def test_serve_daemon(self):
"""Test serving a galaxy tool via a daemon Galaxy process."""
port = network_util.get_free_port()
cat_path = os.path.join(TEST_REPOS_DIR, "single_tool", "cat.xml")
config = galaxy_serve(
self.test_context,
[for_path(cat_path)],
install_galaxy=True,
port=port,
daemon=True,
no_dependency_resolution=True,
)
assert network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
config_dict = config.gi.config.get_config()
assert "allow_user_dataset_purge" in config_dict
config.kill()
assert not network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
def test_serve_daemon(self):
"""Test serving a galaxy tool via a daemon Galaxy process."""
port = network_util.get_free_port()
cat_path = os.path.join(TEST_REPOS_DIR, "single_tool", "cat.xml")
config = galaxy_serve(
self.test_context,
[for_path(cat_path)],
install_galaxy=True,
port=port,
daemon=True,
no_dependency_resolution=True,
)
assert network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
config_dict = config.gi.config.get_config()
assert "allow_user_dataset_purge" in config_dict
config.kill()
assert not network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
def _launch_thread_and_wait(self, func, port):
t = threading.Thread(target=func)
t.daemon = True
t.start()
time.sleep(15)
assert network_util.wait_net_service("127.0.0.1", port)
time.sleep(.1)
assert network_util.wait_net_service("127.0.0.1", port)
def _launch_thread_and_wait(self, func, port):
t = threading.Thread(target=func)
t.daemon = True
t.start()
time.sleep(15)
assert network_util.wait_net_service("127.0.0.1", port)
time.sleep(.1)
assert network_util.wait_net_service("127.0.0.1", port)
def _launch_thread_and_wait(self, func, args=[]):
target = functools.partial(func, args)
port = self._port
t = threading.Thread(target=target)
t.daemon = True
t.start()
time.sleep(10)
assert network_util.wait_net_service("127.0.0.1", port)
time.sleep(.1)
assert network_util.wait_net_service("127.0.0.1", port)
def _launch_thread_and_wait(self, func, args=[]):
target = functools.partial(func, args)
port = self._port
t = threading.Thread(target=target)
t.daemon = True
t.start()
time.sleep(10)
assert network_util.wait_net_service("127.0.0.1", port)
time.sleep(1)
assert network_util.wait_net_service("127.0.0.1", port)
time.sleep(1)
assert network_util.wait_net_service("127.0.0.1", port)
def test_serve(self):
port = network_util.get_free_port()
serve = functools.partial(self._run, port)
t = threading.Thread(target=serve)
t.daemon = True
t.start()
time.sleep(15)
assert network_util.wait_net_service("127.0.0.1", port)
def test_serve(self):
port = network_util.get_free_port()
serve = functools.partial(self._run, port)
t = threading.Thread(target=serve)
t.daemon = True
t.start()
time.sleep(15)
assert network_util.wait_net_service("127.0.0.1", port)
def setup_mock_shed():
port = network_util.get_free_port()
directory = mkdtemp()
model = mock_model(directory)
def run():
app.debug = True
app.config["model"] = model
run_simple('localhost',
port,
app,
use_reloader=False,
use_debugger=True)
t = threading.Thread(target=run)
t.start()
network_util.wait_net_service("localhost", port, DEFAULT_OP_TIMEOUT)
return MockShed("http://localhost:%d" % port, directory, t, model)
def launch_and_wait_for_service(port, func, args=[]):
"""Run func(args) in a thread and wait on port for service.
Service should remain up so check network a few times, this prevents
the code that finds a free port from causing a false positive when
detecting that the port is bound to.
