def test_init_fail():
_init_fail(None, MissingParameterError('userid'))
_init_fail(' \t ', MissingParameterError('userid'))
_init_fail('foo \t bar',
IllegalParameterError('userid contains control characters'))
_init_fail('u' * 257,
IllegalParameterError('userid exceeds maximum length of 256'))
def test_sample_node_address_init_fail():
sa = SampleAddress(uuid.UUID('1234567890abcdef1234567890abcdef'), 5)
_sample_node_address_init_fail(None, 'f', ValueError(
'sample cannot be a value that evaluates to false'))
_sample_node_address_init_fail(sa, None, MissingParameterError('node'))
_sample_node_address_init_fail(sa, ' \t \n ', MissingParameterError('node'))
_sample_node_address_init_fail(sa, '3' * 257, IllegalParameterError(
'node exceeds maximum length of 256'))
def test_get_admin_request_from_object_fail_bad_args():
_get_admin_request_from_object_fail(None, '1', '2', ValueError('params cannot be None'))
_get_admin_request_from_object_fail({'a': 'b'}, None, '2', MissingParameterError('as_admin'))
_get_admin_request_from_object_fail({'a': 'b'}, '1', None, MissingParameterError('as_user'))
_get_admin_request_from_object_fail(
{'asa': True, 'asu': ['foo']}, 'asa', 'asu', IllegalParameterError(
'asu must be a string if present'))
_get_admin_request_from_object_fail(
{'asa': True, 'asu': 'whe\tee'}, 'asa', 'asu', IllegalParameterError(
'userid contains control characters'))
def test_get_version_from_object_fail_bad_args():
get_version_from_object_fail(None, False, ValueError('params cannot be None'))
get_version_from_object_fail({}, True, MissingParameterError('version'))
get_version_from_object_fail(
{'version': None}, True, MissingParameterError('version'))
get_version_from_object_fail(
{'version': 'whee'}, False, IllegalParameterError('Illegal version argument: whee'))
get_version_from_object_fail(
{'version': 0}, True, IllegalParameterError('Illegal version argument: 0'))
get_version_from_object_fail(
{'version': -3}, False, IllegalParameterError('Illegal version argument: -3'))
def test_get_id_from_object_fail_bad_args():
_get_id_from_object_fail({'id': 6}, True, IllegalParameterError(
'Sample ID 6 must be a UUID string'))
_get_id_from_object_fail({
'id': 'f5bd78c3-823e-40b2-9f93-20e78680e41'},
False,
IllegalParameterError(
'Sample ID f5bd78c3-823e-40b2-9f93-20e78680e41 must be a UUID string'))
_get_id_from_object_fail(None, True, MissingParameterError('Sample ID'))
_get_id_from_object_fail({}, True, MissingParameterError('Sample ID'))
_get_id_from_object_fail({'id': None}, True, MissingParameterError('Sample ID'))
def check_string(string: Optional[str],
name: str,
max_len: int = None,
optional: bool = False) -> Optional[str]:
'''
Check that a string meets a set of criteria:
- it is not None or whitespace only (unless the optional parameter is specified)
- it contains no control characters
- (optional) it is less than some specified maximum length
:param string: the string to test.
:param name: the name of the string to be used in error messages.
:param max_len: the maximum length of the string.
:param optional: True if no error should be thrown if the string is None.
:returns: the stripped string or None if the string was optional and None or whitespace only.
:raises MissingParameterError: if the string is None or whitespace only.
:raises IllegalParameterError: if the string is too long or contains illegal characters.
'''
# See the IDMapping service if character classes are needed.
# Maybe package this stuff
if max_len is not None and max_len < 1:
raise ValueError('max_len must be > 0 if provided')
if not string or not string.strip():
if optional:
return None
raise MissingParameterError(name)
string = string.strip()
_no_control_characters(string, name)
if max_len and len(string) > max_len:
raise IllegalParameterError('{} exceeds maximum length of {}'.format(
name, max_len))
return string
def test_sample_build_fail():
# not testing every permutation of failing check_string here, just one test to make sure
# it's there
id_ = uuid.UUID('1234567890abcdef1234567890abcdef')
u = UserID('user')
sn = SampleNode('foo')
tn = SampleNode('bar', SubSampleType.TECHNICAL_REPLICATE, 'foo')
sn2 = SampleNode('baz')
dup = SampleNode('foo')
d = dt(8)
_sample_build_fail(
[sn], 'a' * 257, IllegalParameterError('name exceeds maximum length of 256'))
_sample_build_fail([], None, MissingParameterError('At least one node per sample is required'))
_sample_build_fail(
[tn, sn], 'a', IllegalParameterError('The first node in a sample must be a BioReplicate'))
_sample_build_fail([sn, tn, sn2], 'a', IllegalParameterError(
'BioReplicates must be the first nodes in the list of sample nodes.'))
