def handle(self, *args, **options): required = ['username', 'title', 'file_name', 'source_column_index', 'data_file_column'] for arg in required: if not options[arg]: raise CommandError('%s was not provided.' % arg) parser = SingleFileColumnParser() parser.file_permanent = options['data_file_permanent'] parser.file_column_index = int( options['data_file_column'] ) parser.source_column_index = [int(x.strip()) for x in options['source_column_index'].split(",")] parser.column_index_separator = "/" parser.file_base_path = options['base_path'] if options['auxiliary_file_column'] is not None: parser.auxiliary_file_column_index = int( options['auxiliary_file_column'] ) if options['species_column'] is not None: parser.species_column_index = int( options['species_column'] ) if options['genome_build_column'] is not None: parser.genome_build_column_index = int( options['genome_build_column'] ) if options['annotation_column'] is not None: parser.annotation_column_index = int( options['annotation_column'] ) investigation = parser.run(options['file_name']) investigation.title = options['title'] investigation.save() create_dataset( investigation.uuid, options['username'], dataset_title=options['title'], slug=options['slug'], public=options['is_public'] )
def handle(self, *args, **options): # set pre-defined options for the Refinery default tabular file format options['source_column_index'] = "0" # source = filename options['data_file_column'] = "1" options['auxiliary_file_column'] = "2" options['species_column'] = "3" options['genome_build_column'] = "4" options['annotation_column'] = "5" options['data_file_permanent'] = True required = ['username', 'title', 'file_name'] for arg in required: if not options[arg]: raise CommandError('%s was not provided.' % arg) parser = SingleFileColumnParser() parser.source_column_index = [ int(x.strip()) for x in options['source_column_index'].split(",") ] parser.column_index_separator = "/" parser.file_base_path = options['base_path'] # fixed settings parser.file_column_index = int(options['data_file_column']) parser.auxiliary_file_column_index = int( options['auxiliary_file_column']) parser.species_column_index = int(options['species_column']) parser.genome_build_column_index = int(options['genome_build_column']) parser.annotation_column_index = int(options['annotation_column']) parser.file_permanent = options['data_file_permanent'] investigation = parser.run(options['file_name']) investigation.title = options['title'] investigation.save() create_dataset(investigation.uuid, options['username'], dataset_title=options['title'], slug=options['slug'], public=options['is_public'])
def handle(self, *args, **options): # set pre-defined options for the Refinery default tabular file format options["source_column_index"] = "0" # source = filename options["data_file_column"] = "1" options["auxiliary_file_column"] = "2" options["species_column"] = "3" options["genome_build_column"] = "4" options["annotation_column"] = "5" options["data_file_permanent"] = True required = ["username", "title", "file_name"] for arg in required: if not options[arg]: raise CommandError("%s was not provided." % arg) parser = SingleFileColumnParser() parser.source_column_index = [int(x.strip()) for x in options["source_column_index"].split(",")] parser.column_index_separator = "/" parser.file_base_path = options["base_path"] # fixed settings parser.file_column_index = int(options["data_file_column"]) parser.auxiliary_file_column_index = int(options["auxiliary_file_column"]) parser.species_column_index = int(options["species_column"]) parser.genome_build_column_index = int(options["genome_build_column"]) parser.annotation_column_index = int(options["annotation_column"]) parser.file_permanent = options["data_file_permanent"] investigation = parser.run(options["file_name"]) investigation.title = options["title"] investigation.save() create_dataset( investigation.uuid, options["username"], dataset_title=options["title"], slug=options["slug"], public=options["is_public"], )