connect_goo if block_given?
 
     # Check to make sure url prefix has trailing slash
-    @settings.rest_url_prefix = @settings.rest_url_prefix + '/' unless @settings.rest_url_prefix[-1].eql?('/')
+    @settings.rest_url_prefix = "#{@settings.rest_url_prefix}/" unless @settings.rest_url_prefix[-1].eql?('/')
 
     puts "(LD) >> Using rdf store #{@settings.goo_host}:#{@settings.goo_port}#{@settings.goo_path_query}"
     puts "(LD) >> Using term search server at #{@settings.search_server_url}"
     puts "(LD) >> Using property search server at #{@settings.property_search_server_url}"
-    puts '(LD) >> Using HTTP Redis instance at '+
-            "#{@settings.http_redis_host}:#{@settings.http_redis_port}"
-    puts '(LD) >> Using Goo Redis instance at '+
-            "#{@settings.goo_redis_host}:#{@settings.goo_redis_port}"
+    puts "(LD) >> Using HTTP Redis instance at #{@settings.http_redis_host}:#{@settings.http_redis_port}"
+    puts "(LD) >> Using Goo Redis instance at #{@settings.goo_redis_host}:#{@settings.goo_redis_port}"
 
     connect_goo unless overide_connect_goo
   end
@@ -132,15 +130,14 @@ def connect_goo
                                port: @settings.goo_redis_port)
 
         if @settings.enable_monitoring
-          puts "(LD) >> Enable SPARQL monitoring with cube #{@settings.cube_host}:"+
-                    "#{@settings.cube_port}"
+          puts "(LD) >> Enable SPARQL monitoring with cube #{@settings.cube_host}:#{@settings.cube_port}"
           conf.enable_cube do |opts|
             opts[:host] = @settings.cube_host
             opts[:port] = @settings.cube_port
           end
         end
       end
-    rescue Exception => e
+    rescue StandardError => e
       abort("EXITING: Cannot connect to triplestore and/or search server:\n  #{e}\n#{e.backtrace.join("\n")}")
     end
   end
@@ -153,23 +150,48 @@ def goo_namespaces
       conf.add_namespace(:omv, RDF::Vocabulary.new("http://omv.ontoware.org/2005/05/ontology#"))
       conf.add_namespace(:skos, RDF::Vocabulary.new("http://www.w3.org/2004/02/skos/core#"))
       conf.add_namespace(:owl, RDF::Vocabulary.new("http://www.w3.org/2002/07/owl#"))
+      conf.add_namespace(:rdf, RDF::Vocabulary.new("http://www.w3.org/1999/02/22-rdf-syntax-ns#"))
       conf.add_namespace(:rdfs, RDF::Vocabulary.new("http://www.w3.org/2000/01/rdf-schema#"))
-      conf.add_namespace(:metadata,
-                         RDF::Vocabulary.new("http://data.bioontology.org/metadata/"),
-                         default = true)
-      conf.add_namespace(:metadata_def,
-                         RDF::Vocabulary.new("http://data.bioontology.org/metadata/def/"))
+      conf.add_namespace(:metadata, RDF::Vocabulary.new("http://data.bioontology.org/metadata/"), default = true)
+      conf.add_namespace(:metadata_def, RDF::Vocabulary.new("http://data.bioontology.org/metadata/def/"))
       conf.add_namespace(:dc, RDF::Vocabulary.new("http://purl.org/dc/elements/1.1/"))
       conf.add_namespace(:xsd, RDF::Vocabulary.new("http://www.w3.org/2001/XMLSchema#"))
-      conf.add_namespace(:oboinowl_gen,
-                         RDF::Vocabulary.new("http://www.geneontology.org/formats/oboInOwl#"))
+      conf.add_namespace(:oboinowl_gen, RDF::Vocabulary.new("http://www.geneontology.org/formats/oboInOwl#"))
       conf.add_namespace(:obo_purl, RDF::Vocabulary.new("http://purl.obolibrary.org/obo/"))
-      conf.add_namespace(:umls,
-                         RDF::Vocabulary.new("http://bioportal.bioontology.org/ontologies/umls/"))
-      conf.id_prefix = "http://data.bioontology.org/"
+      conf.add_namespace(:umls, RDF::Vocabulary.new("http://bioportal.bioontology.org/ontologies/umls/"))
+      conf.add_namespace(:door, RDF::Vocabulary.new("http://kannel.open.ac.uk/ontology#"))
+      conf.add_namespace(:dct, RDF::Vocabulary.new("http://purl.org/dc/terms/"))
+
+      conf.add_namespace(:void, RDF::Vocabulary.new("http://rdfs.org/ns/void#"))
+      conf.add_namespace(:foaf, RDF::Vocabulary.new("http://xmlns.com/foaf/0.1/"))
+      conf.add_namespace(:vann, RDF::Vocabulary.new("http://purl.org/vocab/vann/"))
+      conf.add_namespace(:adms, RDF::Vocabulary.new("http://www.w3.org/ns/adms#"))
+      conf.add_namespace(:voaf, RDF::Vocabulary.new("http://purl.org/vocommons/voaf#"))
+      conf.add_namespace(:dcat, RDF::Vocabulary.new("http://www.w3.org/ns/dcat#"))
+      conf.add_namespace(:mod, RDF::Vocabulary.new("http://www.isibang.ac.in/ns/mod#"))
+      conf.add_namespace(:prov, RDF::Vocabulary.new("http://www.w3.org/ns/prov#"))
+      conf.add_namespace(:cc, RDF::Vocabulary.new("http://creativecommons.org/ns#"))
+      conf.add_namespace(:schema, RDF::Vocabulary.new("http://schema.org/"))
+      conf.add_namespace(:doap, RDF::Vocabulary.new("http://usefulinc.com/ns/doap#"))
+      conf.add_namespace(:bibo, RDF::Vocabulary.new("http://purl.org/ontology/bibo/"))
+      conf.add_namespace(:wdrs, RDF::Vocabulary.new("http://www.w3.org/2007/05/powder-s#"))
+      conf.add_namespace(:cito, RDF::Vocabulary.new("http://purl.org/spar/cito/"))
+      conf.add_namespace(:pav, RDF::Vocabulary.new("http://purl.org/pav/"))
+      conf.add_namespace(:oboInOwl, RDF::Vocabulary.new("http://www.geneontology.org/formats/oboInOwl#"))
+      conf.add_namespace(:idot, RDF::Vocabulary.new("http://identifiers.org/idot/"))
+      conf.add_namespace(:sd, RDF::Vocabulary.new("http://www.w3.org/ns/sparql-service-description#"))
+      conf.add_namespace(:org, RDF::Vocabulary.new("http://www.w3.org/ns/org#"))
+      conf.add_namespace(:cclicense, RDF::Vocabulary.new("http://creativecommons.org/licenses/"))
+      conf.add_namespace(:nkos, RDF::Vocabulary.new("http://w3id.org/nkos#"))
+      conf.add_namespace(:skosxl, RDF::Vocabulary.new("http://www.w3.org/2008/05/skos-xl#"))
+      conf.add_namespace(:dcterms, RDF::Vocabulary.new("http://purl.org/dc/terms/"))
+      conf.add_namespace(:uneskos, RDF::Vocabulary.new("http://purl.org/umu/uneskos#"))
+
+
+      conf.id_prefix = 'http://data.bioontology.org/'
       conf.pluralize_models(true)
     end
   end
-  self.goo_namespaces
+  goo_namespaces
 
