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"],
)