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'])
