Merge pull request #199 from ontoportal-lirmm/pr/sync-agroportal-ncbo

Feature: Multilingual Support - Add search and languages serialization
ncbo · May 8, 2024 · f6764a8 · f6764a8
2 parents 02986ff + fc48343
commit f6764a8
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Showing 34 changed files with 382,747 additions and 964 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
+.bundle/
 *.swp
 *.gemtags
 .bundle

diff --git a/Gemfile b/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: 'ontoportal-lirmm/goo', branch: 'pr/sync-agroportal-bioportal'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,7 +1,17 @@
 GIT
-  remote: https://github.com/ncbo/goo.git
-  revision: ef2d816df2d263c905bd034efd449a964fa4890f
-  branch: master
+  remote: https://github.com/ncbo/sparql-client.git
+  revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc
+  branch: develop
+  specs:
+    sparql-client (1.0.1)
+      json_pure (>= 1.4)
+      net-http-persistent (= 2.9.4)
+      rdf (>= 1.0)
+
+GIT
+  remote: https://github.com/ontoportal-lirmm/goo.git
+  revision: f2751fe9324e48a0a5c2a8b15580ab879fc53a2b
+  branch: pr/sync-agroportal-bioportal
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -14,16 +24,6 @@ GIT
       sparql-client
       uuid
 
-GIT
-  remote: https://github.com/ncbo/sparql-client.git
-  revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
-  branch: master
-  specs:
-    sparql-client (1.0.1)
-      json_pure (>= 1.4)
-      net-http-persistent (= 2.9.4)
-      rdf (>= 1.0)
-
 GEM
   remote: https://rubygems.org/
   specs:
@@ -182,8 +182,7 @@ GEM
       macaddr (~> 1.0)
 
 PLATFORMS
-  arm64-darwin-22
-  x86_64-darwin-21
+  x86_64-linux
 
 DEPENDENCIES
   activesupport (~> 4)
@@ -204,6 +203,7 @@ DEPENDENCIES
   rack
   rack-test (~> 0.6)
   rake (~> 10.0)
+  request_store
   rest-client
   rsolr
   rubocop

diff --git a/config/solr/term_search/schema.xml b/config/solr/term_search/schema.xml
diff --git a/lib/ontologies_linked_data/config/config.rb b/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
diff --git a/lib/ontologies_linked_data/models/base.rb b/lib/ontologies_linked_data/models/base.rb
@@ -42,17 +42,17 @@ def self.goo_attrs_to_load(attributes = [], level = 0)
         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 = []