def openbis_instance():
instance = Openbis("http://localhost:20000")
print("\nLOGGING IN...")
instance.login('admin', 'anypassword')
yield instance
instance.logout()
print("LOGGED OUT...")
def test_token(openbis_instance):
assert openbis_instance.hostname is not None
new_instance = Openbis(openbis_instance.url)
new_instance.login('admin', 'any_test_password')
assert new_instance.token is not None
assert new_instance.is_token_valid() is True
new_instance.logout()
assert new_instance.is_token_valid() is False
invalid_connection = Openbis(openbis_instance.url)
with pytest.raises(Exception):
invalid_connection.login('invalid_username', 'invalid_password')
assert invalid_connection.token is None
assert invalid_connection.is_token_valid() is False
run_minvar(o, samples_to_analyse, tqdm_out, files_to_delete)
logging.info('-----------RETROSEQ Analysis session finished-----------')
#time.sleep(300)
logging.info('-----------CONSENSUS Analysis session starting-----------')
# Fetch all consensus samples that are mapped
res_test_mapped = o.get_experiment(
'/IMV/CONSENSUS/CONSENSUS_INFO').get_samples(mapped=True)
rtm = set(res_test_mapped.df['identifier'])
# All consensus samples that have already been analyzed
try:
res_test_analysed = o.get_experiment(
'/IMV/CONSENSUS/CONSENSUS_INFO').get_samples(mapped=True,
analysed=True)
rta = set(res_test_analysed.df['identifier'])
except ValueError:
rta = set()
logging.info('Found %d mapped samples', len(rtm))
logging.info('Found %d analysed samples', len(rta))
samples_to_analyse = list(rtm - rta)[:analyses_per_run]
logging.info('CONSENSUS Analysis will proceed on %d samples',
len(samples_to_analyse))
files_to_delete = [] # store files that will be deleted at the end
run_smaltalign(o, samples_to_analyse, tqdm_out, files_to_delete)
logging.info('-----------CONSENSUS Analysis session finished-----------')
o.logout()