def main():
parser = PromptParser()
parser.add_argument('-p',
'--path',
metavar='',
help='{path} - path of the directory to organize ')
parser1 = PromptParser()
parser1.add_argument(
'-o',
'--order',
default='type',
help='{extension,size,date,type} - the way you need to organize',
metavar='',
choices=['extension', 'size', 'date', 'type'],
)
path = parser.parse_args().path
organizeBy = parser1.parse_args().order
if organizeBy == 'extension':
organize_by_extension(path)
elif organizeBy == 'size':
organize_by_size(path)
elif organizeBy == 'date':
organize_by_date(path)
elif organizeBy == 'type':
organize_by_type(path)
else:
print('Wrong Choice for Organizing')
def test_auto_parser():
"""Test a basic parser when the enviroment variable is set to disable prompts"""
parser = PromptParser()
parser.add_argument(
"--argument", "-a", help="An argument you could provide", default="foo"
)
args = parser.parse_args([])
assert args.argument == "foo"
def test_mismatched_default(input_mock):
"""Test a parser which has a default which isn't the same type as the type"""
input_mock.return_value = ""
parser = PromptParser()
parser.add_argument("--argument", type=str, default=None)
args = parser.parse_args([])
assert args.argument is None
input_mock.assert_called()
def test_default_parser(input_mock):
"""Test a basic parser with a default value"""
input_mock.side_effect = mock_input("")
parser = PromptParser()
parser.add_argument(
"--argument", "-a", help="An argument you could provide", default="foo"
)
args = parser.parse_args([])
assert args.argument == "foo"
def main():
parser = PromptParser()
parser.add_argument('--sequence_number',
help='Enter Sequence Number',
type=int,
default=None)
parser.add_argument('--start_num',
help='Enter first number in sequence',
type=int,
default=1)
parser.add_argument('--end_num',
help='Enter last number in sequence',
type=int,
default=None)
parser.add_argument(
'--block_interval',
help='After how many samples would you like a control block',
type=int,
default=None)
parser.add_argument(
'--beginning_blanks',
help='How many blanks would you like at the top of the run',
type=int,
default=1)
parser.add_argument(
'--standard_format',
help='Is this a pHILIC, lipid, or ZIC run (input 1, 2, or 3)',
type=int,
default=None)
parser.add_argument('--directory',
help='Enter directory to save files',
default='C:\\Users\\ASHL01\\Desktop')
parser.add_argument('--filename1',
help='Enter filename1 (LC)',
default='SQtestLC.csv')
parser.add_argument('--filename2',
help='Enter filename2 (MS)',
default='SQtestMS.csv')
#print(parser.parse_args().argument)
args = parser.parse_args()
trays = Trays(args.start_num, args.end_num)
trays.print_placement()
standard_string = 'ISTD' if args.standard_format == 1 else 'LQC' if args.standard_format == 2 else 'QC' if args.standard_format == 3 else None
if standard_string is None:
raise ValueError('enter 1 for pHILIC, 2 for lipid, or 3 for ZIC')
seqgen = SequenceGenerator(trays, args.sequence_number,
args.block_interval, standard_string,
args.beginning_blanks)
seqgen.directory(args.directory)
if os.path.exists('.\\' + args.filename1):
raise ValueError('This file already exists')
if os.path.exists('.\\' + args.filename2):
raise ValueError('This file already exists')
seqgen.export_format_1(args.filename2)
seqgen.export_format_2(args.filename1)
def test_invalid_type(input_mock):
"""Test a parser with a type argument. Check that it fails when the type is wrong"""
input_mock.side_effect = mock_input("abc")
with pytest.raises(SystemExit):
parser = PromptParser()
parser.add_argument(
"--argument", "-a", help="An argument you could provide", type=int
)
args = parser.parse_args([])
input_mock.assert_called()
def test_valid_type(input_mock):
"""Test a parser with a type argument. Check that it succeeds when the type is correct"""
input_mock.side_effect = mock_input("123")
parser = PromptParser()
parser.add_argument(
"--argument", "-a", help="An argument you could provide", type=int