_sample_build_fail([sn, sn2, dup], 'a', IllegalParameterError(
'Duplicate sample node name: foo'))
_sample_build_fail([sn2, tn], 'a', IllegalParameterError(
'Parent foo of node bar does not appear in node list prior to node.'))
_sample_with_id_build_fail(None, u, [sn], d, None, None,
ValueError('id_ cannot be a value that evaluates to false'))
_sample_with_id_build_fail(id_, None, [sn], d, None, None,
ValueError('user cannot be a value that evaluates to false'))
_sample_with_id_build_fail(id_, u, [sn], None, None, None, ValueError(
'savetime cannot be a value that evaluates to false'))
_sample_with_id_build_fail(id_, u, [sn], datetime.datetime.now(), None, None, ValueError(
'savetime cannot be a naive datetime'))
_sample_with_id_build_fail(id_, u, [sn], d, None, 0, ValueError('version must be > 0'))
def test_get_user_from_object_fail_bad_args():
_get_user_from_object_fail(None, 'us', ValueError('params cannot be None'))
_get_user_from_object_fail({'us': 'foo'}, None, MissingParameterError('key'))
_get_user_from_object_fail({'us': []}, 'us', IllegalParameterError(
'us must be a string if present'))
_get_user_from_object_fail({'us': 'baz\tbaat'}, 'us', IllegalParameterError(
# probably not worth the trouble to change the key name, we'll see
'userid contains control characters'))
def test_get_data_unit_id_from_object_fail_bad_args():
_get_data_unit_id_from_object_fail(None, ValueError('params cannot be None'))
_get_data_unit_id_from_object_fail({}, MissingParameterError('upa'))
_get_data_unit_id_from_object_fail({'upa': '1/0/1'}, IllegalParameterError(
'1/0/1 is not a valid UPA'))
_get_data_unit_id_from_object_fail({'upa': 82}, IllegalParameterError(
'upa key is not a string as required'))
_get_data_unit_id_from_object_fail({'upa': '1/1/1', 'dataid': []}, IllegalParameterError(
'dataid key is not a string as required'))
_get_data_unit_id_from_object_fail({'upa': '1/1/1', 'dataid': 'f\t/b'}, IllegalParameterError(
'dataid contains control characters'))
def test_create_data_link_params_fail_bad_args():
id_ = '706fe9e1-70ef-4feb-bbd9-32295104a119'
_create_data_link_params_fail(None, ValueError('params cannot be None'))
_create_data_link_params_fail({}, MissingParameterError('Sample ID'))
_create_data_link_params_fail({'id': 6}, IllegalParameterError(
'Sample ID 6 must be a UUID string'))
_create_data_link_params_fail({'id': id_[:-1]}, IllegalParameterError(
'Sample ID 706fe9e1-70ef-4feb-bbd9-32295104a11 must be a UUID string'))
_create_data_link_params_fail({'id': id_}, MissingParameterError('version'))
_create_data_link_params_fail(
{'id': id_, 'version': 'ver'},
IllegalParameterError('Illegal version argument: ver'))
_create_data_link_params_fail(
{'id': id_, 'version': -1},
IllegalParameterError('Illegal version argument: -1'))
_create_data_link_params_fail(
{'id': id_, 'version': 1},
MissingParameterError('node'))
_create_data_link_params_fail(
{'id': id_, 'version': 1, 'node': {'a': 'b'}},
IllegalParameterError('node key is not a string as required'))
_create_data_link_params_fail(
{'id': id_, 'version': 1, 'node': 'foo\tbar'},
IllegalParameterError('node contains control characters'))
_create_data_link_params_fail(
{'id': id_, 'version': 1, 'node': 'm'},
MissingParameterError('upa'))
_create_data_link_params_fail(
{'id': id_, 'version': 1, 'node': 'm', 'upa': 3.4},
IllegalParameterError('upa key is not a string as required'))
_create_data_link_params_fail(
{'id': id_, 'version': 1, 'node': 'm', 'upa': '1/0/1'},
IllegalParameterError('1/0/1 is not a valid UPA'))
_create_data_link_params_fail(
{'id': id_, 'version': 1, 'node': 'm', 'upa': '1/1/1', 'dataid': 6},
IllegalParameterError('dataid key is not a string as required'))
_create_data_link_params_fail(
{'id': id_, 'version': 1, 'node': 'm', 'upa': '1/1/1', 'dataid': 'yay\nyo'},
IllegalParameterError('dataid contains control characters'))
def __init__(
self,
nodes: List[SampleNode],
name: Optional[str] = None,
):
'''
Create the the sample.
:param nodes: The tree nodes in the sample. BIOLOGICAL_REPLICATES must come first in
the list, and parents must come before children in the list.
:param name: The name of the sample. Cannot contain control characters or be longer than
255 characters.
:raise MissingParameterError: if no nodes are provided.
