def create_sample_params(
params: Dict[str,
Any]) -> Tuple[Sample, Optional[UUID], Optional[int]]:
'''
Process the input from the create_sample API call and translate it into standard types.
:param params: The unmarshalled JSON recieved from the API as part of the create_sample
call.
:returns: A tuple of the sample to save, the UUID of the sample for which a new version should
be created or None if an entirely new sample should be created, and the previous version
of the sample expected when saving a new version.
:raises IllegalParameterError: if any of the arguments are illegal.
'''
_check_params(params)
if type(params.get('sample')) != dict:
raise _IllegalParameterError(
'params must contain sample key that maps to a structure')
s = params['sample']
if type(s.get('node_tree')) != list:
raise _IllegalParameterError(
'sample node tree must be present and a list')
if s.get('name') is not None and type(s.get('name')) != str:
raise _IllegalParameterError('sample name must be omitted or a string')
nodes = _check_nodes(s)
id_ = get_id_from_object(s, ID, name='sample.id')
pv = params.get('prior_version')
if pv is not None and type(pv) != int:
raise _IllegalParameterError(
'prior_version must be an integer if supplied')
s = Sample(nodes, s.get('name'))
return (s, id_, pv)
def validate_samples_params(params: Dict[str, Any]) -> List[Sample]:
'''
Process the input from the validate_samples API call and translate it into standard types.
:param params: The unmarshalled JSON recieved from the API as part of the create_sample
call.
:returns: A tuple of the sample to save, the UUID of the sample for which a new version should
be created or None if an entirely new sample should be created, and the previous version
of the sample expected when saving a new version.
:raises IllegalParameterError: if any of the arguments are illegal.
'''
_check_params(params)
if type(params.get('samples')) != list or len(params.get('samples',
[])) == 0:
raise _IllegalParameterError('params must contain list of `samples`')
samples = []
for s in params['samples']:
if type(s.get('node_tree')) != list:
raise _IllegalParameterError(
'sample node tree must be present and a list')
if type(s.get('name')) != str or len(s.get('name')) <= 0:
raise _IllegalParameterError(
'sample name must be included as non-empty string')
nodes = _check_nodes(s)
s = Sample(nodes, s.get('name'))
samples.append(s)
return samples
def test_sample_build():
sn = SampleNode('foo')
sn2 = SampleNode('bat')
sn3 = SampleNode('bar', type_=SubSampleType.TECHNICAL_REPLICATE, parent='foo')
sn4 = SampleNode('baz', type_=SubSampleType.SUB_SAMPLE, parent='foo')
sndup = SampleNode('foo')
s = Sample([sn])
assert s.nodes == (sndup,)
assert s.name is None
s = Sample([sn, sn2, sn4, sn3], ' \t foo ')
assert s.nodes == (sndup, sn2, sn4, sn3)
assert s.name == 'foo'
s = Sample([sn], 'a' * 256)
assert s.nodes == (sndup,)
assert s.name == 'a' * 256
id_ = uuid.UUID('1234567890abcdef1234567890abcdef')
s = SavedSample(id_, UserID('user'), [sn], dt(6))
assert s.id == uuid.UUID('1234567890abcdef1234567890abcdef')
assert s.user == UserID('user')
assert s.nodes == (sndup,)
assert s.savetime == dt(6)
assert s.name is None
assert s.version is None
s = SavedSample(id_, UserID('user2'), [sn], dt(6), 'foo')
assert s.id == uuid.UUID('1234567890abcdef1234567890abcdef')
assert s.user == UserID('user2')
assert s.nodes == (sndup,)
assert s.savetime == dt(6)
assert s.name == 'foo'
assert s.version is None
s = SavedSample(id_, UserID('user'), [sn], dt(6), 'foo', 1)
assert s.id == uuid.UUID('1234567890abcdef1234567890abcdef')
assert s.user == UserID('user')
assert s.nodes == (sndup,)
assert s.savetime == dt(6)
assert s.name == 'foo'
assert s.version == 1
s = SavedSample(id_, UserID('user'), [sn], dt(6), 'foo', 8)
assert s.id == uuid.UUID('1234567890abcdef1234567890abcdef')
assert s.user == UserID('user')
assert s.nodes == (sndup,)
assert s.savetime == dt(6)
assert s.name == 'foo'
assert s.version == 8
s = SavedSample(id_, UserID('user'), [sn], dt(6), version=8)
assert s.id == uuid.UUID('1234567890abcdef1234567890abcdef')
assert s.user == UserID('user')
assert s.nodes == (sndup,)
assert s.savetime == dt(6)
assert s.name is None
assert s.version == 8
def create_sample_params(
params: Dict[str,
Any]) -> Tuple[Sample, Optional[UUID], Optional[int]]:
'''
Process the input from the create_sample API call and translate it into standard types.