)
args = parser.parse_args([])
assert args.argument == 123
input_mock.assert_called()
def test_no_default(input_mock, capsys, monkeypatch):
"""If a flag has no default, the prompt should still say ``None``"""
# Mock the input function
input_mock.side_effect = mock_input("abc")
# Create the parser
parser = PromptParser()
parser.add_argument("--argument", "-a", help="An argument you could provide")
args = parser.parse_args([])
captured = capsys.readouterr()
assert "None" in captured.out
def main():
parser = PromptParser()
parser.add_argument('--pcap',
'-p',
help='PCAP file to analyze',
default='foo')
pcap_file = parser.parse_args().pcap
run_bro(pcap_file)
for file in get_files('extract_files'):
scan_file(file)
ha_sandbox(file)
def create_parser():
parser = PromptParser()
parser.add_argument('--server-url',
'-s',
dest='server_url',
default=os.environ.get('BBMIGRATE_SERVER_URL'),
help='URL of the Bitbucket Server')
parser.add_argument('--server-user',
'-su',
dest='server_user',
default=os.environ.get('BBMIGRATE_SERVER_USER'),
help='Bitbucket Server username')
parser.add_argument('--server-pass',
'-sp',
dest='server_pass',
default=os.environ.get('BBMIGRATE_SERVER_PASS'),
help='Bitbucket Server password',
secure=True)
parser.add_argument('--workspace',
'-w',
dest='workspace',
default=os.environ.get('BBMIGRATE_WORKSPACE'),
help='Bitbucket Cloud workspace name')
parser.add_argument('--cloud-user',
'-cu',
dest='cloud_user',
default=os.environ.get('BBMIGRATE_CLOUD_USER'),
help='Bitbucket Cloud username (not e-mail)')
parser.add_argument('--threads',
'-t',
dest='threads',
default=env_or('BBMIGRATE_THREADS', "5"),
help='Number of threads to use (default: 5)')
parser.add_argument('--cloud-pass',
'-cp',
dest='cloud_pass',
default=os.environ.get('BBMIGRATE_CLOUD_PASS'),
help='Bitbucket Cloud password',
secure=True)
parser.add_argument(
'--no-remove-repos',
'-norm',
dest='no_remove_repos',
default=env_or('BBMIGRATE_NO_REMOVE_REPOS', "False"),
help='Do not remove locally-cloned repos (default: false)')
parser.add_argument(
'--repo-path',
'-rp',
dest='repo_path',
default=env_or('BBMIGRATE_REPO_PATH', "/tmp/bbmigrate"),
help='base path to output the projects/repos (default: /tmp/bbmigrate')
return parser
def test_secure_parser(getpass_mock):
"""Test a secure parser, which shouldn't echo the user's input to stdout"""
getpass_mock.return_value = "abc"
parser = PromptParser()
parser.add_argument(
"--argument",
"-a",
help="An argument you could provide",
secure=True,
default="foo",
)
args = parser.parse_args([])
assert args.argument == "abc"
getpass_mock.assert_called()
def main():
print("Artifactory Token Generator %s" % version)
parser = PromptParser(
description='A command line tool to help with generating API Key to Artifactory with SAML access.')
subparsers = parser.add_subparsers(help="", dest="action")
subparsers.required = True
login_args(subparsers)
configure_args(subparsers)
args = parser.parse_args()
if args.action == "login":
config = SAML2ArtConfig()
config.load(DEFAULT_CONFIG_FILE_PATH)
login_saml2art(config, args)
elif args.action == "configure":
configure_saml2art(args, DEFAULT_CONFIG_FILE_PATH)
else:
parser.print_help()
def test_basic_parser(input_mock, capsys):
"""Test a basic parser with no type argument"""
# Mock the input function
input_mock.side_effect = mock_input("abc")
parser = PromptParser()
parser.add_argument(
"--argument", "-a", help="An argument you could provide", default="foo"
)
args = parser.parse_args([])
# If the user inputs "abc", that should be the value of the argument
assert args.argument == "abc"
# The default value "foo" should be shown to the user
captured = capsys.readouterr()
assert "foo" in captured.out
def main():
parser = PromptParser()
add_arguments(parser)
args = parser.parse_args()
if ".txt" in args.path:
files = args.path
else:
files = glob.glob(f"{args.path}/*.txt")
assert len(files) > 1, "Warning not '.txt' files found in directory."
