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"""Test sandboxjs.py and related code."""
import os
import shutil
import threading
from pathlib import Path
from typing import Any
import pytest
from cwl_utils import expression, sandboxjs
from .util import needs_podman, needs_singularity, needs_udocker
node_versions = [
("v0.8.26\n", False),
("v0.10.25\n", False),
("v0.10.26\n", True),
("v4.4.2\n", True),
("v7.7.3\n", True),
]
@pytest.mark.parametrize("version,supported", node_versions)
def test_node_version(version: str, supported: bool, mocker: Any) -> None:
mocked_subprocess = mocker.patch("cwl_utils.sandboxjs.subprocess")
mocked_subprocess.check_output = mocker.Mock(return_value=version)
assert sandboxjs.check_js_threshold_version("node") == supported
def test_value_from_two_concatenated_expressions() -> None:
js_engine = sandboxjs.get_js_engine()
js_engine.have_node_slim = False # type: ignore[attr-defined]
js_engine.localdata = threading.local() # type: ignore[attr-defined]
assert (
expression.do_eval(
'$("a ")$("string")',
{},
[{"class": "InlineJavascriptRequirement"}],
None,
None,
{},
cwlVersion="v1.0",
)
== "a string"
)
def hide_nodejs(temp_dir: Path) -> str:
"""Generate a new PATH that hides node{js,}."""
paths: list[str] = os.environ.get("PATH", "").split(":")
names: list[str] = []
if "/bin" in paths:
bin_path = Path("/bin")
if (
bin_path.is_symlink()
and os.readlink(bin_path) == "usr/bin"
and "/usr/bin" in paths
):
paths.remove("/bin")
for name in ("nodejs", "node"):
path = shutil.which(name, path=":".join(paths))
if path:
names.append(path)
for name in names:
dirname = os.path.dirname(name)
if dirname in paths:
paths.remove(dirname)
new_dir = temp_dir / os.path.basename(dirname)
new_dir.mkdir()
for entry in os.listdir(dirname):
if entry not in ("nodejs", "node"):
os.symlink(os.path.join(dirname, entry), new_dir / entry)
paths.append(str(new_dir))
return ":".join(paths)
@needs_podman
def test_value_from_two_concatenated_expressions_podman(
tmp_path: Path, monkeypatch: pytest.MonkeyPatch
) -> None:
"""Javascript test using podman."""
new_paths = hide_nodejs(tmp_path)
with monkeypatch.context() as m:
m.setenv("PATH", new_paths)
js_engine = sandboxjs.get_js_engine()
js_engine.have_node_slim = False # type: ignore[attr-defined]
js_engine.localdata = threading.local() # type: ignore[attr-defined]
assert (
expression.do_eval(
'$("a ")$("string")',
{},
[{"class": "InlineJavascriptRequirement"}],
None,
None,
{},
cwlVersion="v1.0",
container_engine="podman",
)
== "a string"
)
@needs_udocker
def test_value_from_two_concatenated_expressions_udocker(
tmp_path: Path, monkeypatch: pytest.MonkeyPatch
) -> None:
"""Javascript test using udocker."""
new_paths = hide_nodejs(tmp_path)
with monkeypatch.context() as m:
m.setenv("PATH", new_paths)
js_engine = sandboxjs.get_js_engine()
js_engine.have_node_slim = False # type: ignore[attr-defined]
js_engine.localdata = threading.local() # type: ignore[attr-defined]
assert (
expression.do_eval(
'$("a ")$("string")',
{},
[{"class": "InlineJavascriptRequirement"}],
None,
None,
{},
cwlVersion="v1.0",
container_engine="udocker",
)
== "a string"
)
@needs_singularity
def test_value_from_two_concatenated_expressions_singularity(
tmp_path: Path, monkeypatch: pytest.MonkeyPatch
) -> None:
"""Javascript test using Singularity."""
new_paths = hide_nodejs(tmp_path)
with monkeypatch.context() as m:
m.setenv("PATH", new_paths)
js_engine = sandboxjs.get_js_engine()
js_engine.have_node_slim = False # type: ignore[attr-defined]
js_engine.localdata = threading.local() # type: ignore[attr-defined]
assert (
expression.do_eval(
'$("a ")$("string")',
{},
[{"class": "InlineJavascriptRequirement"}],
None,
None,
{},
cwlVersion="v1.0",
container_engine="singularity",
)
== "a string"
)
@needs_singularity
def test_singularity_cache(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
"""Affirm that CWL_SINGULARIT_CACHE is respected."""
bin_path = tmp_path / "no_nodejs"
bin_path.mkdir()
new_paths = hide_nodejs(bin_path)
cache_path = tmp_path / "singularity_cache"
cache_path.mkdir()
with monkeypatch.context() as m:
m.setenv("PATH", new_paths)
m.setenv("CWL_SINGULARITY_CACHE", str(cache_path))
js_engine = sandboxjs.get_js_engine()
js_engine.localdata = threading.local() # type: ignore[attr-defined]
js_engine.have_node_slim = False # type: ignore[attr-defined]
assert (
expression.do_eval(
"$(42*23)",
{},
[{"class": "InlineJavascriptRequirement"}],
None,
None,
{},
cwlVersion="v1.0",
container_engine="singularity",
)
== 42 * 23
)
assert (cache_path / "node_alpine.sif").exists()
def test_caches_js_processes(mocker: Any) -> None:
sandboxjs.exec_js_process("7", context="{}")
mocked_new_js_proc = mocker.patch("cwl_utils.sandboxjs.new_js_proc")
sandboxjs.exec_js_process("7", context="{}")
mocked_new_js_proc.assert_not_called()
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