add index_all step to submission parsing steps

lib/ontologies_linked_data/models/concerns/submission_process.rb

@@ -18,6 +18,10 @@ def generate_diff(logger)
         LinkedData::Services::SubmissionDiffGenerator.new(self).process(logger)
       end
 
+      def index_all(logger, commit: true)
+        LinkedData::Services::OntologySubmissionAllDataIndexer.new(self).process(logger, commit: commit)
+      end
+
       def index_terms(logger, commit: true, optimize: true)
         LinkedData::Services::OntologySubmissionIndexer.new(self).process(logger, commit: commit, optimize: optimize)
       end

lib/ontologies_linked_data/services/submission_process/submission_processor.rb

@@ -42,6 +42,16 @@ def process_submission(logger, options = {})
 
             parsed = @submission.ready?(status: %i[rdf rdf_labels])
 
+            if process_index_all_data?(options)
+              unless parsed
+                raise StandardError, "The submission #{@submission.ontology.acronym}/submissions/#{@submission.submissionId}
+                                cannot be indexed because it has not been successfully parsed"
+              end
+
+              @submission.index_all(logger, commit: process_index_commit?(options))
+            end
+
+
             if process_index_search?(options)
               unless parsed
                 raise StandardError, "The submission #{@submission.ontology.acronym}/submissions/#{@submission.submissionId}
@@ -95,6 +105,10 @@ def process_rdf?(options)
         options.empty? || options[:process_rdf].eql?(true)
       end
 
+      def process_index_all_data?(options)
+        options.empty? || options[:index_all_data].eql?(true)
+      end
+
       def process_index_search?(options)
         options.empty? || options[:index_search].eql?(true)
       end
@@ -104,7 +118,7 @@ def process_index_properties?(options)
       end
 
       def process_index_commit?(options)
-        options.empty? || (process_index_search?(options) || process_index_properties?(options))
+        options.empty? || (process_index_search?(options) || process_index_properties?(options) || process_index_all_data?(options))
       end
 
       def process_diff?(options)

test/models/test_search.rb

@@ -132,6 +132,7 @@ def test_search_ontology_data
                                                                                         process_rdf: true, extract_metadata: false,
                                                                                         generate_missing_labels: false,
                                                                                         index_search: false,
+                                                                                        index_all_data: true
                                                                                       },
                                                                                       acronym: 'BROTEST',
                                                                                       name: 'ontTEST Bla',
@@ -142,10 +143,7 @@ def test_search_ontology_data
                                                                                     })
     ont_sub = LinkedData::Models::Ontology.find('BROTEST-0').first
     ont_sub = ont_sub.latest_submission
-    time = Benchmark.realtime do
-      ont_sub.index_all_data(Logger.new($stdout))
-    end
-    puts time
+
     conn = Goo.search_client(:ontology_data)
     response = conn.search('*')