def test_sub_parsers_help(capsys):
# do we get the `name` substitution right?
SingleFileExperimentFactory.__doc__ = 'Description of {parser_name}'
cli = CLI()
assert cli.all_subparsers['data'].parser_name == 'data'
with parsing_output(capsys) as text:
parse('data --help')
assert 'Description of data' in text.std
# is custom sub-parser screen displayed and description used included in it?
SingleFileExperimentFactory.description = 'A dummy description'
SingleFileExperimentFactory.epilog = 'A dummy epilog'
with parsing_output(capsys) as text:
parse('data --help')
lines = text.std.split('\n')
half_of_output = len(lines) // 2
# is description in the text and is it in the first 50% of lines?
assert any(SingleFileExperimentFactory.description in line
for line in lines[:half_of_output])
# is the epilog in the text and is it in the last 50% of lines?
assert any(SingleFileExperimentFactory.epilog in line
for line in lines[half_of_output:])
def test_database(capsys):
with parsing_output(capsys) as text:
parse('gsea database --show_gene_sets')
assert 'HALLMARK_HYPOXIA' in text.std
db = create_test_db()
assert len(db.gene_sets) == 2
def test_shows_usage_when_no_args(capsys):
# if there are no arguments provided, the parser should
# show the usage summary (and do not raise any errors)
with parsing_output(capsys) as text:
parse(None)
assert 'usage' in text.err
def test_general_help(capsys):
with parsing_output(capsys) as text:
parse('--help')
for method in Method.members:
assert method in text.std
with parsing_error(match='unrecognized arguments: --controll'):
p_parse('data merged.tsv --case 1 --controll 2 control c.tsv')
def test_methods(capsys, test_files):
suffix = 'case t.tsv control c.tsv'
class MyMethod(Method):
name = 'some_method'
help = 'Some important text help'
other_argument = Argument(
type=int,
help='Only integer numbers!',
default=0,
)
def __init__(self,
mode,
my_argument: float = None,
other_argument=None):
"""
Args:
mode: This argument has to be passed!
my_argument: Help and documentation for my_argument
other_argument: Documentation for the other_argument
"""
if mode == 'active':
raise Success('In active mode!')
if my_argument == 1.4:
raise Success('Correct Argument provided +1')
if type(other_argument) is int:
raise Success(f'Parsed +{other_argument}')
def run(self, experiment):
raise Success('Run +10')
# test mode which is a required argument
with pytest.raises(Success, message='In active mode!'):
parse(f'some_method active {suffix}')
# test my_argument
with pytest.raises(Success, message='Correct Argument provided +1'):
parse(f'some_method a --my_argument 1.4 {suffix}')
# test run
with pytest.raises(Success, message='Run +10'):
run(f'run.py some_method a --my_argument 2.1 {suffix}'.split())
# test other_argument
with pytest.raises(Success, message='Parsed +5'):
parse(f'some_method a --other_argument 5 {suffix}')
# test help
for test_command in ['some_method --help', '-h some_method']:
with parsing_output(capsys, contains='Some important text help'):
parse(test_command)
with parsing_output(capsys, does_not_contain='Some important text help'):
parse('--help')
# test arguments help
arguments_help = {
'This argument has to be passed!': True,
'Help and documentation for my_argument': True,
'Only integer numbers!': True,
# Following should not be shown, as it is overwritten by
# "integers-only" text above from Argument definition:
'Documentation for the other_argument': False
}
for text, is_expected in arguments_help.items():
contains, does_not_contain = None, None
if is_expected:
contains = text
else:
does_not_contain = text
with parsing_output(capsys,
contains=contains,
does_not_contain=does_not_contain):
parse('some_method -h')
def test_help(capsys):
with parsing_output(capsys) as text:
parse('gsea --help')
assert 'GSEA method' in text.std
def test_licence(capsys):
with parsing_output(capsys) as text:
parse('gsea --show_licence')
assert 'copyright (c) 2004-2017 Broad Institute, Inc.' in text.std
def test_database(capsys):
with parsing_output(capsys) as text:
parse('gsea database --show_gene_sets')
assert 'HALLMARK_HYPOXIA' in text.std
def test_help(capsys):
with parsing_output(capsys) as text:
parse('SPIA --help')
assert 'signaling pathway impact analysis (SPIA)' in text.std
