renaming some functions in the new operations files

lib/ontologies_linked_data/models/class.rb

@@ -264,6 +264,8 @@ def index_doc(to_set=nil)
             puts "Exception getting paths to root for search for #{self.id.to_s}: #{e.class}: #{e.message}\n#{e.backtrace.join("\n")}"
           end
 
+          self.submission.ontology.bring(:ontologyType) if self.submission.ontology.bring?(:ontologyType)
+
           doc[:ontologyId] = self.submission.id.to_s
           doc[:submissionAcronym] = self.submission.ontology.acronym
           doc[:submissionId] = self.submission.submissionId

lib/ontologies_linked_data/models/concerns/submission_process.rb

@@ -6,7 +6,7 @@ def process_submission(logger, options = {})
         LinkedData::Services::OntologyProcessor.new(self).process(logger, options)
       end
 
-      def generate_missing_label(logger)
+      def generate_missing_labels(logger)
         puts 'Start generate_mission_label'
         time = Benchmark.realtime do
           LinkedData::Services::GenerateMissingLabels.new(self).process(logger, file_path: self.master_file_path)

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

@@ -7,12 +7,12 @@ class OntologySubmissionArchiver < OntologySubmissionProcess
       FILE_SIZE_ZIPPING_THRESHOLD = 100 * 1024 * 1024 # 100MB
 
       def process
-        submission_archive
+        archive_submission
       end
 
       private
 
-      def submission_archive
+      def archive_submission
         @submission.ontology.bring(:submissions)
         submissions = @submission.ontology.submissions
         return if submissions.nil?
@@ -26,6 +26,8 @@ def submission_archive
         status = LinkedData::Models::SubmissionStatus.find("ARCHIVED").first
         @submission.add_submission_status(status)
 
+        @submission.unindex
+
         # Delete everything except for original ontology file.
         delete_old_submission_files
         @submission.uploadFilePath = zip_submission_uploaded_file

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

@@ -14,13 +14,11 @@ def process_indexation(logger, options)
         begin
           index(logger, options[:commit], false)
           @submission.add_submission_status(status)
-        rescue Exception => e
+        rescue StandardError => e
           logger.error("#{e.class}: #{e.message}\n#{e.backtrace.join("\n\t")}")
           logger.flush
           @submission.add_submission_status(status.get_error_status)
-          if File.file?(@submission.csv_path)
-            FileUtils.rm(@submission.csv_path)
-          end
+          FileUtils.rm(@submission.csv_path) if File.file?(@submission.csv_path)
         ensure
           @submission.save
         end

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

@@ -97,6 +97,14 @@ def generate_metrics_file(class_count, indiv_count, prop_count)
         end
       end
 
+      # TODO to find usage in NCBO code
+      def generate_metrics_file2(class_count, indiv_count, prop_count, max_depth)
+        CSV.open(self.metrics_path, "wb") do |csv|
+          csv << ["Class Count", "Individual Count", "Property Count", "Max Depth"]
+          csv << [class_count, indiv_count, prop_count, max_depth]
+        end
+      end
+
     end
   end
 end

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

@@ -76,57 +76,6 @@ def generate_obsolete_classes(logger, file_path)
             mime_type = "application/x-turtle")
         end
       end
-
-      def generate_rdf(logger, file_path, reasoning: true)
-        mime_type = nil
-
-        if @submission.hasOntologyLanguage.umls?
-          triples_file_path = @submission.triples_file_path
-          logger.info("Using UMLS turtle file found, skipping OWLAPI parse")
-          logger.flush
-          mime_type = LinkedData::MediaTypes.media_type_from_base(LinkedData::MediaTypes::TURTLE)
-          SubmissionMetricsCalculator.new(@submission).generate_umls_metrics_file(triples_file_path)
-        else
-          output_rdf = @submission.rdf_path
-
-          if File.exist?(output_rdf)
-            logger.info("deleting old owlapi.xrdf ..")
-            deleted = FileUtils.rm(output_rdf)
-
-            if deleted.length > 0
-              logger.info("deleted")
-            else
-              logger.info("error deleting owlapi.rdf")
-            end
-          end
-          owlapi = LinkedData::Parser::OWLAPICommand.new(
-            File.expand_path(file_path),
-            File.expand_path(@submission.data_folder.to_s),
-            master_file: @submission.masterFileName)
-
-          owlapi.disable_reasoner unless reasoning
-          triples_file_path, missing_imports = owlapi.parse
-
-          if missing_imports && missing_imports.length > 0
-            @submission.missingImports = missing_imports
-
-            missing_imports.each do |imp|
-              logger.info("OWL_IMPORT_MISSING: #{imp}")
-            end
-          else
-            @submission.missingImports = nil
-          end
-          logger.flush
-        end
-        delete_and_append(triples_file_path, logger, mime_type)
-      end
-
-      def delete_and_append(triples_file_path, logger, mime_type = nil)
-        Goo.sparql_data_client.delete_graph(@submission.id)
-        Goo.sparql_data_client.put_triples(@submission.id, triples_file_path, mime_type)
-        logger.info("Triples #{triples_file_path} appended in #{@submission.id.to_ntriples}")
-        logger.flush
-      end
     end
   end
 end

