def test_timeout_backoff():
condition = WaitCondition(after_call_count=4, return_value="second")
sleeper = Sleeper()
exception_called = False
try:
wait_on(condition, "condition", 8, delta=2, polling_backoff=1, sleep_=sleeper.sleep)
except TimeoutAssertionError:
exception_called = True
assert len(sleeper.sleeps) == 3
assert sleeper.sleeps[0] == 2 # delta of 2
assert sleeper.sleeps[1] == 3 # delta of 2 + 1 backoff
assert sleeper.sleeps[2] == 4 # delta of 2 + 2 backoff
assert exception_called
def test_timeout_third_call():
condition = WaitCondition(after_call_count=4, return_value="second")
sleeper = Sleeper()
exception_called = False
try:
wait_on(condition, "condition", 5, delta=2, sleep_=sleeper.sleep)
except TimeoutAssertionError:
exception_called = True
assert len(sleeper.sleeps) == 3
assert sleeper.sleeps[0] == 2 # delta of 2
assert sleeper.sleeps[1] == 2 # delta of 2
assert sleeper.sleeps[2] == 2 # delta of 2
assert exception_called
def test_timeout_first_call():
condition = WaitCondition(after_call_count=1, return_value="second")
sleeper = Sleeper()
exception_called = False
try:
wait_on(condition, "never met condition", 1, delta=2, sleep_=sleeper.sleep)
except TimeoutAssertionError as e:
assert "never met condition" in str(e)
assert "after 2.0 seconds" in str(e)
exception_called = True
assert len(sleeper.sleeps) == 1
assert sleeper.sleeps[0] == 2 # delta of 2
assert exception_called
def test_application_stack_post_fork(monkeypatch):
app = GalaxyDataTestApp()
monkeypatch.setenv("SERVER_SOFTWARE", SERVER_SOFTWARE)
monkeypatch.setenv("GUNICORN_WORKER_ID", "100")
monkeypatch.setattr(GunicornApplicationStack, "do_post_fork", True)
stack_instance = application_stack_instance(app=app, config=app.config)
assert isinstance(stack_instance, GunicornApplicationStack)
stack_instance.register_postfork_function(
lambda: stack_instance.set_postfork_server_name(app))
assert not app.config.server_name.endswith(".100")
stack_instance.late_postfork()
stack_instance.late_postfork_event.set()
wait_on(lambda: app.config.server_name.endswith(".100") or None,
desc="server name to change",
timeout=1,
delta=0.1)
def test_return_on_third_call():
condition = WaitCondition(after_call_count=2, return_value="second")
sleeper = Sleeper()
assert "second" == wait_on(condition, "condition", 5, delta=2, sleep_=sleeper.sleep)
assert len(sleeper.sleeps) == 2
assert sleeper.sleeps[0] == 2 # delta of 2
assert sleeper.sleeps[1] == 2 # delta of 2
def test_immediate_return():
condition = WaitCondition(return_value="first")
sleeper = Sleeper()
assert "first" == wait_on(condition,
"condition",
100,
sleep_=sleeper.sleep)
assert len(sleeper.sleeps) == 0
import bioblend.galaxy
from galaxy.tool_util.verify.wait import wait_on
log = logging.getLogger('__name__')
N_CHARS = int(os.environ.get('N_CHARS', 14))
N_THREADS = os.environ.get('N_THREADS', 1)
GALAXY_URL = os.environ.get('GALAXY_URL', 'https://your-galaxy')
GALAXY_API_KEY = os.environ.get('GALAXY_API_KEY', 'adminkey')
log.debug(f"Running test tool with {N_CHARS} input dataset")
gi = bioblend.galaxy.GalaxyInstance(GALAXY_URL, GALAXY_API_KEY)
history_id = gi.histories.create_history('test_history')['id']
job = gi.tools.paste_content('A' * N_CHARS, history_id=history_id)
hda_id = job['outputs'][0]['id']
rval = gi.tools.run_tool(history_id, 'testing',
{'input1': {
'src': 'hda',
'id': hda_id
}})
job_id = rval['jobs'][0]['id']
wait_on(lambda: gi.jobs.show_job(job_id)['state'] == 'ok',
'waiting for test job',
timeout=60)
output_id = rval['outputs'][0]['id']
gi.datasets.download_dataset(output_id)
output = gi.datasets.download_dataset(output_id).decode()
assert output == f"Running with '{N_THREADS}' threads\n", f"expecting {N_THREADS} threads, but output was {output}"
