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 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)