def test_serve_daemon(self):
extra_args = ["--daemon", "--pid_file", self._pid_file]
self._launch_thread_and_wait(self._run, extra_args)
user_gi = self._user_gi
assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
user_gi.histories.create_history(TEST_HISTORY_NAME)
kill_pid_file(self._pid_file)
def test_serve_daemon(self):
extra_args = ["--daemon", "--pid_file", self._pid_file]
self._launch_thread_and_wait(self._run, extra_args)
user_gi = self._user_gi
assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
user_gi.histories.create_history(TEST_HISTORY_NAME)
kill_pid_file(self._pid_file)
def cli_daemon_galaxy(runner, pid_file, port, command_list, exit_code=0):
t = launch_and_wait_for_galaxy(port,
check_exit_code,
args=[runner, command_list, exit_code])
yield
io.kill_pid_file(pid_file)
t.join(timeout=60)
def cli_daemon_galaxy(runner, pid_file, port, command_list, exit_code=0):
future = launch_and_wait_for_galaxy(port,
check_exit_code,
args=[runner, command_list, exit_code])
yield
io.kill_pid_file(pid_file)
_wait_on_future_suppress_exception(future)
def kill(self):
if self._ctx.verbose:
shell(["ps", "ax"])
exists = os.path.exists(self.pid_file)
print("Killing pid file [%s]" % self.pid_file)
print("pid_file exists? [%s]" % exists)
if exists:
print("pid_file contents are [%s]" % open(self.pid_file, "r").read())
kill_pid_file(self.pid_file)
def _test_serve_profile(self, *db_options):
new_profile = "planemo_test_profile_%s" % uuid.uuid4()
extra_args = [
"--daemon",
"--pid_file", self._pid_file,
"--profile", new_profile,
]
extra_args.extend(db_options)
self._launch_thread_and_wait(self._run, extra_args)
user_gi = self._user_gi
assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
user_gi.histories.create_history(TEST_HISTORY_NAME)
kill_pid_file(self._pid_file)
self._launch_thread_and_wait(self._run, extra_args)
assert len(user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 1
def test_shed_serve(self):
extra_args = ["--daemon", "--pid_file", self._pid_file, "--shed_target", "toolshed"]
fastqc_path = os.path.join(TEST_REPOS_DIR, "fastqc")
self._serve_artifact = fastqc_path
self._launch_thread_and_wait(self._run_shed, extra_args)
user_gi = self._user_gi
found = False
tool_ids = None
for i in range(30):
tool_ids = [t["id"] for t in user_gi.tools.get_tools()]
if "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71" in tool_ids:
found = True
break
time.sleep(5)
assert found, "Failed to find fastqc id in %s" % tool_ids
kill_pid_file(self._pid_file)
def test_shed_serve(self):
extra_args = ["--daemon", "--pid_file", self._pid_file, "--shed_target", "toolshed"]
fastqc_path = os.path.join(TEST_REPOS_DIR, "fastqc")
self._serve_artifact = fastqc_path
self._launch_thread_and_wait(self._run_shed, extra_args)
user_gi = self._user_gi
found = False
tool_ids = None
for i in range(30):
tool_ids = [t["id"] for t in user_gi.tools.get_tools()]
if any(_.startswith("toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/") for _ in tool_ids):
found = True
break
time.sleep(5)
assert found, "Failed to find fastqc id in %s" % tool_ids
kill_pid_file(self._pid_file)
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_serve_profile(self, *db_options):
new_profile = "planemo_test_profile_%s" % uuid.uuid4()
extra_args = [
"--daemon",
"--pid_file",
self._pid_file,
"--profile",
new_profile,
]
extra_args.extend(db_options)
self._launch_thread_and_wait(self._run, extra_args)
user_gi = self._user_gi
assert len(
user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 0
user_gi.histories.create_history(TEST_HISTORY_NAME)
kill_pid_file(self._pid_file)
self._launch_thread_and_wait(self._run, extra_args)
assert len(
user_gi.histories.get_histories(name=TEST_HISTORY_NAME)) == 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 kill(self):
kill_pid_file(self.pid_file)
def kill(self):
kill_pid_file(self.pid_file)