:param params: The unmarshalled JSON recieved from the API as part of the create_sample
call.
:returns: A tuple of the sample to save, the UUID of the sample for which a new version should
be created or None if an entirely new sample should be created, and the previous version
of the sample expected when saving a new version.
:raises IllegalParameterError: if any of the arguments are illegal.
'''
_check_params(params)
if type(params.get('sample')) != dict:
raise _IllegalParameterError(
'params must contain sample key that maps to a structure')
s = params['sample']
if type(s.get('node_tree')) != list:
raise _IllegalParameterError(
'sample node tree must be present and a list')
if s.get('name') is not None and type(s.get('name')) != str:
raise _IllegalParameterError('sample name must be omitted or a string')
nodes = []
for i, n in enumerate(s['node_tree']):
if type(n) != dict:
raise _IllegalParameterError(
f'Node at index {i} is not a structure')
if type(n.get('id')) != str:
raise _IllegalParameterError(
f'Node at index {i} must have an id key that maps to a string')
try:
type_ = _SubSampleType(n.get('type'))
except ValueError:
raise _IllegalParameterError(
f'Node at index {i} has an invalid sample type: {n.get("type")}'
)
if n.get('parent') and type(n.get('parent')) != str:
raise _IllegalParameterError(
f'Node at index {i} has a parent entry that is not a string')
mc = _check_meta(n.get('meta_controlled'), i, 'controlled metadata')
mu = _check_meta(n.get('meta_user'), i, 'user metadata')
try:
nodes.append(
_SampleNode(n.get('id'), type_, n.get('parent'), mc, mu))
# already checked for the missing param error above, for id
except _IllegalParameterError as e:
raise _IllegalParameterError(f'Error for node at index {i}: ' +
_cast(str, e.message)) from e
id_ = get_id_from_object(s)
pv = params.get('prior_version')
if pv is not None and type(pv) != int:
raise _IllegalParameterError(
'prior_version must be an integer if supplied')
s = Sample(nodes, s.get('name'))
return (s, id_, pv)
def test_sample_eq():
sn = SampleNode('foo')
sn2 = SampleNode('bar')
assert Sample([sn], 'yay') == Sample([sn], 'yay')
assert Sample([sn], 'yay') != Sample([sn2], 'yay')
assert Sample([sn], 'yay') != Sample([sn], 'yooo')
id1 = uuid.UUID('1234567890abcdef1234567890abcdef')
id2 = uuid.UUID('1234567890abcdef1234567890abcdea')
dt1 = dt(5)
dt2 = dt(8)
u = UserID('u')
u2 = UserID('u2')
assert SavedSample(id1, u, [sn], dt1) == SavedSample(id1, u, [sn], dt(5))
assert SavedSample(id1, u, [sn], dt1) != SavedSample(id2, u, [sn], dt1)
assert SavedSample(id1, u, [sn], dt1) != SavedSample(id1, u2, [sn], dt1)
assert SavedSample(id1, u, [sn], dt1) != SavedSample(id1, u, [sn2], dt1)
assert SavedSample(id1, u, [sn], dt1) != SavedSample(id1, u, [sn], dt2)
assert SavedSample(id1, u, [sn], dt1, 'yay') == SavedSample(id1, u, [sn], dt1, 'yay')
assert SavedSample(id1, u, [sn], dt1, 'yay') != SavedSample(id1, u, [sn], dt1, 'yooo')
assert SavedSample(id1, u, [sn], dt2, 'yay', 6) == SavedSample(id1, u, [sn], dt2, 'yay', 6)
assert SavedSample(id1, u, [sn], dt1, 'yay', 6) != SavedSample(id1, u, [sn], dt1, 'yay', 7)
assert SavedSample(id1, u, [sn], dt1, 'yay') != Sample([sn], 'yay')
assert Sample([sn], 'yay') != SavedSample(id1, u, [sn], dt1, 'yay')
def test_create_sample_params_minimal():
params = {'sample': {'version': 7, # should be ignored
'save_date': 9, # should be ignored
'node_tree': [{'id': 'foo',
'type': 'BioReplicate'}]
}}
expected = Sample([SampleNode('foo')])
assert create_sample_params(params) == (expected, None, None)
def _sample_build_fail(nodes, name, expected):
with raises(Exception) as got:
