extract the parsing step "append triples to the store" from the "generate_rdf" step

[syphax-bouazzouni]

Currently, we append the triples to the store each time we generate the RDF file to be always sync

    def generate_rdf(logger, reasoning: true, user_params: {})
        mime_type = nil
        user_params = {} if user_params.nil?

        if self.hasOntologyLanguage.umls?
          triples_file_path = self.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)
          generate_umls_metrics_file(triples_file_path)
        else
          output_rdf = self.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 = owlapi_parser(logger: nil)

        end
        delete_and_append(triples_file_path, logger, mime_type)
       .....
      end

The feature request is to have the possibility with ncbo_cron to do only the "append" without re-parsing the submission file

[syphax-bouazzouni]

done in #132