def test_to_synapse_annotations__called_convert_to_annotations_list(mock_convert_to_annotations_list):
"""Test the helper function _convert_to_annotations_list called properly"""
a = Annotations('syn123', '7bdb83e9-a50a-46e4-987a-4962559f090f',
{'foo': 'bar', 'zoo': ['zing', 'zaboo'], 'species': 'Platypus'})
to_synapse_annotations(a)
mock_convert_to_annotations_list.assert_called_once_with({'foo': 'bar', 'zoo': ['zing', 'zaboo'],
'species': 'Platypus'})
def test_annotations():
"""Test string annotations"""
a = Annotations('syn123', '7bdb83e9-a50a-46e4-987a-4962559f090f', {
'foo': 'bar',
'zoo': ['zing', 'zaboo'],
'species': 'Platypus'
})
sa = to_synapse_annotations(a)
expected = {
'id': 'syn123',
'etag': '7bdb83e9-a50a-46e4-987a-4962559f090f',
'annotations': {
'foo': {
'value': ['bar'],
'type': 'STRING'
},
'zoo': {
'value': ['zing', 'zaboo'],
'type': 'STRING'
},
'species': {
'value': ['Platypus'],
'type': 'STRING'
}
}
}
assert expected == sa
def test_annotations_unicode():
a = Annotations(
'syn123', '7bdb83e9-a50a-46e4-987a-4962559f090f', {
'files': [u'文件.txt'],
'cacheDir': u'/Users/chris/.synapseCache/python/syn1809087',
u'foo': 1266
})
sa = to_synapse_annotations(a)
expected = {
'id': 'syn123',
'etag': '7bdb83e9-a50a-46e4-987a-4962559f090f',
'annotations': {
'cacheDir': {
'type': 'STRING',
'value': ['/Users/chris/.synapseCache/python/syn1809087']
},
'files': {
'type': 'STRING',
'value': ['文件.txt']
},
'foo': {
'type': 'LONG',
'value': ['1266']
}
}
}
assert expected == sa
def test_to_synapse_annotations__empty():
python_client_annos = Annotations('syn123', '7bdb83e9-a50a-46e4-987a-4962559f090f', {})
assert (
{
'id': 'syn123',
'etag': '7bdb83e9-a50a-46e4-987a-4962559f090f',
'annotations': {}
} == to_synapse_annotations(python_client_annos)
)
def test_idempotent_annotations():
"""test that to_synapse_annotations won't mess up a dictionary that's already in the synapse format"""
a = Annotations('syn123', '7bdb83e9-a50a-46e4-987a-4962559f090f',
{'species': 'Moose', 'n': 42, 'birthday': Datetime(1969, 4, 28), 'fact': True})
sa = to_synapse_annotations(a)
a2 = {}
a2.update(sa)
sa2 = to_synapse_annotations(a2)
assert sa == sa2
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_more_annotations():
"""Test long, float and data annotations"""
a = Annotations(
'syn123', '7bdb83e9-a50a-46e4-987a-4962559f090f', {
'foo':
1234,
'zoo': [123.1, 456.2, 789.3],
'species':
'Platypus',
'birthdays': [
Datetime(1969, 4, 28),
Datetime(1973, 12, 8),
Datetime(2008, 1, 3)
],
'test_boolean':
True,
'test_mo_booleans': [False, True, True, False]
})
sa = to_synapse_annotations(a)
expected = {
'id': 'syn123',
'etag': '7bdb83e9-a50a-46e4-987a-4962559f090f',
'annotations': {
'foo': {
'value': ['1234'],
'type': 'LONG'
},
'zoo': {
'value': ['123.1', '456.2', '789.3'],
'type': 'DOUBLE'
},
'species': {
'value': ['Platypus'],
'type': 'STRING'
},
'birthdays': {
'value': ['-21427200000', '124156800000', '1199318400000'],
'type': 'TIMESTAMP_MS'
},
'test_boolean': {
'value': ['true'],
'type': 'STRING'
},
'test_mo_booleans': {
'value': ['false', 'true', 'true', 'false'],
'type': 'STRING'
}
}
}
assert expected == sa
def test_submission_status_annotations_round_trip():
april_28_1969 = Datetime(1969, 4, 28)
a = Annotations(
'syn123', '7bdb83e9-a50a-46e4-987a-4962559f090f', {
'screen_name': 'Bullwinkle',
'species': 'Moose',
'lucky': 13,
'pi': pi,
'birthday': april_28_1969
})
sa = to_submission_status_annotations(a)
assert {'screen_name',
'species'} == set([kvp['key'] for kvp in sa['stringAnnos']])
assert {'Bullwinkle',
'Moose'} == set([kvp['value'] for kvp in sa['stringAnnos']])
# test idempotence
assert sa == to_submission_status_annotations(sa)
assert {'lucky',
'birthday'} == set([kvp['key'] for kvp in sa['longAnnos']])
for kvp in sa['longAnnos']:
key = kvp['key']
value = kvp['value']
if key == 'lucky':
assert value == 13
if key == 'birthday':
assert utils.from_unix_epoch_time(value) == april_28_1969
assert {'pi'} == set([kvp['key'] for kvp in sa['doubleAnnos']])
assert {pi} == set([kvp['value'] for kvp in sa['doubleAnnos']])
set_privacy(sa, key='screen_name', is_private=False)
pytest.raises(KeyError,
set_privacy,
sa,
key='this_key_does_not_exist',
is_private=False)
for kvp in sa['stringAnnos']:
if kvp['key'] == 'screen_name':
assert not kvp['isPrivate']
a2 = from_submission_status_annotations(sa)
# TODO: is there a way to convert dates back from longs automatically?
a2['birthday'] = utils.from_unix_epoch_time(a2['birthday'])
assert a == a2
# test idempotence
assert a == from_submission_status_annotations(a)
def test__None_id_and_etag(self):
# in constuctor
pytest.raises(ValueError, Annotations, 'syn123', None)
pytest.raises(ValueError, Annotations, None, '0f2977b9-0261-4811-a89e-c13e37ce4604')
# after constuction
annot = Annotations('syn123', '0f2977b9-0261-4811-a89e-c13e37ce4604', {'asdf': 'qwerty'})
def change_id_to_None():
annot.id = None
pytest.raises(ValueError, change_id_to_None)
def change_etag_to_None():
annot.etag = None
pytest.raises(ValueError, change_etag_to_None)
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 test_annotations(self):
annot = Annotations('syn123', '0f2977b9-0261-4811-a89e-c13e37ce4604', {'asdf': 'qwerty'})
assert 'syn123' == annot.id
assert '0f2977b9-0261-4811-a89e-c13e37ce4604' == annot.etag
assert {'asdf': 'qwerty'} == annot
