def test_round_trip_annotations():
"""Test that annotations can make the round trip from a simple dictionary to the synapse format and back"""
a = dict(foo=1234, zoo=[123.1, 456.2, 789.3], species='Moose',
birthdays=[Datetime(1969, 4, 28), Datetime(1973, 12, 8), Datetime(2008, 1, 3), Datetime(2013, 3, 15)])
sa = to_synapse_annotations(a)
a2 = from_synapse_annotations(sa)
a = a2
def test_mixed_annotations():
"""test that to_synapse_annotations will coerce a list of mixed types to strings"""
a = dict(foo=[1, 'a', Datetime(1969, 4, 28, 11, 47)])
sa = to_synapse_annotations(a)
a2 = from_synapse_annotations(sa)
assert a2['foo'][0] == '1'
assert a2['foo'][1] == 'a'
assert a2['foo'][2].find('1969') > -1
def test_from_synapse_annotations__empty():
ssa = {'id': 'syn123',
'etag': '7bdb83e9-a50a-46e4-987a-4962559f090f',
'annotations': {}}
annos = from_synapse_annotations(ssa)
assert {} == annos
assert 'syn123' == annos.id
assert '7bdb83e9-a50a-46e4-987a-4962559f090f' == annos.etag
def test_mixed_annotations():
"""test that to_synapse_annotations will coerce a list of mixed types to strings"""
a = dict(foo=[1, 'a', Datetime(1969, 4, 28, 11, 47)])
sa = to_synapse_annotations(a)
a2 = from_synapse_annotations(sa)
assert_equals(a2['foo'][0], '1')
assert_equals(a2['foo'][1], 'a')
assert_greater(a2['foo'][2].find('1969'), -1)
def test_mixed_annotations():
"""test that to_synapse_annotations will coerce a list of mixed types to strings"""
a = dict(foo=[1, 'a', Datetime(1969,4,28,11,47)])
sa = to_synapse_annotations(a)
# print(sa)
a2 = from_synapse_annotations(sa)
# print(a2)
assert a2['foo'][0] == '1'
assert a2['foo'][1] == 'a'
assert a2['foo'][2].find('1969') > -1
def test_mixed_annotations():
"""test that to_synapse_annotations will coerce a list of mixed types to strings"""
a = Annotations('syn123', '7bdb83e9-a50a-46e4-987a-4962559f090f',
{'foo': [1, 'a', Datetime(1969, 4, 28, 11, 47)]})
sa = to_synapse_annotations(a)
a2 = from_synapse_annotations(sa)
assert a2['foo'][0] == '1'
assert a2['foo'][1] == 'a'
assert a2['foo'][2].find('1969') > -1
assert 'syn123' == a2.id
assert '7bdb83e9-a50a-46e4-987a-4962559f090f' == a2.etag
def test_annotation_name_collision():
"""Test handling of a name collisions between typed user generated and untyped
system generated annotations, see SYNPY-203 and PLFM-3248"""
## order is important: to repro the erro, the key uri has to come before stringAnnotations
sa = OrderedDict()
sa[u'uri'] = u'/entity/syn47396/annotations'
sa[u'doubleAnnotations'] = {}
sa[u'longAnnotations'] = {}
sa[u'stringAnnotations'] = {
'tissueType': ['Blood'],
'uri': ['/repo/v1/dataset/47396']}
sa[u'creationDate'] = u'1321168909232'
sa[u'id'] = u'syn47396'
a = from_synapse_annotations(sa)
assert a['tissueType'] == ['Blood']
def _convert_to_annotation_cls(
id: str, etag: str, values: typing.Union[Annotations,
dict]) -> Annotations:
"""Convert synapse style annotation or dict to synapseclient.Annotation
:param id: The id of the entity / submission
:param etag: The etag of the entity / submission
:param values: A synapseclient.Annotations or dict
:returns: A synapseclient.Annotations
"""
if isinstance(values, Annotations):
return values
if is_synapse_annotations(values):
values = from_synapse_annotations(values)
else:
values = Annotations(id=id, etag=etag, values=values)
return values
def test_round_trip_annotations():
"""Test that annotations can make the round trip from a simple dictionary to the synapse format and back"""
a = Annotations(
'syn123', '7bdb83e9-a50a-46e4-987a-4962559f090f', {
'foo': [1234],
'zoo': [123.1, 456.2, 789.3],
'species': ['Moose'],
'birthdays': [
Datetime(1969, 4, 28),
Datetime(1973, 12, 8),
Datetime(2008, 1, 3),
Datetime(2013, 3, 15)
]
})
sa = to_synapse_annotations(a)
a2 = from_synapse_annotations(sa)
assert a == a2
assert a.id == a2.id
assert a.etag == a2.etag
def _convert_to_annotation_cls(
sub_status: SubmissionStatus,
values: typing.Union[Annotations, dict]) -> Annotations:
"""Convert synapse style annotation or dict to synapseclient.Annotation
Args:
sub_status: A synapseclient.SubmissionStatus
values: A synapseclient.Annotations or dict
Returns:
A synapseclient.Annotations
"""
if isinstance(values, Annotations):
return values
if is_synapse_annotations(values):
values = from_synapse_annotations(values)
else:
values = Annotations(id=sub_status.id,
etag=sub_status.etag,
values=values)
return values