"""
target = functools.partial(func, *args)
t = threading.Thread(target=target)
t.daemon = True
t.start()
time.sleep(5)
assert network_util.wait_net_service("127.0.0.1", port, timeout=600)
time.sleep(1)
assert network_util.wait_net_service("127.0.0.1", port, timeout=600)
time.sleep(1)
assert network_util.wait_net_service("127.0.0.1", port, timeout=600)
return t
def _assert_service_up(config):
assert network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
galaxy_config_api = config.gi.config
config_dict = galaxy_config_api.get_config()
assert "allow_user_dataset_purge" in config_dict
def setup_mock_shed():
port = network_util.get_free_port()
directory = mkdtemp()
model = mock_model(directory)
def run():
app.debug = True
app.config["model"] = model
run_simple(
'localhost',
port,
app,
use_reloader=False,
use_debugger=True
)
t = threading.Thread(target=run)
t.start()
network_util.wait_net_service("localhost", port, DEFAULT_OP_TIMEOUT)
return MockShed("http://localhost:%d" % port, directory, t, model)
def serve(ctx, paths, **kwds):
# TODO: Preceate a user.
# TODO: Setup an admin user.
# TODO: Pass through more parameters.
# TODO: Populate test-data directory as FTP directory.
daemon = kwds.get("daemon", False)
if daemon:
kwds["no_cleanup"] = True
with galaxy_config(ctx, paths, **kwds) as config:
pid_file = config.pid_file
# TODO: Allow running dockerized Galaxy here instead.
setup_venv_command = setup_venv(ctx, kwds)
run_script = os.path.join(config.galaxy_root, "run.sh")
run_script += " $COMMON_STARTUP_ARGS"
if daemon:
run_script += " --pid-file '%s' --daemon" % pid_file
config.env["GALAXY_RUN_ALL"] = "1"
else:
run_script += " --server-name '%s' --reload" % config.server_name
server_ini = os.path.join(config.config_directory, "galaxy.ini")
config.env["GALAXY_CONFIG_FILE"] = server_ini
cd_to_galaxy_command = "cd %s" % config.galaxy_root
cmd = io.shell_join(
cd_to_galaxy_command,
setup_venv_command,
run_script,
)
action = "Starting galaxy"
run_galaxy_command(
ctx,
cmd,
config.env,
action,
)
host = kwds.get("host", "127.0.0.1")
port = kwds.get("port")
assert network_util.wait_net_service(host, port)
time.sleep(.1)
assert network_util.wait_net_service(host, port)
return config
def serve(ctx, paths, **kwds):
# TODO: Preceate a user.
# TODO: Setup an admin user.
# TODO: Pass through more parameters.
# TODO: Populate test-data directory as FTP directory.
daemon = kwds.get("daemon", False)
if daemon:
kwds["no_cleanup"] = True
with galaxy_config(ctx, paths, **kwds) as config:
pid_file = config.pid_file
# TODO: Allow running dockerized Galaxy here instead.
setup_venv_command = setup_venv(ctx, kwds)
run_script = os.path.join(config.galaxy_root, "run.sh")
run_script += " $COMMON_STARTUP_ARGS"
if daemon:
run_script += " --pid-file '%s' --daemon" % pid_file
config.env["GALAXY_RUN_ALL"] = "1"
else:
run_script += " --server-name '%s' --reload" % config.server_name
server_ini = os.path.join(config.config_directory, "galaxy.ini")
config.env["GALAXY_CONFIG_FILE"] = server_ini
cd_to_galaxy_command = "cd %s" % config.galaxy_root
cmd = io.shell_join(
cd_to_galaxy_command,
setup_venv_command,
run_script,
)
action = "Starting galaxy"
run_galaxy_command(
ctx,
cmd,
config.env,
action,
)
host = kwds.get("host", "127.0.0.1")
port = kwds.get("port")
assert network_util.wait_net_service(host, port)
time.sleep(.1)
assert network_util.wait_net_service(host, port)
return config
def _serve(ctx, runnables, **kwds):
engine = kwds.get("engine", "galaxy")
if engine == "docker_galaxy":
kwds["dockerize"] = True
daemon = kwds.get("daemon", False)
if daemon:
kwds["no_cleanup"] = True
with galaxy_config(ctx, runnables, **kwds) as config:
cmd = config.startup_command(ctx, **kwds)
action = "Starting galaxy"
exit_code = run_galaxy_command(
ctx,
cmd,
config.env,
action,
)
if exit_code:
message = "Problem running Galaxy command [%s]." % config.log_contents
io.warn(message)
raise Exception(message)
