class TestKB(KBObjectCreator):
def __init__(self, name):
super(TestKB, self).__init__(name)
self.kill_list = []
def setUp(self):
self.kb = KB(driver='omero')(OME_HOST, OME_USER, OME_PASS)
def tearDown(self):
self.kill_list.reverse()
for x in self.kill_list:
self.kb.delete(x)
self.kill_list = []
def check_object(self, o, conf, otype):
try:
self.assertTrue(isinstance(o, otype))
for k in conf.keys():
v = conf[k]
# FIXME this is omero specific...
if hasattr(v, 'ome_obj'):
self.assertEqual(getattr(o, k).id, v.id)
self.assertEqual(type(getattr(o, k)), type(v))
elif hasattr(v, '_id'):
self.assertEqual(getattr(o, k)._id, v._id)
else:
self.assertEqual(getattr(o, k), v)
except:
pass
def test_parallel_save(self):
aconf, action = self.create_action()
self.kill_list.append(action.save())
N = 1000
people = []
for i in range(N):
conf, i = self.create_individual(action=action,
gender=self.kb.Gender.MALE)
self.kill_list.append(i)
people.append(i)
start = time.time()
self.kb.save_array(people)
print ' \n\ttime needed to save %s object: %s' % (N,
time.time() - start)
class TestKB(KBObjectCreator):
def __init__(self, name):
super(TestKB, self).__init__(name)
self.kill_list = []
def setUp(self):
self.kb = KB(driver='omero')(OME_HOST, OME_USER, OME_PASS)
def tearDown(self):
self.kill_list.reverse()
for x in self.kill_list:
self.kb.delete(x)
self.kill_list = []
def check_object(self, o, conf, otype):
try:
self.assertTrue(isinstance(o, otype))
for k in conf.keys():
v = conf[k]
# FIXME this is omero specific...
if hasattr(v, 'ome_obj'):
self.assertEqual(getattr(o, k).id, v.id)
self.assertEqual(type(getattr(o, k)), type(v))
elif hasattr(v, '_id'):
self.assertEqual(getattr(o, k)._id, v._id)
else:
self.assertEqual(getattr(o, k), v)
except:
pass
def test_parallel_save(self):
aconf, action = self.create_action()
self.kill_list.append(action.save())
N = 1000
people = []
for i in range(N):
conf, i = self.create_individual(action=action,
gender=self.kb.Gender.MALE)
self.kill_list.append(i)
people.append(i)
start = time.time()
self.kb.save_array(people)
print' \n\ttime needed to save %s object: %s' % (N, time.time() - start)
for en_code1, en_code2 in couples:
logger.info('Swapping couple %s - %s' % (en_code1, en_code2))
try:
en1 = en_lookup[en_code1]
en2 = en_lookup[en_code2]
except KeyError, ke:
logger.error('Code %s not found in study %s' % (ke, args.study))
sys.exit(2)
logger.info('Starting swap procedure for couple %s -- %s' %
(en_code1, en_code2))
logger.debug('Enrollment %s --- Individual ID %s' %
(en1.studyCode, en1.individual.id))
logger.debug('Enrollment %s --- Individual ID %s' %
(en2.studyCode, en2.individual.id))
en1.individual, en2.individual = en2.individual, en1.individual
kb.save_array([en1, en2])
logger.info('Swap completed')
kb.reload_object(en1)
logger.debug('Enrollment %s --- Individual ID %s' %
(en1.studyCode, en1.individual.id))
kb.reload_object(en2)
logger.debug('Enrollment %s --- Individual ID %s' %
(en2.studyCode, en2.individual.id))
if __name__ == '__main__':
main(sys.argv[1:])
for en_code1, en_code2 in couples:
logger.info('Swapping couple %s - %s' % (en_code1, en_code2))
try:
en1 = en_lookup[en_code1]
en2 = en_lookup[en_code2]
except KeyError, ke:
logger.error('Code %s not found in study %s' % (ke, args.study))
sys.exit(2)
logger.info('Starting swap procedure for couple %s -- %s' % (en_code1, en_code2))
logger.debug('Enrollment %s --- Individual ID %s' % (en1.studyCode,
en1.individual.id))
logger.debug('Enrollment %s --- Individual ID %s' % (en2.studyCode,
en2.individual.id))
en1.individual, en2.individual = en2.individual, en1.individual
kb.save_array([en1, en2])
logger.info('Swap completed')
kb.reload_object(en1)
logger.debug('Enrollment %s --- Individual ID %s' % (en1.studyCode,
en1.individual.id))
kb.reload_object(en2)
logger.debug('Enrollment %s --- Individual ID %s' % (en2.studyCode,
en2.individual.id))
if __name__ == '__main__':
main(sys.argv[1:])