added --container-engine (#206)

Co-authored-by: Jake Fennick <[email protected]>

Author: jfennick

cwl_utils/docker_extract.py

@@ -32,6 +32,12 @@ def arg_parser() -> argparse.ArgumentParser:
         help="Use singularity to pull the image",
         action="store_true",
     )
+    parser.add_argument(
+        "--container-engine",
+        dest="container_engine",
+        default="docker",
+        help="Specify which command to use to run OCI containers.",
+    )
     return parser
 
 
@@ -51,9 +57,13 @@ def run(args: argparse.Namespace) -> int:
             print(f"Unable to save image from {req} due to lack of 'dockerPull'.")
             continue
         if args.singularity:
-            image_puller: ImagePuller = SingularityImagePuller(req.dockerPull, args.dir)
+            image_puller: ImagePuller = SingularityImagePuller(
+                req.dockerPull, args.dir, "singularity"
+            )
         else:
-            image_puller = DockerImagePuller(req.dockerPull, args.dir)
+            image_puller = DockerImagePuller(
+                req.dockerPull, args.dir, args.container_engine
+            )
         image_puller.save_docker_image()
     return 0
 

cwl_utils/image_puller.py

@@ -15,10 +15,11 @@
 
 
 class ImagePuller(ABC):
-    def __init__(self, req: str, save_directory: str) -> None:
+    def __init__(self, req: str, save_directory: str, cmd: str) -> None:
         """Create an ImagePuller."""
         self.req = req
         self.save_directory = save_directory
+        self.cmd = cmd
 
     @abstractmethod
     def get_image_name(self) -> str:
@@ -45,7 +46,11 @@ class DockerImagePuller(ImagePuller):
 
     def get_image_name(self) -> str:
         """Get the name of the tarball."""
-        return "".join(self.req.split("/")) + ".tar"
+        name = "".join(self.req.split("/")) + ".tar"
+        # Replace colons with underscores in the name.
+        # See https://github.com/containers/podman/issues/489
+        name = name.replace(":", "_")
+        return name
 
     def generate_udocker_loading_command(self) -> str:
         """Generate the udocker loading command."""
@@ -54,10 +59,10 @@ def generate_udocker_loading_command(self) -> str:
     def save_docker_image(self) -> None:
         """Download and save the software container image to disk as a docker tarball."""
         _LOGGER.info(f"Pulling {self.req} with Docker...")
-        cmd_pull = ["docker", "pull", self.req]
+        cmd_pull = [self.cmd, "pull", self.req]
         ImagePuller._run_command_pull(cmd_pull)
         cmd_save = [
-            "docker",
+            self.cmd,
             "save",
             "-o",
             os.path.join(self.save_directory, self.get_image_name()),
@@ -76,9 +81,9 @@ class SingularityImagePuller(ImagePuller):
     CHARS_TO_REPLACE = ["/"]
     NEW_CHAR = "_"
 
-    def __init__(self, req: str, save_directory: str) -> None:
+    def __init__(self, req: str, save_directory: str, cmd: str) -> None:
         """Create a Singularity-based software container image downloader."""
-        super().__init__(req, save_directory)
+        super().__init__(req, save_directory, cmd)
 
     def get_image_name(self) -> str:
         """Determine the file name appropriate to the installed version of Singularity."""
@@ -99,7 +104,7 @@ def save_docker_image(self) -> None:
         """Pull down the Docker container image in the Singularity image format."""
         _LOGGER.info(f"Pulling {self.req} with Singularity...")
         cmd_pull = [
-            "singularity",
+            self.cmd,
             "pull",
             "--name",
             os.path.join(self.save_directory, self.get_image_name()),

tests/test_docker_extract.py

@@ -24,7 +24,22 @@ def test_traverse_workflow() -> None:
         assert len(reqs) == 1
         for req in reqs:
             assert req.dockerPull
-            image_puller = DockerImagePuller(req.dockerPull, tmpdir)
+            image_puller = DockerImagePuller(req.dockerPull, tmpdir, "docker")
+            image_puller.save_docker_image()
+            _ = image_puller.generate_udocker_loading_command()
+
+
+@mark.skipif(which("podman") is None, reason="podman is not available")
+def test_traverse_workflow_podman() -> None:
+    """Test container extraction tool using Podman."""
+    loaded = parser.load_document(TEST_CWL)
+
+    with TemporaryDirectory() as tmpdir:
+        reqs = set(traverse(loaded))
+        assert len(reqs) == 1
+        for req in reqs:
+            assert req.dockerPull
+            image_puller = DockerImagePuller(req.dockerPull, tmpdir, "podman")
             image_puller.save_docker_image()
             _ = image_puller.generate_udocker_loading_command()
 
@@ -39,5 +54,5 @@ def test_traverse_workflow_singularity() -> None:
         assert len(reqs) == 1
         for req in reqs:
             assert req.dockerPull
-            image_puller = SingularityImagePuller(req.dockerPull, tmpdir)
+            image_puller = SingularityImagePuller(req.dockerPull, tmpdir, "singularity")
             image_puller.save_docker_image()