host = kwds.get("host", "127.0.0.1")
port = kwds.get("port", None)
if port is None:
port = network_util.get_free_port()
ctx.vlog("Waiting for service on (%s, %s)" % (host, port))
assert network_util.wait_net_service(host, port)
time.sleep(.1)
ctx.vlog("Waiting for service on (%s, %s)" % (host, port))
assert network_util.wait_net_service(host, port)
time.sleep(5)
ctx.vlog("Waiting for service on (%s, %s)" % (host, port))
assert network_util.wait_net_service(host, port)
config.install_workflows()
return config
def _serve(ctx, runnables, **kwds):
engine = kwds.get("engine", "galaxy")
if engine == "docker_galaxy":
kwds["dockerize"] = True
daemon = kwds.get("daemon", False)
if daemon:
kwds["no_cleanup"] = True
with galaxy_config(ctx, runnables, **kwds) as config:
cmd = config.startup_command(ctx, **kwds)
action = "Starting galaxy"
exit_code = run_galaxy_command(
ctx,
cmd,
config.env,
action,
)
if exit_code:
message = "Problem running Galaxy command [%s]." % config.log_contents
io.warn(message)
raise Exception(message)
host = kwds.get("host", "127.0.0.1")
port = kwds.get("port", None)
if port is None:
port = network_util.get_free_port()
ctx.vlog("Waiting for service on (%s, %s)" % (host, port))
assert network_util.wait_net_service(host, port)
time.sleep(.1)
ctx.vlog("Waiting for service on (%s, %s)" % (host, port))
assert network_util.wait_net_service(host, port)
time.sleep(5)
ctx.vlog("Waiting for service on (%s, %s)" % (host, port))
assert network_util.wait_net_service(host, port)
config.install_workflows()
return config
def test_serve_daemon(self):
port = network_util.get_free_port()
cat_path = os.path.join(TEST_REPOS_DIR, "single_tool", "cat.xml")
config = galaxy_serve(
self.test_context,
cat_path,
install_galaxy=True,
port=port,
daemon=True,
)
assert network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
config_dict = config.gi.config.get_config()
assert "allow_user_dataset_purge" in config_dict
config.kill()
assert not network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
def test_serve_profile(self):
port = network_util.get_free_port()
pid_file = os.path.join(self._home, "test.pid")
extra_args = [
"--daemon", "--pid_file", pid_file, "--profile", "moo",
]
serve = functools.partial(self._run, port, extra_args)
self._launch_thread_and_wait(serve, port)
assert network_util.wait_net_service("127.0.0.1", port)
admin_gi = api.gi(port)
user_api_key = api.user_api_key(admin_gi)
user_gi = api.gi(port, user_api_key)
assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
user_gi.histories.create_history(TEST_HISTORY_NAME)
kill_pid_file(pid_file)
self._launch_thread_and_wait(serve, port)
assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 1
def test_shed_serve_daemon(self):
port = network_util.get_free_port()
fastqc_path = os.path.join(TEST_REPOS_DIR, "fastqc")
ctx = self.test_context
install_args_list = shed.install_arg_lists(
ctx, [fastqc_path],
shed_target="toolshed",
)
with shed_serve(
ctx, install_args_list,
port=port,
skip_dependencies=True,
install_galaxy=True,
) as config:
assert network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)
def test_serve_profile(self):
port = network_util.get_free_port()
pid_file = os.path.join(self._home, "test.pid")
extra_args = [
"--daemon",
"--pid_file",
pid_file,
"--profile",
"moo",
]
serve = functools.partial(self._run, port, extra_args)
self._launch_thread_and_wait(serve, port)
assert network_util.wait_net_service("127.0.0.1", port)
admin_gi = api.gi(port)
user_api_key = api.user_api_key(admin_gi)
user_gi = api.gi(port, user_api_key)
assert len(
user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
user_gi.histories.create_history(TEST_HISTORY_NAME)
kill_pid_file(pid_file)
self._launch_thread_and_wait(serve, port)
assert len(
user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 1
def _assert_service_down(config):
assert not network_util.wait_net_service(
"localhost",
config.port,
timeout=.1,
)