Sample(nodes, name)
assert_exception_correct(got.value, expected)
id_ = uuid.UUID('1234567890abcdef1234567890abcdef')
with raises(Exception) as got:
SavedSample(id_, UserID('u'), nodes, dt(8), name)
assert_exception_correct(got.value, expected)
def test_create_sample_params_maximal():
params = {'sample': {'version': 7, # should be ignored
'save_date': 9, # should be ignored
'id': '706fe9e1-70ef-4feb-bbd9-32295104a119',
'name': 'myname',
'node_tree': [{'id': 'foo',
'type': 'BioReplicate'},
{'id': 'bar',
'parent': 'foo',
'type': 'TechReplicate',
'meta_controlled':
{'concentration/NO2':
{'species': 'NO2',
'units': 'ppm',
'value': 78.91,
'protocol_id': 782,
'some_boolean_or_other': True
}
},
'meta_user': {'location_name': {'name': 'my_buttocks'}}
}
]
},
'prior_version': 1}
assert create_sample_params(params) == (
Sample([
SampleNode('foo'),
SampleNode(
'bar',
SubSampleType.TECHNICAL_REPLICATE,
'foo',
{'concentration/NO2':
{'species': 'NO2',
'units': 'ppm',
'value': 78.91,
'protocol_id': 782,
'some_boolean_or_other': True
}
},
{'location_name': {'name': 'my_buttocks'}}
)
],
'myname'
),
UUID('706fe9e1-70ef-4feb-bbd9-32295104a119'),
1)
def test_sample_build_fail_sample_count():
nodes = [SampleNode('s' + str(i)) for i in range(10000)]
s = Sample(nodes)
assert s.nodes == tuple(nodes)
assert s.name is None
id_ = uuid.UUID('1234567890abcdef1234567890abcdef')
s = SavedSample(id_, UserID('u'), nodes, dt(8))
assert s.id == uuid.UUID('1234567890abcdef1234567890abcdef')
assert s.user == UserID('u')
assert s.nodes == tuple(nodes)
assert s.savetime == dt(8)
assert s.name is None
assert s.version is None
nodes.append(SampleNode('s10000'))
_sample_build_fail(nodes, None, IllegalParameterError(
'At most 10000 nodes are allowed per sample'))
def test_sample_hash():
# hashes will change from instance to instance of the python interpreter, and therefore
# tests can't be written that directly test the hash value. See
# https://docs.python.org/3/reference/datamodel.html#object.__hash__
sn = SampleNode('foo')
sn2 = SampleNode('bar')
id1 = uuid.UUID('1234567890abcdef1234567890abcdef')
id2 = uuid.UUID('1234567890abcdef1234567890abcdea')
dt1 = dt(5)
dt2 = dt(8)
u = UserID('u')
u2 = UserID('u2')
assert hash(Sample([sn], 'yay')) == hash(Sample([sn], 'yay'))
assert hash(Sample([sn], 'foo')) == hash(Sample([sn], 'foo'))
assert hash(Sample([sn], 'yay')) != hash(Sample([sn2], 'yay'))
assert hash(Sample([sn], 'yay')) != hash(Sample([sn], 'yo'))
assert hash(SavedSample(id1, u, [sn], dt1, 'yay')) == hash(SavedSample(
id1, u, [sn], dt(5), 'yay'))
assert hash(SavedSample(id2, u, [sn], dt1, 'foo')) == hash(SavedSample(
id2, u, [sn], dt1, 'foo'))
assert hash(SavedSample(id1, u, [sn], dt1, 'foo')) != hash(SavedSample(
id2, u, [sn], dt1, 'foo'))
assert hash(SavedSample(id1, u, [sn], dt1, 'foo')) != hash(SavedSample(
id1, u2, [sn], dt1, 'foo'))
assert hash(SavedSample(id2, u, [sn], dt1, 'foo')) != hash(SavedSample(
id2, u, [sn2], dt1, 'foo'))
assert hash(SavedSample(id2, u, [sn], dt1, 'foo')) != hash(SavedSample(
id2, u, [sn], dt2, 'foo'))
assert hash(SavedSample(id2, u, [sn], dt1, 'foo')) != hash(SavedSample(
id2, u, [sn], dt1, 'bar'))
assert hash(SavedSample(id1, u, [sn], dt1, 'foo', 6)) == hash(SavedSample(
id1, u, [sn], dt1, 'foo', 6))
assert hash(SavedSample(id1, u, [sn], dt1, 'foo', 6)) != hash(SavedSample(
id1, u, [sn], dt1, 'foo', 7))
def _sample_with_id_build_fail(id_, user, nodes, savetime, name, version, expected):
with raises(Exception) as got:
SavedSample(id_, user, nodes, savetime, name, version)
Sample(nodes, name)
assert_exception_correct(got.value, expected)