def main():
args = parser.parse_args()
files, size = get_files(args.paths)
print('Collected %s files with total size: %s' % (len(files), friendly_number(size)))
try:
connection = get_connection(args)
except GenestackVersionException as e:
sys.stderr.write(str(e))
sys.stderr.write('\n')
exit(13)
new_folder, folder_name, accessions = upload_files(connection, files, args.folder_name)
print('%s files were uploaded to %s / %s' % (len(accessions), new_folder, folder_name))
if args.no_recognition:
exit(0)
try:
recognize_files(connection, accessions, new_folder)
except GenestackServerException as e:
sys.stderr.write("Recognition failed: %s\n" % e)
exit(1)
def main():
args = parser.parse_args()
files, size = get_files(args.paths)
print('Collected %s files with total size: %s' %
(len(files), friendly_number(size)))
try:
connection = get_connection(args)
except GenestackVersionException as e:
sys.stderr.write(str(e))
sys.stderr.write('\n')
exit(13)
new_folder, folder_name, accessions = upload_files(connection, files,
args.folder_name,
args.upload_to)
print('%s files were uploaded to %s / %s' %
(len(accessions), new_folder, folder_name))
if args.no_recognition:
exit(0)
try:
recognize_files(connection, accessions, new_folder)
except GenestackServerException as e:
sys.stderr.write("Recognition failed: %s\n" % e)
exit(1)
parser.add_argument(
'csv_file',
help='Path to the local comma-delimited CSV file containing the data')
parser.add_argument('--name',
help='Name of the experiment to create in Genestack')
parser.add_argument(
'--description',
help='Description of the experiment to display in Genestack')
args = parser.parse_args()
csv_input = args.csv_file
print "Connecting to Genestack..."
# get connection and application handlers
connection = get_connection(args)
importer = DataImporter(connection)
# file format of the reads to import
file_format = UnalignedReads.compose_format_map(UnalignedReads.Space.BASESPACE,
UnalignedReads.Format.PHRED33,
UnalignedReads.Type.SINGLE)
# create the experiment where we will store the data in Genestack
experiment = importer.create_experiment(name=args.name
or "Imported experiment",
description=args.description
or "No description provided")
print "Created a new experiment with accession %s..." % experiment
if __name__ == "__main__":
# parse script arguments
parser = make_connection_parser()
parser.add_argument('csv_file', help='Path to the local comma-delimited CSV file containing the data')
parser.add_argument('local_key', help='Name of the local key to match CSV records and Genestack files names')
parser.add_argument('folder', help='Accession of the Genestack folder containing the files')
args = parser.parse_args()
csv_input = args.csv_file
local_key = args.local_key
print "Connecting to Genestack..."
# get connection and application handlers
connection = get_connection(args)
files_util = FilesUtil(connection)
print "Collecting files..."
files = files_util.get_file_children(args.folder)
print "Found %d files. Collecting metadata..." % len(files)
infos = files_util.get_infos(files)
identifier_map = {info['name']: info['accession'] for info in infos}
# parse the CSV file
with open(csv_input, 'r') as the_file:
reader = csv.DictReader(the_file, delimiter=",")
field_names = reader.fieldnames
if args.local_key not in field_names:
def conn(args):
if get_user(args).host != "internal-dev.genestack.com":
sys.stderr.write("Tests must be run on internal-dev")
sys.exit(1)
connection = get_connection(args)
return connection
def files_utils():
connection = get_connection(make_connection_parser().parse_args([]))
files_utils = FilesUtil(connection)
return files_utils
def conn():
conn = get_connection(make_connection_parser().parse_args())
return conn
def conn(args):
if get_user(args).host != "internal-dev.genestack.com":
sys.stderr.write("Tests must be run on internal-dev")
sys.exit(1)
connection = get_connection(args)
return connection
def conn():
conn = get_connection(make_connection_parser().parse_args())
return conn
def test_future_version():
connection = get_connection()
assert connection.check_version('99.99.99') == ''
def test_too_old():
connection = get_connection()
with pytest.raises(GenestackException):
assert connection.check_version('0.0.1')
def test_current_version():
connection = get_connection()
assert connection.check_version(__version__) == ''
from builtins import *
from genestack_client import TaskLogViewer, get_connection, make_connection_parser
# add extra arguments to the Genestack arguments parser for this script
parser = make_connection_parser()
parser.add_argument('-f',
'--follow',
action='store_true',
help="Follow the logs' output if the task is not done")
parser.add_argument(
'-t',
'--type',
metavar='<log_type>',
choices=[TaskLogViewer.STDERR, TaskLogViewer.STDOUT],
default=TaskLogViewer.STDOUT,
help="Type of logs to display ('{0}' or '{1}' ; default is '{0}')".format(
TaskLogViewer.STDOUT, TaskLogViewer.STDERR))
parser.add_argument('accession',
metavar='<accession>',
help='Accession of the file for which to display the logs')
arguments = parser.parse_args()
# connect to Genestack
connection = get_connection(arguments)
log_viewer = TaskLogViewer(connection)
# print task logs
log_viewer.print_log(arguments.accession,
log_type=arguments.type,
follow=arguments.follow)
#!/usr/bin/env python2.7
# -*- coding: utf-8 -*-
from genestack_client import TaskLogViewer, get_connection, make_connection_parser
# add extra arguments to the Genestack arguments parser for this script
parser = make_connection_parser()
parser.add_argument('-f', '--follow', action='store_true', help="Follow the logs' output if the task is not done")
parser.add_argument('-t', '--type', metavar='<log_type>',
choices=[TaskLogViewer.STDERR, TaskLogViewer.STDOUT],
default=TaskLogViewer.STDOUT,
help="Type of logs to display ('{0}' or '{1}' ; default is '{0}')".format(
TaskLogViewer.STDOUT, TaskLogViewer.STDERR))
parser.add_argument('accession', metavar='<accession>', help='Accession of the file for which to display the logs')
arguments = parser.parse_args()
# connect to Genestack
connection = get_connection(arguments)
log_viewer = TaskLogViewer(connection)
# print task logs
log_viewer.print_log(arguments.accession, log_type=arguments.type, follow=arguments.follow)
def files_utils():
connection = get_connection(make_connection_parser().parse_args([]))
files_utils = FilesUtil(connection)
return files_utils