Fixed the issues revealed by the failing unit tests

Gemfile

@@ -34,5 +34,5 @@ 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: 'develop'
+gem 'goo', github: 'ncbo/goo', branch: 'multilingual_preflabels'
 gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'

Gemfile.lock

@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 74a012eebb9433d031eb00df5abbe488cb8b4512
-  branch: develop
+  revision: d6b84e12d61317dbddc1b86cb1451acb37915369
+  branch: multilingual_preflabels
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -37,6 +37,7 @@ GEM
       public_suffix (>= 2.0.2, < 7.0)
     ansi (1.5.0)
     ast (2.4.2)
+    base64 (0.2.0)
     bcrypt (3.1.20)
     bigdecimal (3.1.8)
     builder (3.3.0)
@@ -55,9 +56,11 @@ GEM
       launchy (>= 2.1, < 4.0)
       mail (~> 2.7)
     eventmachine (1.2.7)
-    faraday (1.2.0)
-      multipart-post (>= 1.2, < 3)
-      ruby2_keywords
+    faraday (2.8.1)
+      base64
+      faraday-net_http (>= 2.0, < 3.1)
+      ruby2_keywords (>= 0.0.4)
+    faraday-net_http (3.0.2)
     ffi (1.17.0)
     hashie (5.0.0)
     htmlentities (4.3.4)
@@ -94,9 +97,8 @@ GEM
       minitest (>= 2.12, < 5.0)
       powerbar
     multi_json (1.15.0)
-    multipart-post (2.4.1)
     net-http-persistent (2.9.4)
-    net-imap (0.4.16)
+    net-imap (0.4.17)
       date
       net-protocol
     net-pop (0.1.2)
@@ -125,7 +127,7 @@ GEM
       method_source (~> 1.0)
     public_suffix (5.1.1)
     racc (1.8.1)
-    rack (2.2.9)
+    rack (2.2.10)
     rack-test (0.8.3)
       rack (>= 1.0, < 3)
     rainbow (3.1.1)
@@ -148,7 +150,7 @@ GEM
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.66.1)
+    rubocop (1.67.0)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)

lib/ontologies_linked_data/services/submission_process/operations/submission_rdf_generator.rb

@@ -11,7 +11,16 @@ def process(logger, options = {})
 
       def handle_missing_labels(file_path, logger)
         callbacks = {
+
+
+
+
           include_languages: true,
+
+
+
+
+
           missing_labels: {
             op_name: 'Missing Labels Generation',
             required: true,
@@ -189,21 +198,24 @@ def generate_missing_labels_pre_page(artifacts = {}, logger, paging, page_classe
 
       def generate_missing_labels_each(artifacts = {}, logger, paging, page_classes, page, c)
         prefLabel = nil
+        portal_lang = Goo.portal_language
+        prefLabel_lang = c.prefLabel(include_languages: true)
+        no_default_prefLabel = prefLabel_lang.nil? || (prefLabel_lang.keys & [portal_lang, :none]).empty?
 
-        if c.prefLabel.nil?
+        if prefLabel_lang.nil? || no_default_prefLabel
           lang_rdfs_labels = c.label(include_languages: true)
-          lang_rdfs_labels = {none: []} if lang_rdfs_labels.empty?
+          lang_rdfs_labels = {none: []} if lang_rdfs_labels.to_a.empty? ||
+              (no_default_prefLabel && (lang_rdfs_labels.keys & [portal_lang, :none]).empty?)
 
