def test_token_without_username():
parser = make_connection_parser()
some_token = 'some_token'
args = parser.parse_args(['--token', some_token])
user = get_user(args)
assert user.token == some_token
assert user.host == DEFAULT_HOST
def test_parse_user_by_email():
user = get_user(make_connection_parser().parse_args(
['-u', '*****@*****.**']))
expected = User('*****@*****.**',
alias='*****@*****.**',
host='platform.genestack.org')
assert user == expected
def generate_rst_doc(shell_name, file_name, class_name, footer_file_name, save_path):
with open(os.path.join(os.path.dirname(__file__), '..', '..', 'genestack_client', 'scripts', file_name)) as f:
shell_module = imp.new_module('shell_name')
exec(f.read(), shell_module.__dict__)
shell = getattr(shell_module, class_name)
tool_file_name = os.path.basename(shell_name)
commands = []
script_help = get_help(shell().get_shell_parser()).replace("\n", "\n ").replace('sphinx-build',
tool_file_name)
for command in sorted(shell.COMMAND_LIST, key=lambda x: x.COMMAND):
command = command()
parser = command.get_command_parser(parser=None if command.OFFLINE else make_connection_parser())
help_text = get_help(parser).replace("\n", "\n ").replace('sphinx-build', tool_file_name)
text = '- **%s**:\n\n .. code-block:: text\n\n %s\n\n' % (command.COMMAND, help_text)
commands.append(text)
if footer_file_name:
with open(footer_file_name) as f:
footer = f.read()
else:
footer = ''
with open(save_path, 'w') as f:
f.write(template.format(
name=tool_file_name,
name_underline='=' * len(tool_file_name),
commands='\n'.join(commands),
description=shell.DESCRIPTION,
usage=script_help,
footer=footer,
))
def test_token_without_username():
parser = make_connection_parser()
some_token = 'some_token'
args = parser.parse_args(['--token', some_token])
user = get_user(args)
assert user.token == some_token
assert user.host == DEFAULT_HOST
def args():
p = make_connection_parser()
p.add_argument(
'--keep',
action='store_true',
help='Keep created test files for manual inspection or initialization')
return p.parse_args()
def test_parse_default_user():
user = get_user(make_connection_parser().parse_args())
expected = User('*****@*****.**',
alias='tester',
host='localhost:8080',
password='******',
token=None)
assert user == expected
def test_parse_default():
parser = make_connection_parser()
args = parser.parse_args()
expected = Namespace(debug=False,
host=None,
pwd=None,
show_logs=False,
user=None,
token=None)
assert args == expected
def generate_rst_doc(shell_name, file_name, class_name, footer_file_name,
save_path):
with open(
os.path.join(os.path.dirname(__file__), '..', '..',
'genestack_client', 'scripts', file_name)) as f:
shell_module = imp.new_module('shell_name')
exec(f.read(), shell_module.__dict__)
shell = getattr(shell_module, class_name)
tool_file_name = os.path.basename(shell_name)
commands = []
script_help = get_help(shell().get_shell_parser()).replace(
"\n", "\n ").replace('sphinx-build', tool_file_name)
for command in sorted(shell.COMMAND_LIST, key=lambda x: x.COMMAND):
command = command()
parser = command.get_command_parser(
parser=None if command.OFFLINE else make_connection_parser())
help_text = get_help(parser).replace("\n", "\n ").replace(
'sphinx-build', tool_file_name)
text = '- **%s**:\n\n .. code-block:: text\n\n %s\n\n' % (
command.COMMAND, help_text)
commands.append(text)
if footer_file_name:
with open(footer_file_name) as f:
footer = f.read()
else:
footer = ''
with open(save_path, 'w') as f:
f.write(
template.format(
name=tool_file_name,
name_underline='=' * len(tool_file_name),
commands='\n'.join(commands),
description=shell.DESCRIPTION,
usage=script_help,
footer=footer,
))
def test_token_and_user(capsys):
parser = make_connection_parser()
with pytest.raises(SystemExit):
parser.parse_args(['-u', 'some_user', '--token', 'some_token'])
# Test stderr output that was written by parser before raising error:
# Expected output consist of usage section and line with filename and tested error
expected_error_message = 'Token and user should not be specified together'
# Save parser.print_usage output to the variable
f = StringIO()
parser.print_usage(file=f)
expected_output = f.getvalue()
expected_output += '%s: error: %s\n' % (os.path.basename(__file__),
expected_error_message)
# capture stdout and stderr that was produced during test
# https://docs.pytest.org/en/latest/capture.html#accessing-captured-output-from-a-test-function
out, err = capsys.readouterr()
assert err == expected_output
def test_token_and_user(capsys):
parser = make_connection_parser()
with pytest.raises(SystemExit):
parser.parse_args(['-u', 'some_user', '--token', 'some_token'])
# Test stderr output that was written by parser before raising error:
# Expected output consist of usage section and line with filename and tested error
expected_error_message = 'Token and user should not be specified together'
# Save parser.print_usage output to the variable
f = StringIO()
parser.print_usage(file=f)
expected_output = f.getvalue()
expected_output += '%s: error: %s\n' % (
os.path.basename(__file__), expected_error_message)
# capture stdout and stderr that was produced during test
# https://docs.pytest.org/en/latest/capture.html#accessing-captured-output-from-a-test-function
out, err = capsys.readouterr()
assert err == expected_output
GenestackException)
# keys that must be supplied in the CSV file
MANDATORY_KEYS = ['name', 'link']
# keys that have existing dedicated "Genestack" metainfo key names
SPECIAL_KEYS = {
'name': BioMetainfo.NAME,
'organism': BioMetainfo.ORGANISM,
'method': BioMetainfo.METHOD,
'sex': BioMetainfo.SEX,
'cell line': BioMetainfo.CELL_LINE
}
# 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('--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
# Logic to parse 'boolean-like' values as metainfo booleans
TRUE_VALUES = {'true', 'yes', 'y'}
FALSE_VALUES = {'false', 'no', 'n'}
def parse_as_boolean(s):
if s.lower().strip() in TRUE_VALUES:
return True
elif s.lower().strip() in FALSE_VALUES:
return False
return None
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..."
def test_parse_default_user():
user = get_user(make_connection_parser().parse_args())
expected = User('*****@*****.**', alias='tester',
host='localhost:8080', password='******', token=None)
assert user == expected
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 args():
p = make_connection_parser()
p.add_argument('--keep', action='store_true', help='Keep created test files for manual inspection or initialization')
return p.parse_args()
def conn():
conn = get_connection(make_connection_parser().parse_args())
return conn
def files_utils():
connection = get_connection(make_connection_parser().parse_args([]))
files_utils = FilesUtil(connection)
return files_utils
def test_parse_user_by_email():
user = get_user(make_connection_parser().parse_args(['-u', '*****@*****.**']))
expected = User('*****@*****.**', alias='*****@*****.**',
host='platform.genestack.org')
assert user == expected
def test_parse_default():
parser = make_connection_parser()
args = parser.parse_args()
expected = Namespace(debug=False, host=None, pwd=None, show_logs=False,
user=None, token=None)
assert args == expected
