def test_initialization(tmpdir, popen):
t1 = Target.empty("Target1")
t2 = Target.empty("Target2")
t3 = Target.empty("Target3")
t4 = Target.empty("Target4")
gwf_dir = tmpdir.ensure_dir(".gwf")
tracked_file = gwf_dir.join("slurm-backend-tracked.json")
tracked_file.write(
'{"Target1": "1", "Target2": "2", "Target3": "3", "Target4": "4"}'
)
popen.return_value.returncode = 0
popen.return_value.communicate.return_value = ("3;SE\n2;BF\n1;R\n", "")
with tmpdir.as_cwd():
backend = SlurmBackend()
assert backend.status(t1) == Status.RUNNING
assert backend.status(t2) == Status.UNKNOWN
assert backend.status(t3) == Status.SUBMITTED
assert backend.status(t4) == Status.UNKNOWN
popen.return_value.returncode = 1
popen.return_value.communicate.return_value = ("", "This is stderr")
with pytest.raises(BackendError):
with SlurmBackend():
pass
def test_submit_1(popen):
t1 = Target.empty("Target1")
t2 = Target.empty("Target2")
t3 = Target.empty("Target3")
t4 = Target.empty("Target4")
popen.return_value.returncode = 0
popen.return_value.communicate.return_value = ("", "")
backend = SlurmBackend()
popen.return_value.returncode = 0
popen.return_value.communicate.side_effect = [
("1\n", ""),
("2\n", ""),
("3\n", ""),
("", "This is stderr\n"),
]
backend.submit(t1, [])
backend.submit(t2, [])
backend.submit(t3, [t1, t2])
assert (
call(
["/bin/sbatch", "--parsable"],
stderr=-1,
stdin=-1,
stdout=-1,
universal_newlines=True,
)
in popen.call_args_list
)
assert (
call(
["/bin/sbatch", "--parsable"],
stderr=-1,
stdin=-1,
stdout=-1,
universal_newlines=True,
)
in popen.call_args_list
)
assert (
call(
["/bin/sbatch", "--parsable", "--dependency=afterok:1:2"],
stderr=-1,
stdin=-1,
stdout=-1,
universal_newlines=True,
)
in popen.call_args_list
)
with pytest.raises(DependencyError):
backend.submit(t3, [t4])
popen.return_value.returncode = 1
with pytest.raises(BackendError):
backend.submit(t4, [])
def test_cancel(popen):
t = Target.empty("Target")
popen.return_value.returncode = 0
popen.return_value.communicate.return_value = ("", "")
backend = SlurmBackend()
with pytest.raises(TargetError):
backend.cancel(t)
popen.return_value.communicate.return_value = ("1\n", "")
backend.submit(t, [])
assert backend.status(t) == Status.SUBMITTED
backend.cancel(t)
assert backend.status(t) == Status.UNKNOWN
assert (
call(
["/bin/scancel", "--verbose", "1"],
stderr=-1,
stdin=-1,
stdout=-1,
universal_newlines=True,
)
in popen.call_args_list
)
popen.return_value.returncode = 1
popen.return_value.communicate.return_value = ("", "This is stderr")
with pytest.raises(BackendError):
backend.cancel(t)
def test_executable_unavailable_after_initialization(popen, monkeypatch):
exes = {"squeue": "/bin/squeue"}
monkeypatch.setattr("gwf.backends.slurm.find_executable", lambda e: exes.get(e))
t = Target.empty("TestTarget")
popen.return_value.returncode = 0
popen.return_value.communicate.return_value = ("", "")
backend = SlurmBackend()
with pytest.raises(BackendError):
backend.cancel(t)
with pytest.raises(BackendError):
backend.submit(t, dependencies=[])
def test_file_log_manager_remove(log_manager, tmpdir):
target = Target.empty("TestTarget")
stdout_file = tmpdir.join(".gwf", "logs", "TestTarget.stdout").ensure()
stderr_file = tmpdir.join(".gwf", "logs", "TestTarget.stderr").ensure()
log_manager.remove_stdout(target)
assert not stdout_file.exists()
log_manager.remove_stderr(target)
assert not stderr_file.exists()
with pytest.raises(LogError):
log_manager.remove_stdout(target)
with pytest.raises(LogError):
log_manager.remove_stderr(target)
def test_file_log_manager_open(log_manager, tmpdir):
target = Target.empty("TestTarget")
with pytest.raises(LogError):
log_manager.open_stdout(target)
with pytest.raises(LogError):
log_manager.open_stderr(target)
stdout_file = tmpdir.join(".gwf", "logs", "TestTarget.stdout")
stdout_file.write("This is standard output...")
stderr_file = tmpdir.join(".gwf", "logs", "TestTarget.stderr")
stderr_file.write("This is standard error...")
assert log_manager.open_stdout(target).read() == "This is standard output..."
assert log_manager.open_stderr(target).read() == "This is standard error..."
def test_file_log_manager_remove(log_manager, tmpdir):
target = Target.empty("TestTarget")
stdout_file = tmpdir.join(".gwf", "logs", "TestTarget.stdout").ensure()
stderr_file = tmpdir.join(".gwf", "logs", "TestTarget.stderr").ensure()
log_manager.remove_stdout(target)
assert not stdout_file.exists()
log_manager.remove_stderr(target)
assert not stderr_file.exists()
with pytest.raises(LogError):
log_manager.remove_stdout(target)
with pytest.raises(LogError):
log_manager.remove_stderr(target)
def test_file_log_manager_open(log_manager, tmpdir):
target = Target.empty("TestTarget")
with pytest.raises(LogError):
log_manager.open_stdout(target)
with pytest.raises(LogError):
log_manager.open_stderr(target)
stdout_file = tmpdir.join(".gwf", "logs", "TestTarget.stdout")
stdout_file.write("This is standard output...")
stderr_file = tmpdir.join(".gwf", "logs", "TestTarget.stderr")
stderr_file.write("This is standard error...")
assert log_manager.open_stdout(
target).read() == "This is standard output..."
assert log_manager.open_stderr(
target).read() == "This is standard error..."
def test_file_log_manager_path(log_manager):
target = Target.empty("TestTarget")
assert log_manager.stderr_path(target) == ".gwf/logs/TestTarget.stderr"
assert log_manager.stdout_path(target) == ".gwf/logs/TestTarget.stdout"
def test_file_log_manager_path(log_manager):
target = Target.empty("TestTarget")
assert log_manager.stderr_path(target) == ".gwf/logs/TestTarget.stderr"
assert log_manager.stdout_path(target) == ".gwf/logs/TestTarget.stdout"