def test_runtimeContext_respects_tmpdir_prefix(tmp_path: Path) -> None:
"""Test that RuntimeContext helper methods respects tmpdir_prefix."""
tmpdir_prefix = str(tmp_path / "foo")
runtime_context = RuntimeContext({"tmpdir_prefix": tmpdir_prefix})
assert runtime_context.get_tmpdir().startswith(tmpdir_prefix)
assert runtime_context.get_stagedir().startswith(tmpdir_prefix)
assert runtime_context.create_tmpdir().startswith(tmpdir_prefix)
assert create_tmp_dir(tmpdir_prefix).startswith(tmpdir_prefix)
def test_docker_tmpdir_prefix(tmp_path: Path) -> None:
"""Test that DockerCommandLineJob respects temp directory directives."""
(tmp_path / "3").mkdir()
tmpdir_prefix = str(tmp_path / "3" / "ttmp")
runtime_context = RuntimeContext({
"tmpdir_prefix": tmpdir_prefix,
"user_space_docker_cmd": None
})
builder = Builder(
{},
[],
[],
{},
schema.Names(),
[],
[],
{},
None,
None,
StdFsAccess,
StdFsAccess(""),
None,
0.1,
False,
False,
False,
"",
runtime_context.get_outdir(),
runtime_context.get_tmpdir(),
runtime_context.get_stagedir(),
INTERNAL_VERSION,
)
job = DockerCommandLineJob(builder, {}, PathMapper, [], [], "")
runtime: List[str] = []
volume_writable_file = MapperEnt(resolved=get_data("tests/2.fastq"),
target="foo",
type=None,
staged=None)
(tmp_path / "1").mkdir()
job.add_writable_file_volume(runtime, volume_writable_file, None,
str(tmp_path / "1" / "writable_file"))
children = sorted((tmp_path / "1").glob("*"))
assert len(children) == 1
subdir = tmp_path / children[0]
assert subdir.name.startswith("writable_file")
assert len(sorted(subdir.glob("*"))) == 1
assert (subdir / "2.fastq").exists()
resolved_writable_dir = tmp_path / "data_orig"
resolved_writable_dir.mkdir(parents=True)
volume_dir = MapperEnt(resolved=str(resolved_writable_dir),
target="bar",
type=None,
staged=None)
(tmp_path / "2").mkdir()
job.add_writable_directory_volume(runtime, volume_dir, None,
str(tmp_path / "2" / "dir"))
children = sorted((tmp_path / "2").glob("*"))
assert len(children) == 1
subdir = tmp_path / "2" / children[0]
assert subdir.name.startswith("dir")
assert len(sorted(subdir.glob("*"))) == 1
assert (subdir / "data_orig").exists()
cidfile = job.create_runtime({}, runtime_context)[1]
assert cidfile and cidfile.startswith(tmpdir_prefix)
volume_file = MapperEnt(resolved="Hoopla!",
target="baz",
type=None,
staged=None)
(tmp_path / "4").mkdir()
job.create_file_and_add_volume(runtime, volume_file, None, None,
str(tmp_path / "4" / "file"))
children = sorted((tmp_path / "4").glob("*"))
assert len(children) == 1
subdir = tmp_path / "4" / children[0]
assert subdir.name.startswith("file")
assert len(sorted(subdir.glob("*"))) == 1
assert (subdir / "baz").exists()