 end

lib/ontologies_linked_data/diff/bubastis_diff.rb

@@ -37,11 +37,11 @@ class BubastisDiffCommand < DiffTool
       # Loading one file locally and one from the web and outputting results to plain text:
       # java -jar bubastis_1_2.jar -ontology1 "H://disease_ontology_version_1.owl" -ontology2 "http://www.disease.org/diseaseontology_latest.owl" -output "C://my_diff.txt"
 
-      def initialize(old_file_path, new_file_path)
+      def initialize(old_file_path, new_file_path, output_repo)
         @bubastis_jar_path = LinkedData.bindir + "/bubastis.jar"
         @input_fileOld = old_file_path
         @input_fileNew = new_file_path
-        @output_repo = File.expand_path(@input_fileNew).gsub(File.basename(@input_fileNew),'')
+        @output_repo = output_repo
         @file_diff_path = nil
         @java_heap_size = LinkedData.settings.java_max_heap_size
       end

lib/ontologies_linked_data/models/base.rb

@@ -42,17 +42,17 @@
         raise ArgumentError, "`attributes` should be an array" unless attributes.is_a?(Array)
 
         # Get attributes, either provided, all, or default
-        if !attributes.empty?
-          if attributes.first == :all
-            default_attrs = self.attributes
-          else
-            default_attrs = attributes
-          end
-        elsif self.hypermedia_settings[:serialize_default].empty?
-          default_attrs = self.attributes
-        else
-          default_attrs = self.hypermedia_settings[:serialize_default].dup
-        end
+        default_attrs = if !attributes.empty?
+                          if attributes.first == :all
+                            (self.attributes + self.hypermedia_settings[:serialize_default]).uniq
+                          else
+                            attributes
+                          end
+                        elsif self.hypermedia_settings[:serialize_default].empty?
+                          self.attributes
+                        else
+                          self.hypermedia_settings[:serialize_default].dup
+                        end
 
         embed_attrs = {}
         extra_attrs = []