def test_aggregate_sample_only(stasis):
aggregator = Aggregator(args=parser.parse_args(
['--dir', f'{parent}/../results']),
stasis=stasis)
aggregator.aggregate_samples(samples=samples,
destination=f"{parent}/../results")
def test_aggregate(stasis):
aggregator = Aggregator(
{
'infiles': [f'{parent}/../test.txt'],
'dir': f'{parent}/../results'
}, stasis)
aggregator.aggregate()
def test_build_worksheet(stasis):
aggregator = Aggregator({'infiles': 'filename'}, stasis)
results = _build_result(stasis, samples)
targets = aggregator.get_target_list(results)
intensity = aggregator.build_worksheet(targets, 'intensity matrix')
assert len(targets) == intensity.index.size
def test_get_target_list_negative_mode(stasis):
aggregator = Aggregator({'infiles': 'filename'}, stasis)
results = _build_result(stasis, samples2)
assert len(results) > 0
targets = aggregator.get_target_list(results)
assert len(targets) > 0
def test_aggregate_no_args(stasis):
aggregator = Aggregator({}, stasis)
try:
aggregator.aggregate()
fail()
except KeyError:
pass
def test_aggregate_file_not_found(stasis):
aggregator = Aggregator(args=parser.parse_args(['--files', 'bad.txt']),
stasis=stasis)
try:
aggregator.aggregate()
fail()
except FileNotFoundError:
pass
def test_aggregate_extra_files(stasis):
aggregator = Aggregator(
{
'infiles': [f'{parent}/../test.txt'],
'dir': f'{parent}/../results',
'extra_files': True
}, stasis)
aggregator.aggregate()
def test_aggregate_norepl(stasis):
aggregator = Aggregator(
{
'infiles': [f'{parent}/../test.txt'],
'dir': f'{parent}/../results',
'exclude_replacement': True
}, stasis)
aggregator.aggregate()
def test_get_target_list_new_model(stasis):
aggregator = Aggregator({'infiles': 'filename'}, stasis)
results = _build_result(stasis, newsample)
assert len(results) > 0
targets = aggregator.get_target_list(results)
pprint(targets)
assert len(targets) > 0
def test_format_sample(stasis):
sample = 'PNACIC_UnkLip_IntQC_P2_QE_A_NEG_14Oct20_Lola-WCSH315112'
samplefile = 'PNACIC_UnkLip_IntQC_P2_QE_A_NEG_14Oct20_Lola-WCSH315112'
aggregator = Aggregator({'infile': 'filename', 'save': True}, stasis)
result = stasis.sample_result_as_json(samplefile)
formatted = aggregator.format_sample(result)
assert '152.994812:7832.22 158.026062:7178.55 172.474503:3949.74 187.616302:4657.92 ' \
'202.055176:16934.99 231.554276:4670.40 237.226807:3772.17 254.032379:4215.71 ' \
'269.248138:149924.94 292.144012:3959.56 339.703491:4769.80 ' \
'368.308716:4431.29 437.528534:4201.56 502.319580:122849.00 ' \
'532.803040:4007.13 631.061951:4249.08' == formatted[7][sample][74]
def test_add_metadata(stasis):
# Test correct indexing of samples in header
aggregator = Aggregator(
{
'infiles': 'filename',
'save': True,
'dir': f'{parent}/../data'
}, stasis)
results = _build_result(stasis, samples)
md = aggregator.add_metadata(samples, results)
assert md.iloc[4, 6:].to_list() == list(range(1, 6))
def test_process_sample_list(stasis):
excel_list = {
'test-intensity_matrix-results-norepl.xlsx',
'test-mass_matrix-results-norepl.xlsx',
'test-original_rt_matrix-results-norepl.xlsx',
'test-replaced_values-results-norepl.xlsx',
'test-retention_index_matrix-results-norepl.xlsx',
'test-correction_curve-results-norepl.xlsx',
'test-msms_spectrum-results-norepl.xlsx'
}
samples = [
'PlasmaBiorec001_MX524916_posCSH_preSOP001',
'PlasmaBiorec002_MX524916_posCSH_postSOP010',
'PlasmaBiorec003_MX524916_posCSH_postSOP020'
]
aggregator = Aggregator({'infiles': 'filename'}, stasis)
aggregator.process_sample_list(samples, f'{parent}/../results')
def test_find_intensity(stasis):
# test find_intensity on non replaced data
aggregator = Aggregator({'infiles': 'filename'}, stasis)
value = {'intensity': 1, 'replaced': False}
assert 1 == aggregator.find_intensity(value)
# test find_intensity on zero replaced data not requesting replaced data
value = {'intensity': 2, 'replaced': True}
assert 2 == aggregator.find_intensity(value)
# test find_intensity on zero replaced data requesting replaced data
aggregator = Aggregator(
{
'infiles': 'filename',
'exclude_replacement': True
}, stasis)
value = {'intensity': 2, 'replaced': True}
assert 0 == aggregator.find_intensity(value)
def _aggregate(self, samples: List[str], job: Job):
aggregator = Aggregator({}, stasis=self._get_stasis_client())
aggregator.aggregate_samples(samples=samples,
destination=self.destination)
def test_find_replaced():
assert 2 == Aggregator.find_replaced({'intensity': 2, 'replaced': True})
assert 0 == Aggregator.find_replaced({'intensity': 2, 'replaced': False})
default=False)
parser.add_argument('--mz-tolerance',
help='m/z alignment tolerance',
type=float,
default=0.01)
parser.add_argument('--rt-tolerance',
help='retention time alignment tolerance',
type=float,
default=0.1)
return parser
if __name__ == '__main__':
parser = create_parser()
args = parser.parse_args()
# Validate arguments
if args.save and not args.dir:
parser.error(
'--save argument requires a local directory to be provided with --dir'
)
# try:
Aggregator(vars(args)).aggregate()
# except Exception as ex:
# print(str(ex.args))
# parser.print_help()
# exit(-1)