Merge pull request #72 from xcube-dev/pont-57-container-args

Make 'xcengine image run' pass extra args to container

Author: pont-us

CHANGES.md

@@ -7,6 +7,7 @@
 * Improve type annotations and checks (#68)
 * Include Dockerfile in built images (#55)
 * Look for environment.yml automatically (#41)
+* Allow 'xcengine image run' to pass arguments to the container (#57)
 
 ## Changes in 0.1.1
 

docs/xcetool.md

@@ -39,7 +39,7 @@ Options:
 
 ### `xcetool image run`
 
-Usage: `xcetool image run [OPTIONS] IMAGE`
+Usage: `xcetool image run [OPTIONS] IMAGE [CONTAINER_ARGUMENT]...`
 
 Options:
 
@@ -59,9 +59,11 @@ Options:
     running.
 -   `--help`: Show a help message for this subcommand and exit.
 
-This subcommand runs an xcengine container image. An image can also be run
-using the `docker run` command, but `xcetool image run` provides some
-additional convenience (e.g. easy configuration of a server HTTP port).
+This subcommand runs an xcengine container image. Any arguments provided
+after IMAGE will be passed on to the command executed inside the container.
+An image can also be run using the `docker run` command, but
+`xcetool image run` provides some additional convenience (e.g. easy
+configuration of a server HTTP port).
 
 If you use the `--server` option with `xcetool image run`, the image will be
 run in xcube server mode: after the code from the input notebook is used to

environment.yml

@@ -18,6 +18,7 @@ dependencies:
   - cwltool
   - pytest
   - pytest-cov
+  - pytz
 
 # Note: xcube is not required for the conversion itself, but is required
 # to run generated scripts outside containers ("create" mode). xcube is

pyproject.toml

@@ -56,7 +56,8 @@ xcetool = "xcengine.cli:cli"
 dev = [
   "cwltool",
   "pytest",
-  "pytest-cov"
+  "pytest-cov",
+  "pytz"
 ]
 doc = [
   "mkdocs",

test/test_cli.py

@@ -102,6 +102,7 @@ def test_image_run(runner_mock):
         host_port=None,
         from_saved=False,
         keep=False,
+        script_args=[],
     )
 
 
@@ -120,10 +121,30 @@ def test_image_run_print_urls(runner_mock):
         host_port=port,
         from_saved=False,
         keep=False,
+        script_args=[],
     )
     assert re.search(
         f"server.*http://localhost:{port}", result.stdout, re.IGNORECASE
     )
     assert re.search(
         f"viewer.*http://localhost:{port}/viewer", result.stdout, re.IGNORECASE
     )
+
+
+@patch("xcengine.cli.ContainerRunner")
+def test_image_run_script_args(runner_mock):
+    cli_runner = CliRunner()
+    instance_mock = runner_mock.return_value = MagicMock()
+    port = 32168
+    result = cli_runner.invoke(
+        cli, ["image", "run", "--server", "--port", str(port), "foo", "--bar"]
+    )
+    runner_mock.assert_called_once_with(image="foo", output_dir=None)
+    assert result.exit_code == 0
+    instance_mock.run.assert_called_once_with(
+        run_batch=False,
+        host_port=port,
+        from_saved=False,
+        keep=False,
+        script_args=["--bar"],
+    )

test/test_core.py

@@ -29,7 +29,9 @@
 
 @patch("xcengine.core.ScriptCreator.__init__")
 @pytest.mark.parametrize("tag", [None, "bar"])
-@pytest.mark.parametrize("env_file_name", ["environment.yml", "foo.yaml", None])
+@pytest.mark.parametrize(
+    "env_file_name", ["environment.yml", "foo.yaml", None]
+)
 @pytest.mark.parametrize("use_env_file_param", [False, True])
 def test_image_builder_init(
     init_mock,
@@ -56,7 +58,11 @@ def test_image_builder_init(
     )
     assert ib.notebook == nb_path
     assert ib.build_dir == build_path
-    expected_env = environment_path if (use_env_file_param or env_file_name == "environment.yml") else None
+    expected_env = (
+        environment_path
+        if (use_env_file_param or env_file_name == "environment.yml")
+        else None
+    )
     assert ib.environment == expected_env
     if tag is None:
         assert abs(
@@ -123,6 +129,28 @@ def test_runner_run_keep(keep: bool):
         container.remove.assert_called_once_with(force=True)
 