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

@@ -32,7 +32,7 @@ def index_properties(logger, commit: true, optimize: true)
           @submission.ontology.bring(:acronym) if @submission.ontology.bring?(:acronym)
           logger.info("Indexing ontology properties: #{@submission.ontology.acronym}...")
           t0 = Time.now
-          @submission.ontology.unindex_all_data(commit)
+          @submission.ontology.unindex_properties(commit)
           logger.info("Removed ontology properties index in #{Time.now - t0} seconds."); logger.flush
 
           props = @submission.ontology.properties

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

@@ -5,7 +5,7 @@ class SubmissionRDFGenerator < OntologySubmissionProcess
 
       def process(logger, options)
         reasoning = options[:reasoning]
-        
+
         # Remove processing status types before starting RDF parsing etc.
         @submission.submissionStatus = nil
         status = LinkedData::Models::SubmissionStatus.find('UPLOADED').first
@@ -27,7 +27,7 @@ def process(logger, options)
           generate_rdf(logger, reasoning: reasoning)
           @submission.add_submission_status(status)
           @submission.save
-        rescue Exception => e
+        rescue StandardError => e
           logger.error("#{e.class}: #{e.message}\n#{e.backtrace.join("\n\t")}")
           logger.flush
           @submission.add_submission_status(status.get_error_status)
@@ -64,7 +64,7 @@ def generate_rdf(logger, reasoning: true)
 
           owlapi = @submission.owlapi_parser(logger: logger)
           owlapi.disable_reasoner unless reasoning
-          
+
           triples_file_path, missing_imports = owlapi.parse
 
           if missing_imports && !missing_imports.empty?

lib/ontologies_linked_data/services/submission_process/submission_processor.rb

@@ -79,43 +79,43 @@ def process_archive?(options)
       end
 
       def process_rdf?(options)
-        options[:process_rdf].nil? || options[:process_rdf].eql?(true)
+        options.empty? || options[:process_rdf].eql?(true)
       end
 
       def generate_missing_labels?(options)
-        options[:generate_missing_labels].nil? || options[:generate_missing_labels].eql?(true)
+        options[:generate_missing_labels].nil? && process_rdf?(options) || options[:generate_missing_labels].eql?(true)
       end
 
       def generate_obsolete_classes?(options)
-        options[:generate_obsolete_classes].nil? || options[:generate_obsolete_classes].eql?(true)
+        options[:generate_obsolete_classes].nil? && process_rdf?(options) || options[:generate_obsolete_classes].eql?(true)
       end
 
       def index_search?(options)
-        options[:index_search].nil? || options[:index_search].eql?(true)
+        options.empty? || options[:index_search].eql?(true)
       end
 
       def index_properties?(options)
-        options[:index_properties].nil? || options[:index_properties].eql?(true)
+        options.empty? || options[:index_properties].eql?(true)
       end
 
       def process_index_commit?(options)
         index_search?(options) || index_properties?(options)
       end
 
       def process_diff?(options)
-        options[:diff].nil? || options[:diff].eql?(true)
+        options.empty? || options[:diff].eql?(true)
       end
 
       def process_metrics?(options)
-        options[:run_metrics].nil? || options[:run_metrics].eql?(true)
+        options.empty? || options[:run_metrics].eql?(true)
       end
 
       def process_reasoning?(options)
-        options[:reasoning].nil? && options[:reasoning].eql?(true)
+        options.empty? && options[:reasoning].eql?(true)
       end
 
       def extract_metadata?(options)
-        options[:extract_metadata].nil? || options[:extract_metadata].eql?(true)
+        options.empty? || options[:extract_metadata].eql?(true)
       end
 
     end