:raises IllegalParameterError: if the name is too long or contains illegal characters,
the first node in the list is not a BIOLOGICAL_REPLICATE, all the BIOLOGICAL_REPLICATES
are not at the start of this list, node names are not unique, or parent nodes
do not appear in the list prior to their children.
'''
self.name = _check_string(name,
'name',
max_len=_MAX_SAMPLE_NAME_LEN,
optional=True)
if not nodes:
raise MissingParameterError(
'At least one node per sample is required')
if len(nodes) > _MAX_SAMPLE_NODES:
raise IllegalParameterError(
f'At most {_MAX_SAMPLE_NODES} nodes are allowed per sample')
if nodes[0].type != SubSampleType.BIOLOGICAL_REPLICATE:
raise IllegalParameterError(
f'The first node in a sample must be a {SubSampleType.BIOLOGICAL_REPLICATE.value}'
)
no_more_bio = False
seen_names: _Set[str] = set()
for n in nodes:
if no_more_bio and n.type == SubSampleType.BIOLOGICAL_REPLICATE:
raise IllegalParameterError(
f'{SubSampleType.BIOLOGICAL_REPLICATE.value}s must be the first '
+ 'nodes in the list of sample nodes.')
if n.type != SubSampleType.BIOLOGICAL_REPLICATE:
no_more_bio = True
if n.name in seen_names:
raise IllegalParameterError(
f'Duplicate sample node name: {n.name}')
if n.parent and n.parent not in seen_names:
raise IllegalParameterError(
f'Parent {n.parent} of node {n.name} does not ' +
'appear in node list prior to node.')
seen_names.add(n.name)
self.nodes = tuple(nodes) # make hashable
def test_get_sample_address_from_object_fail_bad_args():
get_sample_address_from_object_fail(None, False, MissingParameterError('Sample ID'))
get_sample_address_from_object_fail({}, False, MissingParameterError('Sample ID'))
get_sample_address_from_object_fail({'id': None}, False, MissingParameterError('Sample ID'))
get_sample_address_from_object_fail({'id': 6}, False, IllegalParameterError(
'Sample ID 6 must be a UUID string'))
get_sample_address_from_object_fail(
{'id': 'f5bd78c3-823e-40b2-9f93-20e78680e41'}, False,
IllegalParameterError(
'Sample ID f5bd78c3-823e-40b2-9f93-20e78680e41 must be a UUID string'))
id_ = 'f5bd78c3-823e-40b2-9f93-20e78680e41e'
get_sample_address_from_object_fail(
{'id': id_}, True, MissingParameterError('version'))
get_sample_address_from_object_fail(
{'id': id_, 'version': [1]}, False, IllegalParameterError('Illegal version argument: [1]'))
get_version_from_object_fail(
{'id': id_, 'version': 'whee'},
True,
IllegalParameterError('Illegal version argument: whee'))
get_version_from_object_fail(
{'id': id_, 'version': 0}, True, IllegalParameterError('Illegal version argument: 0'))
get_version_from_object_fail(
{'id': id_, 'version': -3}, True, IllegalParameterError('Illegal version argument: -3'))
def test_sample_node_build_fail():
# not testing every permutation of failing check_string here, just one test to make sure
# it's there
_sample_node_build_fail('', SubSampleType.BIOLOGICAL_REPLICATE, None,
MissingParameterError('subsample name'))
_sample_node_build_fail('a' * 257, SubSampleType.BIOLOGICAL_REPLICATE, None,
IllegalParameterError('subsample name exceeds maximum length of 256'))
_sample_node_build_fail('a', None, None,
ValueError('type cannot be a value that evaluates to false'))
_sample_node_build_fail('a', SubSampleType.TECHNICAL_REPLICATE, 'b' * 257,
IllegalParameterError('parent exceeds maximum length of 256'))
_sample_node_build_fail(
'a', SubSampleType.BIOLOGICAL_REPLICATE, 'badparent', IllegalParameterError(
'Node a is of type BioReplicate and therefore cannot have a parent'))
_sample_node_build_fail(
'a', SubSampleType.TECHNICAL_REPLICATE, None, IllegalParameterError(
'Node a is of type TechReplicate and therefore must have a parent'))
_sample_node_build_fail(
'a', SubSampleType.SUB_SAMPLE, None, IllegalParameterError(
'Node a is of type SubSample and therefore must have a parent'))
def test_get_upa_from_object_fail_bad_args():
_get_upa_from_object_fail(None, ValueError('params cannot be None'))
_get_upa_from_object_fail({}, MissingParameterError('upa'))
_get_upa_from_object_fail({'upa': '1/0/1'}, IllegalParameterError('1/0/1 is not a valid UPA'))
_get_upa_from_object_fail({'upa': 82}, IllegalParameterError(
'upa key is not a string as required'))
def test_check_string_optional_false():
for string in [None, ' \t ']:
with raises(Exception) as got:
check_string(string, 'var name')
assert_exception_correct(got.value, MissingParameterError('var name'))