def test_commandLineTool_job_tmpdir_prefix(tmp_path: Path) -> None:
"""Test that non-docker enabled CommandLineTool respects temp directory directives."""
loading_context = LoadingContext({
"metadata": {
"cwlVersion": INTERNAL_VERSION,
"http://commonwl.org/cwltool#original_cwlVersion":
INTERNAL_VERSION,
}
})
clt = CommandLineTool(
cast(
CommentedMap,
cmap({
"cwlVersion": INTERNAL_VERSION,
"class": "CommandLineTool",
"inputs": [],
"outputs": [],
"requirements": [],
}),
),
loading_context,
)
tmpdir_prefix = str(tmp_path / "1")
tmp_outdir_prefix = str(tmp_path / "2")
runtime_context = RuntimeContext({
"tmpdir_prefix": tmpdir_prefix,
"tmp_outdir_prefix": tmp_outdir_prefix,
})
job = next(clt.job({}, None, runtime_context))
assert isinstance(job, JobBase)
assert job.stagedir and job.stagedir.startswith(tmpdir_prefix)
assert job.tmpdir and job.tmpdir.startswith(tmpdir_prefix)
assert job.outdir and job.outdir.startswith(tmp_outdir_prefix)
def test_input_can_be_named_pipe(tmp_path: Path, streamable: bool,
streaming_allowed: bool,
raise_exception: bool) -> None:
"""Test that input can be a named pipe."""
clt = CommandLineTool(
toolpath_object,
loading_context,
)
runtime_context = RuntimeContext()
runtime_context.streaming_allowed = streaming_allowed
path = tmp_path / "tmp"
os.mkfifo(path)
joborder: CWLObjectType = {
"inp": {
"class": "File",
"location": str(path),
"streamable": streamable,
}
}
job = next(clt.job(joborder, None, runtime_context))
assert isinstance(job, JobBase)
if raise_exception:
with pytest.raises(WorkflowException):
job._setup(runtime_context)
else:
job._setup(runtime_context)
def test_regular_file() -> None:
"""Test that regular files do not raise any exception when they are checked in job._setup."""
clt = CommandLineTool(
toolpath_object,
loading_context,
)
runtime_context = RuntimeContext()
joborder: CWLObjectType = {
"inp": {
"class": "File",
"location": get_data("tests/wf/whale.txt"),
}
}
job = next(clt.job(joborder, None, runtime_context))
assert isinstance(job, JobBase)
job._setup(runtime_context)
def test_docker_commandLineTool_job_tmpdir_prefix(tmp_path: Path) -> None:
"""Test that docker enabled CommandLineTool respects temp directory directives."""
loading_context = LoadingContext({
"metadata": {
"cwlVersion": INTERNAL_VERSION,
ORIGINAL_CWLVERSION: INTERNAL_VERSION,
}
})
clt = CommandLineTool(
cast(
CommentedMap,
cmap({
"cwlVersion":
INTERNAL_VERSION,
"class":
"CommandLineTool",
"inputs": [],
"outputs": [],
"requirements": [{
"class": "DockerRequirement",
"dockerPull": "docker.io/debian:stable",
}],
}),
),
loading_context,
)
tmpdir_prefix = str(tmp_path / "1")
tmp_outdir_prefix = str(tmp_path / "2")
runtime_context = RuntimeContext({
"tmpdir_prefix": tmpdir_prefix,
"tmp_outdir_prefix": tmp_outdir_prefix,
})
job = next(clt.job({}, None, runtime_context))
assert isinstance(job, JobBase)
assert job.stagedir and job.stagedir.startswith(tmpdir_prefix)
assert job.tmpdir and job.tmpdir.startswith(tmpdir_prefix)
assert job.outdir and job.outdir.startswith(tmp_outdir_prefix)