procobj = nd.ProcessingObject(files,
args.bead_radius,
opt_kwargs={'baseline_percentage': 0.2})
models = [x.strip() for x in args.models.split(',')]
procobj.fit_models(*models, save_plot=args.save_plot)
procobj.to_csv(f"results.csv")
def main():
parser = PromptParser()
add_arguments(parser)
args = parser.parse_args()
PATH = "data" # OR IT TAKES A .TXT FILE
BEAD_RADIUS = 18.5e-6
MODELS = "hertz_model, line"
SAVE = False
if ".txt" in args.path:
files = args.path
else:
files = glob.glob(f"{args.path}/*.txt")
obj = nd.ProcessingObject(files, args.bead_radius)
models = [x.strip() for x in args.models.split(",")]
obj.fit_models(*models, save_plot=args.save_plot)
obj.to_csv("results_demo2.csv", index=None)
def parse_args():
parser = PromptParser(description='Create gn3 databags')
parser.add_argument('-i',
'--instance',
dest='geonetwork_instance',
help='geonetwork 2 instance '
'e.g. https://catalogue-imos.aodn.org.au')
parser.add_argument('-u',
'--username',
dest='username',
help='username for basic auth')
parser.add_argument('-p',
'--password',
dest='password',
help='password for basic auth. '
'If a username is given but not a password, the '
'password will be prompted for.',
secure=True)
parser.add_argument('-o',
'--output-directory',
default='.',
dest='output_directory',
help='directory at which to backup the repositories')
return parser.parse_args()
from argparse_prompt import PromptParser
parser = PromptParser()
parser.add_argument('--argument',
'-a',
help='An argument you could provide',
type=int)
print(parser.parse_args().argument)
out_file_path = Path(out_file_path)
asset_folder = Path(asset_folder)
out_file_path.parent.mkdir(parents=True, exist_ok=True)
with open(out_file_path, "w+") as f:
f.write("---\n")
for key, value in self.metadata.items():
f.write(f"{key}: {value}\n")
f.write("---\n")
f.write(HEADER)
for cell in self.cells:
cell.render(f, asset_folder)
if __name__ == "__main__":
parser = PromptParser(
description=
"A utility for converting Jupyter Notebooks into UBI Center posts.")
parser.add_argument("notebook", help="The notebook file to convert.")
parser.add_argument("--layout", default="post", help="The layout style")
parser.add_argument("--current", default="post")
parser.add_argument("--cover", default="", help="The cover image path")
parser.add_argument("--navigation", default=True)
parser.add_argument("--title", default="Title goes here", help="The title")
parser.add_argument("--date",
default="2012-09-01",
help="The publishing date")
parser.add_argument("--tags", default="[]", help="The tags")
parser.add_argument("--class_", default="post-template")
parser.add_argument("--subclass", default="'post'")
parser.add_argument("--author", default="max", help="The author name")
parser.add_argument("--excerpt",
## merge all datasets/images associated with tags with labels 'arch%' and 'amoeb%' into one existing tag with ID 233
$ python -m tag_manager.tag_manager_cli -u root -s 172.17.0.3 -i 233 -e arch% amoeb%
## merge all datasets/images associated with tags with labels 'arch%' and 'amoeb%' and tags with IDs 245 and 253
## into one existing tag with ID 233
$ python -m tag_manager.tag_manager_cli -u root -s 172.17.0.3 -i 233 -e arch% amoeb% -r 245 253
## merge all datasets/images associated with tags with label '"Screaming" Hairy l'éléphan%'
## into one existing tag with ID 233
$ python -m tag_manager.tag_manager_cli -u root -s 172.17.0.3 -i 233 \
-e "\"Screaming\" Hairy l'éléphan%"
'''
# Instantiate the parser
# see https://pypi.org/project/argparse-prompt/
parser = PromptParser(description='Tag Manager CLI Application')
# set of connection params
parser.add_argument(
'-u',
'--username',
dest='username',
required=True,
metavar='username',
help="specifies the username for connection to the remote OMERO server",
type=str,
prompt=False)
parser.add_argument(
'-s',
'--server',