Merge pull request #205 from ncbo/develop

Develop to multilingual branch merge

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/ontology_submission.rb

@@ -283,6 +283,10 @@ def zip_folder
         File.join([data_folder, 'unzipped'])
       end
 
+      def master_file_folder
+        zipped? ? zip_folder : data_folder
+      end
+
       def csv_path
         return File.join(self.data_folder, self.ontology.acronym.to_s + ".csv.gz")
       end
@@ -336,7 +340,6 @@ def unzip_submission(logger)
         zip_dst
       end
 
-
       def class_count(logger=nil)
         logger ||= LinkedData::Parser.logger || Logger.new($stderr)
         count = -1
@@ -699,6 +702,14 @@ def parsable?(logger: Logger.new($stdout))
         parsable
       end
 
+      def owlapi_parser(logger: Logger.new($stdout))
+        unzip_submission(logger)
+        LinkedData::Parser::OWLAPICommand.new(
+          owlapi_parser_input,
+          File.expand_path(self.data_folder.to_s),
+          master_file: self.masterFileName,
+          logger: logger)
+      end
 
       private
 
@@ -711,8 +722,6 @@ def owlapi_parser_input
         File.expand_path(path)
       end
 
-
-
       def check_http_file(url)
         session = Net::HTTP.new(url.host, url.port)
         session.use_ssl = true if url.port == 443

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

@@ -18,8 +18,9 @@ def init_diff_tool(older)
         older.bring(:uploadFilePath)
 
         LinkedData::Diff::BubastisDiffCommand.new(
-          File.expand_path(older.uploadFilePath),
-          File.expand_path(@submission.uploadFilePath))
+          File.expand_path(older.uploadFilePath.to_s),
+          File.expand_path(@submission.uploadFilePath.to_s),
+          File.expand_path(@submission.data_folder.to_s))
       end
 
       def process_diff(logger)

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

@@ -307,11 +307,11 @@ def process_rdf(logger, reasoning)
           raise e
         end
 
-        MissingLabelsHandler.new(@submission).process(logger, file_path: @submission.master_file_path)
+        MissingLabelsHandler.new(@submission).process(logger, file_path: @submission.uploadFilePath.to_s)
 
         status = LinkedData::Models::SubmissionStatus.find('OBSOLETE').first
         begin
-          generate_obsolete_classes(logger, @submission.master_file_path)
+          generate_obsolete_classes(logger, @submission.uploadFilePath.to_s)
           @submission.add_submission_status(status)
           @submission.save
         rescue Exception => e
@@ -329,7 +329,7 @@ def generate_rdf(logger, reasoning: true)
 
         if @submission.hasOntologyLanguage.umls?
           triples_file_path = @submission.triples_file_path
-          logger.info("Using UMLS turtle file found, skipping OWLAPI parse")
+          logger.info("UMLS turtle file found; doing OWLAPI parse to extract metrics")
           logger.flush
           mime_type = LinkedData::MediaTypes.media_type_from_base(LinkedData::MediaTypes::TURTLE)
           SubmissionMetricsCalculator.new(@submission).generate_umls_metrics_file(triples_file_path)
@@ -348,10 +348,7 @@ def generate_rdf(logger, reasoning: true)
           end
 
           owlapi = @submission.owlapi_parser(logger: logger)
-
-          if !reasoning
-            owlapi.disable_reasoner
-          end
+          owlapi.disable_reasoner unless reasoning
           triples_file_path, missing_imports = owlapi.parse
 
           if missing_imports && missing_imports.length > 0
@@ -364,6 +361,9 @@ def generate_rdf(logger, reasoning: true)
             @submission.missingImports = nil
           end
           logger.flush
+          # debug code when you need to avoid re-generating the owlapi.xrdf file,
+          # comment out the block above and uncomment the line below
+          # triples_file_path = output_rdf
         end
 
         begin
@@ -372,41 +372,15 @@ def generate_rdf(logger, reasoning: true)
           logger.error("Error sending data to triple store - #{e.response.code} #{e.class}: #{e.response.body}") if e.response&.body
           raise e
         end
-        version_info = extract_version
-
-        if version_info
-          @submission.version = version_info
-        end
       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
 
-
-
-
-      def extract_version
-
-        query_version_info = <<eos
-SELECT ?versionInfo
-FROM #{@submission.id.to_ntriples}
-WHERE {
-<http://bioportal.bioontology.org/ontologies/versionSubject>
- <http://www.w3.org/2002/07/owl#versionInfo> ?versionInfo .
-}
-eos
-        Goo.sparql_query_client.query(query_version_info).each_solution do |sol|
-          return sol[:versionInfo].to_s
-        end
-        return nil
-      end
-
       def process_callbacks(logger, callbacks, action_name, &block)
         callbacks.delete_if do |_, callback|
           begin

lib/ontologies_linked_data/services/submission_process/submission_processor.rb

@@ -36,9 +36,7 @@ def process_submission(logger, options = {})
           if archive
             @submission.archive
           else
-
             @submission.generate_rdf(logger, reasoning: reasoning) if process_rdf
-
             parsed = @submission.ready?(status: [:rdf, :rdf_labels])
 
             if index_search