Support using udocker to run nodejs

Fixes: #153

Author: mr-c

cwl_utils/sandboxjs.py

@@ -118,7 +118,7 @@ def __del__(self) -> None:
                     try:
                         with open(cidfile[0]) as inp_stream:
                             p = subprocess.Popen(  # nosec
-                                ["docker", "kill", inp_stream.read()],
+                                [args[0], "kill", inp_stream.read()],
                                 shell=False,  # nosec
                             )
                             try:
@@ -318,6 +318,8 @@ def new_js_proc(
                 nodeimg = "docker.io/node:alpine"
                 if container_engine == "singularity":
                     nodeimg = f"docker://{nodeimg}"
+                elif container_engine == "podman":
+                    nodeimg = "docker.io/library/node:alpine"
 
                 if not self.have_node_slim:
                     singularity_cache: Optional[str] = None
@@ -338,6 +340,16 @@ def new_js_proc(
                             )
                         if singularityimgs:
                             nodeimg = singularityimgs[0]
+                    elif container_engine == "udocker":
+                        matches = re.search(
+                            re.escape(nodeimg),
+                            subprocess.check_output(  # nosec
+                                [container_engine, "images"],
+                                universal_newlines=True,
+                            ),
+                        )
+                        if matches:
+                            dockerimgs = matches[0]
                     else:
                         raise Exception(
                             f"Unknown container_engine: {container_engine}."
@@ -367,7 +379,10 @@ def new_js_proc(
                         )
                     self.have_node_slim = True
                 nodejs_commands = [container_engine]
-                if container_engine != "singularity":
+                if (
+                    container_engine != "singularity"
+                    and "udocker" not in container_engine
+                ):
                     nodejs_commands.extend(
                         [
                             "run",
@@ -379,7 +394,7 @@ def new_js_proc(
                             "--rm",
                         ]
                     )
-                else:
+                elif "singularity" in container_engine:
                     nodejs_commands.extend(
                         [
                             "exec",
@@ -389,6 +404,15 @@ def new_js_proc(
                             "--userns" if singularity_supports_userns() else "--pid",
                         ]
                     )
+                elif "udocker" in container_engine:
+                    nodejs_commands.extend(
+                        [
+                            "run",
+                            "--device=/dev/stdin",
+                            "--device=/dev/stdout",
+                            "--device=/dev/stderr",
+                        ]
+                    )
                 nodejs_commands.extend(
                     [
                         nodeimg,

tests/test_js_sandbox.py

@@ -9,7 +9,7 @@
 
 from cwl_utils import expression, sandboxjs
 
-from .util import needs_podman, needs_singularity
+from .util import needs_podman, needs_singularity, needs_udocker
 
 node_versions = [
     ("v0.8.26\n", False),
@@ -101,6 +101,32 @@ def test_value_from_two_concatenated_expressions_podman(
         )
 
 
+@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

tests/util.py

@@ -33,3 +33,8 @@ def get_data(filename: str) -> str:
     not bool(shutil.which("podman")),
     reason="Requires the podman executable on the system path.",
 )
+
+needs_udocker = pytest.mark.skipif(
+    not bool(shutil.which("udocker")),
+    reason="Requires the udocker executable on the system path.",
+)