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_idempotent_annotations():
"""test that to_synapse_annotations won't mess up a dictionary that's already in the synapse format"""
a = dict(species='Moose', n=42, birthday=Datetime(1969, 4, 28))
sa = to_synapse_annotations(a)
a2 = dict()
a2.update(sa)
sa2 = to_synapse_annotations(a2)
assert_equals(sa, sa2)
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_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_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_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():
"""Test string annotations"""
a = dict(foo='bar', zoo=['zing', 'zaboo'], species='Platypus')
sa = to_synapse_annotations(a)
assert_equals(sa['stringAnnotations']['foo'], ['bar'])
assert_equals(sa['stringAnnotations']['zoo'], ['zing', 'zaboo'])
assert_equals(sa['stringAnnotations']['species'], ['Platypus'])
def test_annotations():
"""Test string annotations"""
a = dict(foo='bar', zoo=['zing', 'zaboo'], species='Platypus')
sa = to_synapse_annotations(a)
assert sa['stringAnnotations']['foo'] == ['bar']
assert sa['stringAnnotations']['zoo'] == ['zing', 'zaboo']
assert sa['stringAnnotations']['species'] == ['Platypus']
def update_submission_status(sub_status: SubmissionStatus,
values: typing.Union[Annotations, dict],
status: str = None) -> SubmissionStatus:
"""Updates submission status and annotations
Args:
sub_status: A synapseclient.SubmissionStatus
values: A synapseclient.Annotations or dict
status: A submission status (e.g. RECEIVED, SCORED...)
Returns:
A updated synapseclient.SubmissionStatus
"""
if status is not None:
sub_status.status = status
existing = sub_status.get("submissionAnnotations", {})
# Convert to synapseclient.Annotation class
existing_annotations = _convert_to_annotation_cls(sub_status, existing)
new_annotations = _convert_to_annotation_cls(sub_status, values)
# Can use dict.update to update annotations
existing_annotations.update(new_annotations)
# Must turn synapseclient.Annotation into a synapse style annotations
syn_annotations = to_synapse_annotations(existing_annotations)
sub_status.submissionAnnotations = syn_annotations
return sub_status
def test_more_annotations():
"""Test long, float and data annotations"""
a = dict(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)
print sa
assert sa['longAnnotations']['foo'] == [1234]
assert sa['doubleAnnotations']['zoo'] == [123.1, 456.2, 789.3]
assert sa['stringAnnotations']['species'] == ['Platypus']
assert sa['stringAnnotations']['test_boolean'] == ['true']
assert sa['stringAnnotations']['test_mo_booleans'] == [
'false', 'true', 'true', 'false'
]
## this part of the test is kinda fragile. It it breaks again, it should be removed
bdays = [
utils.from_unix_epoch_time(t)
for t in sa['dateAnnotations']['birthdays']
]
assert all([
t in bdays for t in
[Datetime(1969, 4, 28),
Datetime(1973, 12, 8),
Datetime(2008, 1, 3)]
])
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)
a2 = from_synapse_annotations(sa)
assert a2['foo'][0] == '1'
assert a2['foo'][1] == 'a'
assert a2['foo'][2].find('1969') > -1
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_annotations_unicode():
a = {
'files': [u'tmp6y5tVr.txt'],
'cacheDir': u'/Users/chris/.synapseCache/python/syn1809087',
u'foo': 1266
}
sa = to_synapse_annotations(a)
assert_equals(sa['stringAnnotations']['cacheDir'],
[u'/Users/chris/.synapseCache/python/syn1809087'])
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_more_annotations():
"""Test long, float and data annotations"""
a = dict(foo=1234, zoo=[123.1, 456.2, 789.3], species='Platypus', birthdays=[Datetime(1969,4,28), Datetime(1973,12,8), Datetime(2008,1,3)])
sa = to_synapse_annotations(a)
# print sa
assert sa['longAnnotations']['foo'] == [1234]
assert sa['doubleAnnotations']['zoo'] == [123.1, 456.2, 789.3]
assert sa['stringAnnotations']['species'] == ['Platypus']
## this part of the test is kinda fragile. It it breaks again, it should be removed
bdays = [utils.from_unix_epoch_time(t) for t in sa['dateAnnotations']['birthdays']]
assert all([t in bdays for t in [Datetime(1969,4,28), Datetime(1973,12,8), Datetime(2008,1,3)]])
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_more_annotations():
"""Test long, float and data annotations"""
a = dict(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)
assert_equals(sa['longAnnotations']['foo'], [1234])
assert_equals(sa['doubleAnnotations']['zoo'], [123.1, 456.2, 789.3])
assert_equals(sa['stringAnnotations']['species'], ['Platypus'])
assert_equals(sa['stringAnnotations']['test_boolean'], ['true'])
assert_equals(sa['stringAnnotations']['test_mo_booleans'], ['false', 'true', 'true', 'false'])
# this part of the test is kinda fragile. It it breaks again, it should be removed
bdays = [utils.from_unix_epoch_time(t) for t in sa['dateAnnotations']['birthdays']]
assert_true(all([t in bdays for t in [Datetime(1969, 4, 28), Datetime(1973, 12, 8), Datetime(2008, 1, 3)]]))
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 json(self, ensure_ascii=True):
"""Overloaded json function, turning submissionAnnotations into
synapse style annotations"""
json_dict = self
# If not synapse annotations, turn them into synapseclient.Annotations
# must have id and etag to turn into synapse annotations
if not is_synapse_annotations(self.submissionAnnotations):
json_dict = self.copy()
annotations = _convert_to_annotation_cls(
id=self.id, etag=self.etag, values=self.submissionAnnotations)
# Turn into synapse annotation
json_dict['submissionAnnotations'] = to_synapse_annotations(
annotations)
return json.dumps(json_dict,
sort_keys=True,
indent=2,
ensure_ascii=ensure_ascii)
def test_annotations_unicode():
a = {'files': [u'tmp6y5tVr.txt'], 'cacheDir': u'/Users/chris/.synapseCache/python/syn1809087', u'foo': 1266}
sa = to_synapse_annotations(a)
assert sa['stringAnnotations']['cacheDir'] == [u'/Users/chris/.synapseCache/python/syn1809087']
