def main():
argparse = ArgumentParser(
description=
'Upgrade ELOAD config to a format compatible with current automation')
argparse.add_argument('--eload',
required=True,
type=int,
help='The ELOAD number for this submission')
argparse.add_argument('--analysis_alias',
required=False,
type=str,
help='Analysis alias to use')
argparse.add_argument(
'--debug',
action='store_true',
default=False,
help='Set the script to output logging information at debug level')
args = argparse.parse_args()
log_cfg.add_stdout_handler()
if args.debug:
log_cfg.set_log_level(logging.DEBUG)
# Load the config_file from default location
load_config()
with Eload(args.eload) as eload:
eload.upgrade_config_if_needed(args.analysis_alias)
def setUp(self):
config_file = os.path.join(self.resources_folder, 'submission_config.yml')
load_config(config_file)
# Need to set the directory so that the relative path set in the config file works from the top directory
os.chdir(ROOT_DIR)
self.eload = Eload(55)
self.updated_config = EloadConfig(os.path.join(self.eload.eload_dir, 'updated_config.yml'))
# Used to restore test config after each test
self.original_cfg = deepcopy(self.eload.eload_cfg.content)
self.original_updated_cfg = deepcopy(self.updated_config.content)
self.updated_config.set('version', value=__version__)
def test_create_log_file(self):
# Creating a second eload object to test whether the logging file handler
# has been created twice
eload2 = Eload(self.eload.eload_num)
self.eload.info("Testing the creation of logging file")
assert os.path.exists(self.logfile_name)
with open(self.logfile_name, "r") as test_logfile:
k = [i for i in test_logfile.readlines() if "Testing the creation of logging file" in i]
# Checking if the log message is written only once in the log file
assert len(k) == 1
def setUp(self):
config_file = os.path.join(self.resources_folder, 'submission_config.yml')
load_config(config_file)
# Need to set the directory so that the relative path set in the config file works from the top directory
os.chdir(ROOT_DIR)
self.eload = Eload(55)
self.original_config = EloadConfig(os.path.join(self.eload.eload_dir, 'original_config.yml'))
self.updated_config = EloadConfig(os.path.join(self.eload.eload_dir, 'updated_config.yml'))
# Setup the config
self.eload.eload_cfg.content = deepcopy(self.original_config.content)
self.original_updated_cfg = deepcopy(self.updated_config.content)
self.updated_config.set('version', value=__version__)
# Get the log file name
self.logfile_name = os.path.join(self.eload.eload_dir, str(self.eload.eload) + "_submission.log")
def test_context_manager(self):
with Eload(55) as eload:
assert eload.eload_cfg.query('submission',
'assembly_accession') is None
eload.eload_cfg.set('submission',
'assembly_accession',
value='GCA_00009999.9')
assert eload.eload_cfg.query(
'submission', 'assembly_accession') == 'GCA_00009999.9'
# Config file gets written
with open(eload.eload_cfg.config_file) as open_file:
config_dict = yaml.safe_load(open_file)
assert config_dict['submission'][
'assembly_accession'] == 'GCA_00009999.9'