def test_cli_compact_settings_envs(
cli: typer.Typer,
fake_settings_class: Type[BaseCustomSettings],
fake_granular_env_file_content: str,
export_as_dict: Callable,
cli_runner: CliRunner,
monkeypatch: pytest.MonkeyPatch,
):
with monkeypatch.context() as patch:
mocked_envs_1: EnvVarsDict = setenvs_as_envfile(
patch, fake_granular_env_file_content
)
settings_1 = fake_settings_class()
settings_1_dict_wo_secrets = export_as_dict(settings_1)
assert settings_1_dict_wo_secrets == {
"APP_HOST": "localhost",
"APP_PORT": 80,
"APP_OPTIONAL_ADDON": {"MODULE_VALUE": 10, "MODULE_VALUE_DEFAULT": 42},
"APP_REQUIRED_PLUGIN": {
"POSTGRES_HOST": "localhost",
"POSTGRES_PORT": 5432,
"POSTGRES_USER": "******",
"POSTGRES_PASSWORD": "******",
"POSTGRES_DB": "foodb",
"POSTGRES_MINSIZE": 1,
"POSTGRES_MAXSIZE": 50,
"POSTGRES_CLIENT_NAME": None,
},
}
setting_env_content_compact = cli_runner.invoke(
cli,
["settings", "--compact", "--show-secrets"],
catch_exceptions=False,
).stdout
# now we use these as env vars
print(setting_env_content_compact)
with monkeypatch.context() as patch:
mocked_envs_2: EnvVarsDict = setenvs_as_envfile(
patch,
setting_env_content_compact,
)
assert mocked_envs_2 == {
"APP_HOST": "localhost",
"APP_PORT": "80",
"APP_OPTIONAL_ADDON": '{"MODULE_VALUE": 10, "MODULE_VALUE_DEFAULT": 42}',
"APP_REQUIRED_PLUGIN": '{"POSTGRES_HOST": "localhost", "POSTGRES_PORT": 5432, "POSTGRES_USER": "******", "POSTGRES_PASSWORD": "******", "POSTGRES_DB": "foodb", "POSTGRES_MINSIZE": 1, "POSTGRES_MAXSIZE": 50, "POSTGRES_CLIENT_NAME": null}',
}
settings_2 = fake_settings_class()
assert settings_1 == settings_2
def test_env_passing(monkeypatch: pytest.MonkeyPatch) -> None:
"""Confirm that MPI extension passes environment variables correctly."""
config = MpiConfig(
env_pass=["A", "B", "LONG_NAME"],
env_pass_regex=["TOOLNAME", "MPI_.*_CONF"],
)
env: MutableMapping[str, str] = {}
with monkeypatch.context() as m:
m.setattr(os, "environ", {})
env = {}
config.pass_through_env_vars(env)
assert env == {}
with monkeypatch.context() as m:
m.setattr(os, "environ", {"A": "a"})
env = {}
config.pass_through_env_vars(env)
assert env == {"A": "a"}
with monkeypatch.context() as m:
m.setattr(os, "environ", {"A": "a", "C": "c"})
env = {}
config.pass_through_env_vars(env)
assert env == {"A": "a"}
with monkeypatch.context() as m:
m.setattr(os, "environ", {"A": "a", "B": "b", "C": "c"})
env = {"PATH": "one:two:three", "HOME": "/tmp/dir", "TMPDIR": "/tmp/dir"}
config.pass_through_env_vars(env)
assert env == {
"PATH": "one:two:three",
"HOME": "/tmp/dir",
"TMPDIR": "/tmp/dir",
"A": "a",
"B": "b",
}
with monkeypatch.context() as m:
m.setattr(os, "environ", {"TOOLNAME": "foobar"})
env = {}
config.pass_through_env_vars(env)
assert env == {"TOOLNAME": "foobar"}
with monkeypatch.context() as m:
m.setattr(os, "environ", {"_TOOLNAME_": "foobar"})
env = {}
config.pass_through_env_vars(env)
# Cos we are matching not searching
assert env == {}
with monkeypatch.context() as m:
m.setattr(os, "environ", {"MPI_A_CONF": "A", "MPI_B_CONF": "B"})
env = {}
config.pass_through_env_vars(env)
# Cos we are matching not searching
assert env == {"MPI_A_CONF": "A", "MPI_B_CONF": "B"}
def test_windows_warning(monkeypatch: pytest.MonkeyPatch) -> None:
"""Confirm that the windows warning is given."""
with pytest.warns(UserWarning, match=r"Windows Subsystem for Linux 2"):
# would normally just use the MonkeyPatch object directly
# but if we don't use a context then os.name being "nt" causes problems
# for pytest on non-Windows systems. So the context unravels the change
# to os.name quickly, and then pytest will check for the desired warning
with monkeypatch.context() as m:
m.setattr(os, "name", "nt")
main.windows_check()
def use_fixed_time(
monkeypatch: pytest.MonkeyPatch, mocker: MockerFixture
) -> Iterator[None]:
with monkeypatch.context() as m:
m.setenv("TZ", "EST5EDT,M3.2.0,M11.1.0")
time.tzset()
mocker.patch("time.time", return_value=1612373696)
# Time is now 2021-02-03T12:34:56-05:00
yield
time.tzset()
def test_value_from_two_concatenated_expressions_singularity(
tmp_path: Path, monkeypatch: pytest.MonkeyPatch
) -> None:
"""Javascript test using Singularity."""
sandboxjs.have_node_slim = False
sandboxjs.localdata = threading.local()
new_paths = hide_nodejs(tmp_path)
factory = Factory()
factory.loading_context.singularity = True
factory.loading_context.debug = True
factory.runtime_context.debug = True
with monkeypatch.context() as m:
m.setenv("PATH", new_paths)
echo = factory.make(get_data("tests/wf/vf-concat.cwl"))
file = {"class": "File", "location": get_data("tests/wf/whale.txt")}
assert echo(file1=file) == {"out": "a string\n"}
def mark(cls, monkeypatch: pytest.MonkeyPatch) -> Generator[None, None, None]:
"""
Mark connections under in that context.
"""
orig_request = HTTPConnection.request
def call_and_mark(target: Callable[..., None]) -> Callable[..., None]:
def part(self: HTTPConnection, *args: Any, **kwargs: Any) -> None:
target(self, *args, **kwargs)
self.sock.sendall(cls._get_socket_mark(self.sock, False))
return part
with monkeypatch.context() as m:
m.setattr(HTTPConnection, "request", call_and_mark(orig_request))
yield