def test_permutate_job_108():
handler = JobHandler()
counter = 0
def callback(job: Job, parameters: dict, profiles: dict):
nonlocal counter
counter = counter + 1
pass
test_job = Job(samples=['a', 'b', 'c'],
method='abc',
profiles={
'regression': ['a', 'b'],
'similarity': ['d', 'e', 'f']
},
parameters={
'first': [1, 2],
'second': [3, 4, 5],
'third': [6, 7, 8]
})
handler.permutate_job(test_job, callback=callback)
assert counter == 108
def test_job_with_profile_activation_in_tree_format():
LCB_TUNING_CONFIG['schedule']['limit']['sample_count'].set(0)
handler = JobHandler()
job = handler.read_job(f"{ROOT_DIR}/job.example.qtof.yml")
assert len(job.samples) == 11
assert job.method == "soqtof[M+H][M+NH4] | 6530a | c18 | positive"
# assert len(job.parameters) == 7
assert len(job.profiles) == 3
assert len(job.default_profiles) == 4
assert len(job.default_parameters) == 1
counter = 0
counter_linear = 0
counter_polynomial = 0
counter_offset = 0
def callback(job: Job, parameters: list, profiles: list):
nonlocal counter
nonlocal counter_offset
nonlocal counter_linear
nonlocal counter_polynomial
assert isinstance(parameters, list)
assert isinstance(profiles, list)
counter = counter + 1
if "carrot.lcms.correction.regression.offset" in profiles:
keys = list(map(lambda x: x.split("=")[0], parameters))
assert 'wcmc.workflow.lcms.process.correction.regression.offset.n' in keys
assert 'wcmc.workflow.lcms.process.correction.regression.offset.linearSamplesEnd' in keys
counter_offset = counter_offset + 1
elif "carrot.lcms.correction.regression.linear" in profiles:
keys = list(map(lambda x: x.split("=")[0], parameters))
assert 'wcmc.workflow.lcms.process.correction.regression.offset.n' not in keys
assert 'wcmc.workflow.lcms.process.correction.regression.offset.linearSamplesEnd' not in keys
counter_linear = counter_linear + 1
elif "carrot.lcms.correction.regression.polynomial" in profiles:
keys = list(map(lambda x: x.split("=")[0], parameters))
assert 'wcmc.workflow.lcms.process.correction.regression.polynomial.n' in keys
assert 'wcmc.workflow.lcms.process.correction.regression.offset.linearSamplesEnd' not in keys
counter_polynomial = counter_polynomial + 1
else:
raise Exception("invalid combination, should never happen")
pass
handler.permutate_job(job, callback=callback)
assert counter > 0
assert counter_linear > 0
assert counter_offset > 0
assert counter_polynomial == 0
def test_read_job():
handler = JobHandler()
job = handler.read_job(f"{ROOT_DIR}/job.example.yml")
assert len(job.samples) == 12
assert job.method == "soqe[M+H][M+NH4] | QExactive | test | positive"
assert len(job.parameters) == 7
assert len(job.profiles) == 3
assert len(job.default_profiles) == 5
assert len(job.default_parameters) == 1
def test_job_with_profile_activation():
handler = JobHandler()
job = handler.read_job(f"{ROOT_DIR}/job.example.yml")
assert len(job.samples) == 12
assert job.method == "soqe[M+H][M+NH4] | QExactive | test | positive"
assert len(job.parameters) == 7
assert len(job.profiles) == 3
assert len(job.default_profiles) == 5
assert len(job.default_parameters) == 1
counter = 0
counter_linear = 0
counter_polynomial = 0
counter_offset = 0
def callback(job: Job, parameters: dict, profiles: dict):
nonlocal counter
nonlocal counter_offset
nonlocal counter_linear
nonlocal counter_polynomial
counter = counter + 1
if "carrot.lcms.correction.regression.offset" in profiles:
keys = list(map(lambda x: x.split("=")[0], parameters))
assert 'wcmc.workflow.lcms.process.correction.polynomialOrder' in keys
assert 'wcmc.workflow.lcms.process.correction.linearSamplesEnd' in keys
counter_offset = counter_offset + 1
elif "carrot.lcms.correction.regression.linear" in profiles:
keys = list(map(lambda x: x.split("=")[0], parameters))
assert 'wcmc.workflow.lcms.process.correction.polynomialOrder' not in keys
assert 'wcmc.workflow.lcms.process.correction.linearSamplesEnd' not in keys
counter_linear = counter_linear + 1
elif "carrot.lcms.correction.regression.polynomial" in profiles:
keys = list(map(lambda x: x.split("=")[0], parameters))
assert 'wcmc.workflow.lcms.process.correction.polynomialOrder' in keys
assert 'wcmc.workflow.lcms.process.correction.linearSamplesEnd' not in keys
counter_polynomial = counter_polynomial + 1
else:
raise Exception("invalid combination, should never happen")
pass
handler.permutate_job(job, callback=callback)
assert counter > 0
assert counter_linear > 0
assert counter_offset > 0
assert counter_polynomial > 0
def test_permutate_job_8():
handler = JobHandler()
counter = 0
def callback(job: Job, parameters: dict, profiles: dict):
nonlocal counter
counter = counter + 1
pass
test_job = Job(samples=['sample_1', 'sample_2', 'sample_3'],
method='abc',
profiles={'profile': ['a', 'b']},
parameters={
'number_1_2': [1, 2],
'number_3_4': [3, 4]
})
handler.permutate_job(test_job, callback=callback)
assert counter == 8
def test_complex_job():
handler = JobHandler()
test_job = Job(
samples=[
"PNACIC_UnkLip_BTLE_P2_QE_A_POS_13Oct20_Lola-WCSH315112.mzml"
],
method="soqe[M+H][M+NH4] | QExactive | test | positive",
parameters={
'wcmc.workflow.lcms.process.correction.polynomialOrder': [3, 5],
'wcmc.workflow.lcms.process.correction.linearOffsetEnd':
[3, 5, 8, 13],
'wcmc.workflow.lcms.process.correction.linearOffsetBegin':
[3, 5, 8, 13],
},
profiles={
"correction": ["carrot.correction.sliding"],
"test": ["1", "2", "3"]
},
default_profiles=[
"carrot.similarity.entropy.weighted",
"carrot.targets.yaml.correction",
"carrot.targets.yaml.annotation",
"carrot.resource.loader.bucket",
"carrot.resource.store.local",
],
default_parameters=[
"wcmc.workflow.resource.store.multibucket.rawDataBucket=data-carrot"
])
counter = 0
def callback(job: Job, parameters: dict, profiles: dict):
nonlocal counter
counter = counter + 1
pass
handler.permutate_job(test_job, callback=callback)
assert counter == 96