-          lang_rdfs_labels&.each do |lang, rdfs_labels|
+          lang_rdfs_labels.each do |lang, rdfs_labels|
             if rdfs_labels && rdfs_labels.length > 1 && c.synonym.length > 0
               rdfs_labels = (Set.new(c.label) - Set.new(c.synonym)).to_a.first
-
               rdfs_labels = c.label if rdfs_labels.nil? || rdfs_labels.length == 0
             end
 
             rdfs_labels = [rdfs_labels] if rdfs_labels and not (rdfs_labels.instance_of? Array)
-            label = nil
 
+            label = nil
             if rdfs_labels && rdfs_labels.length > 0
               # this sort is needed for a predictable label selection
               label = rdfs_labels.sort[0]
@@ -215,13 +227,15 @@ def generate_missing_labels_each(artifacts = {}, logger, paging, page_classes, p
               lang = nil
               prefLabel = label
             end
-            prefLabel = label if !prefLabel && lang === Goo.portal_language
+            prefLabel = label if !prefLabel && lang === portal_lang
             prefLabel = label unless prefLabel
             artifacts[:label_triples] << LinkedData::Utils::Triples.label_for_class_triple(
-              c.id, Goo.vocabulary(:metadata_def)[:prefLabel], label, lang)
+              c.id, Goo.vocabulary(:metadata_def)[:prefLabel], prefLabel, lang)
           end
-        else
+        elsif prefLabel_lang
           prefLabel = c.prefLabel
+        else
+          prefLabel = LinkedData::Utils::Triples.last_iri_fragment c.id.to_s
         end
 
         if @submission.ontology.viewOf.nil?

test/data/ontology_files/BRO_v3.2.owl

@@ -642,6 +642,7 @@
     <owl:Class rdf:about="&activity;Biospecimen_Management">
         <rdfs:subClassOf rdf:resource="&activity;Activity"/>
         <desc:definition rdf:datatype="&xsd;string">Activity related to the creation, use, or maintenance of a biorepository (http://en.wikipedia.org/wiki/Biorepository)</desc:definition>
+        <rdfs:label xml:lang="fr">Gestion des échantillons biologiques</rdfs:label>
         <core:prefLabel xml:lang="fr">Biospecimen Management</core:prefLabel>
     </owl:Class>
 
@@ -652,7 +653,7 @@
     <owl:Class rdf:about="&activity;Community_Engagement">
         <rdfs:subClassOf rdf:resource="&activity;Activity"/>
         <desc:definition rdf:datatype="&xsd;string">As defined in http://en.wikipedia.org/wiki/Community_engagement</desc:definition>
-        <core:prefLabel rdf:datatype="&xsd;string">Community Engagement</core:prefLabel>
+        <core:prefLabel xml:lang="fr">Engagement communautaire</core:prefLabel>
     </owl:Class>
 
 
@@ -672,7 +673,7 @@
     <owl:Class rdf:about="&activity;Gene_Therapy">
         <rdfs:subClassOf rdf:resource="&activity;Therapeutics"/>
         <desc:definition rdf:datatype="&xsd;string">As defined in http://en.wikipedia.org/wiki/Gene_therapy</desc:definition>
-        <core:prefLabel rdf:datatype="&xsd;string">Gene Therapy</core:prefLabel>
+        <rdfs:label xml:lang="fr">Thérapie génique</rdfs:label>
     </owl:Class>
 
 

test/models/test_ontology_submission.rb

@@ -316,7 +316,6 @@ def test_generate_language_preflabels
     submission_parse("D3OTEST", "DSMZ Digital Diversity Ontology Test",
                      "./test/data/ontology_files/d3o.owl", 1,
                      process_rdf: true, index_search: true, extract_metadata: false)
-
     res = LinkedData::Models::Class.search("prefLabel_en:Anatomic Structure", {:fq => "submissionAcronym:D3OTEST", :start => 0, :rows => 100})
     refute_equal 0, res["response"]["numFound"]
     refute_nil res["response"]["docs"].select{|doc| doc["resource_id"].eql?('https://purl.dsmz.de/schema/AnatomicStructure')}.first
@@ -1190,7 +1189,6 @@ def test_submission_extract_metadata
     end
   end
 
-
   def test_submission_delete_remove_files
     #This one has resources wih accents.
     submission_parse("ONTOMATEST",