restore udocker (#1293)

Fixes #1292

Author: mr-c

cwltool/argparser.py

@@ -395,10 +395,17 @@ def arg_parser() -> argparse.ArgumentParser:
     dockergroup.add_argument(
         "--user-space-docker-cmd",
         metavar="CMD",
-        help="(Linux/OS X only) Specify a user space docker "
-        "command (like udocker or dx-docker) that will be "
-        "used to call 'pull' and 'run'",
+        help="(Linux/OS X only) Specify the path to udocker. Implies --udocker",
     )
+    dockergroup.add_argument(
+        "--udocker",
+        help="(Linux/OS X only) Use the udocker runtime for running containers "
+        "(equivalent to --user-space-docker-cmd=udocker).",
+        action="store_const",
+        const="udocker",
+        dest="user_space_docker_cmd",
+    )
+
     dockergroup.add_argument(
         "--singularity",
         action="store_true",

cwltool/command_line_tool.py

@@ -63,6 +63,7 @@
 )
 from .singularity import SingularityCommandLineJob
 from .stdfsaccess import StdFsAccess
+from .udocker import UDockerCommandLineJob
 from .utils import (
     aslist,
     convert_pathsep_to_unix,
@@ -357,6 +358,8 @@ def make_job_runner(self, runtimeContext: RuntimeContext) -> Type[JobBase]:
         if dockerReq is not None and runtimeContext.use_container:
             if runtimeContext.singularity:
                 return SingularityCommandLineJob
+            elif runtimeContext.user_space_docker_cmd:
+                return UDockerCommandLineJob
             return DockerCommandLineJob
         for t in reversed(self.requirements):
             if t["class"] == "DockerRequirement":

cwltool/udocker.py

@@ -0,0 +1,18 @@
+"""Enables Docker software containers via the udocker runtime."""
+
+from typing import List
+
+from .docker import DockerCommandLineJob
+
+
+class UDockerCommandLineJob(DockerCommandLineJob):
+    """Runs a CommandLineJob in a sofware container using the udocker engine."""
+
+    @staticmethod
+    def append_volume(
+        runtime: List[str], source: str, target: str, writable: bool = False
+    ) -> None:
+        """Add binding arguments to the runtime list."""
+        runtime.append(
+            "--volume={}:{}:{}".format(source, target, "rw" if writable else "ro")
+        )

tests/test_examples.py

@@ -1057,6 +1057,7 @@ def test_no_compute_chcksum(tmpdir, factor):
     assert "checksum" not in stdout
 
 
+@pytest.mark.skipif(onWindows(), reason="udocker is Linux/macOS only")
 @pytest.mark.parametrize("factor", test_factors)
 def test_bad_userspace_runtime(factor):
     test_file = "tests/wf/wc-tool.cwl"

tests/test_udocker.py

@@ -12,10 +12,7 @@
 LINUX = sys.platform in ("linux", "linux2")
 
 
-# @pytest.mark.skipif(not LINUX, reason="LINUX only")
-@pytest.mark.skip(
-    "Udocker install is broken, see https://github.com/indigo-dc/udocker/issues/221"
-)
+@pytest.mark.skipif(not LINUX, reason="LINUX only")
 class TestUdocker:
     udocker_path = None