def test_submission_status_annotations_round_trip():
april_28_1969 = Datetime(1969, 4, 28)
a = dict(screen_name='Bullwinkle',
species='Moose',
lucky=13,
pi=pi,
birthday=april_28_1969)
sa = to_submission_status_annotations(a)
print sa
assert set(['screen_name',
'species']) == set([kvp['key'] for kvp in sa['stringAnnos']])
assert set(['Bullwinkle',
'Moose']) == set([kvp['value'] for kvp in sa['stringAnnos']])
## test idempotence
assert sa == to_submission_status_annotations(sa)
assert set(['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 set(['pi']) == set([kvp['key'] for kvp in sa['doubleAnnos']])
assert set([pi]) == set([kvp['value'] for kvp in sa['doubleAnnos']])
set_privacy(sa, key='screen_name', is_private=False)
assert_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 kvp['isPrivate'] == False
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_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 cast_values(values, headers):
"""
Convert a row of table query results from strings to the correct column type.
See: http://rest.synapse.org/org/sagebionetworks/repo/model/table/ColumnType.html
"""
if len(values) != len(headers):
raise ValueError('Each field in the row must have a matching column header. %d fields, %d headers' % (len(values), len(headers)))
result = []
for header, field in izip(headers, values):
columnType = header.get('columnType', 'STRING')
## convert field to column type
if field is None or field=='':
result.append(None)
elif columnType in ['STRING', 'ENTITYID', 'FILEHANDLEID']:
result.append(field)
elif columnType=='DOUBLE':
result.append(float(field))
elif columnType=='INTEGER':
result.append(int(field))
elif columnType=='BOOLEAN':
result.append(to_boolean(field))
elif columnType=='DATE':
result.append(utils.from_unix_epoch_time(field))
else:
raise ValueError("Unknown column type: %s" % columnType)
return result
def cast_values(values, headers):
"""
Convert a row of table query results from strings to the correct column type.
See: http://rest.synapse.org/org/sagebionetworks/repo/model/table/ColumnType.html
"""
if len(values) != len(headers):
raise ValueError(
'Each field in the row must have a matching column header. %d fields, %d headers'
% (len(values), len(headers)))
result = []
for header, field in izip(headers, values):
columnType = header.get('columnType', 'STRING')
## convert field to column type
if field is None or field == '':
result.append(None)
elif columnType in ['STRING', 'ENTITYID', 'FILEHANDLEID']:
result.append(field)
elif columnType == 'DOUBLE':
result.append(float(field))
elif columnType == 'INTEGER':
result.append(int(field))
elif columnType == 'BOOLEAN':
result.append(to_boolean(field))
elif columnType == 'DATE':
result.append(utils.from_unix_epoch_time(field))
else:
raise ValueError("Unknown column type: %s" % columnType)
return result
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_submission_status_annotations_round_trip():
from math import pi
april_28_1969 = Datetime(1969,4,28)
a = dict(screen_name='Bullwinkle', species='Moose', lucky=13, pi=pi, birthday=april_28_1969)
sa = to_submission_status_annotations(a)
print sa
assert set(['screen_name','species']) == set([kvp['key'] for kvp in sa['stringAnnos']])
assert set(['Bullwinkle','Moose']) == set([kvp['value'] for kvp in sa['stringAnnos']])
## test idempotence
assert sa == to_submission_status_annotations(sa)
assert set(['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
set(['pi']) == set([kvp['key'] for kvp in sa['doubleAnnos']])
set([pi]) == set([kvp['value'] for kvp in sa['doubleAnnos']])
set_privacy(sa, key='screen_name', is_private=False)
assert_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 kvp['isPrivate'] == False
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)