 
+def test_runner_extra_args():
+    runner = xcengine.core.ContainerRunner(
+        image := Mock(docker.models.images.Image),
+        None,
+        client := Mock(DockerClient),
+    )
+    image.tags = []
+    client.containers.run.return_value = (container := MagicMock(Container))
+    container.status = "exited"
+    script_args = ["--foo", "--bar", "42", "--baz", "somestring"]
+    runner.run(
+        run_batch=False,
+        host_port=None,
+        from_saved=False,
+        keep=False,
+        script_args=script_args,
+    )
+    run_args = client.containers.run.call_args
+    command = run_args[1]["command"]
+    assert command == ["python", "execute.py"] + script_args
+
+
 def test_runner_sigint():
     runner = xcengine.core.ContainerRunner(
         image := Mock(docker.models.images.Image),

xcengine/cli.py

@@ -103,7 +103,7 @@ def image_cli():
 
 @image_cli.command(
     help="Build a compute engine as a Docker image, optionally generating an "
-         "Application Package"
+    "Application Package"
 )
 @click.option(
     "-b",
@@ -119,7 +119,7 @@ def image_cli():
     help="Conda environment file to use in Docker image. "
     "If no environment file is specified here or in the notebook, and if "
     "there is no file named environment.yml in the notebook's directory, "
-    "xcetool will try to reproduce the current environment."
+    "xcetool will try to reproduce the current environment.",
 )
 @click.option(
     "-t",
@@ -147,10 +147,12 @@ def build(
 ) -> None:
     if environment is None:
         LOGGER.info("No environment file specified on command line.")
+
     class InitArgs(TypedDict):
         notebook: pathlib.Path
         environment: pathlib.Path
         tag: str
+
     init_args = InitArgs(notebook=notebook, environment=environment, tag=tag)
     if build_dir:
         image_builder = ImageBuilder(build_dir=build_dir, **init_args)
@@ -163,9 +165,11 @@ class InitArgs(TypedDict):
             )
             image = image_builder.build()
     if eoap:
+
         class IndentDumper(yaml.Dumper):
             def increase_indent(self, flow=False, indentless=False):
                 return super(IndentDumper, self).increase_indent(flow, False)
+
         eoap.write_text(
             yaml.dump(
                 image_builder.create_cwl(),
@@ -176,7 +180,14 @@ def increase_indent(self, flow=False, indentless=False):
     print(f"Built image with tags {image.tags}")
 
 
-@image_cli.command(help="Run a compute engine image as a Docker container.")
+@image_cli.command(
+    help="Run a compute engine image as a Docker container. "
+    "Any arguments provided after IMAGE will be passed on to the command "
+    "executed inside the container.",
+    context_settings=dict(
+        ignore_unknown_options=True,
+    ),
+)
 @click.option(
     "-b",
     "--batch",
@@ -213,6 +224,12 @@ def increase_indent(self, flow=False, indentless=False):
     help="Keep container after it has finished running.",
 )
 @click.argument("image", type=str)
+@click.argument(
+    "script_args",
+    nargs=-1,
+    type=click.UNPROCESSED,
+    metavar="[CONTAINER_ARGUMENT]...",
+)
 @click.pass_context
 def run(
     ctx: click.Context,
@@ -223,6 +240,7 @@ def run(
     keep: bool,
     image: str,
     output: pathlib.Path,
+    script_args,
 ) -> None:
     runner = ContainerRunner(image=image, output_dir=output)
     port_specified_explicitly = (
@@ -243,4 +261,5 @@ def run(
         host_port=actual_port,
         from_saved=from_saved,
         keep=keep,
+        script_args=list(script_args),
     )

xcengine/core.py

@@ -33,6 +33,7 @@
 LOGGER = logging.getLogger(__name__)
 logging.basicConfig(level=logging.INFO)
 
+
 class ScriptCreator:
     """Turn a Jupyter notebook into a set of scripts"""
 
@@ -221,7 +222,7 @@ def __init__(
                 self.environment = notebook.parent / nb_env
             else:
                 LOGGER.info(f"No environment specified in notebook.")
-                LOGGER.info(f"Looking for a file named \"environment.yml\".")
+                LOGGER.info(f'Looking for a file named "environment.yml".')
                 notebook_sibling = notebook.parent / "environment.yml"
                 if notebook_sibling.is_file():
                     self.environment = notebook_sibling
@@ -375,9 +376,11 @@ def run(
         host_port: int | None,
         from_saved: bool,
         keep: bool,
+        script_args: list[str] | None = None,
     ):
         LOGGER.info(f"Running container from image {self.image.short_id}")
         LOGGER.info(f"Image tags: {' '.join(self.image.tags)}")
+        assert isinstance(script_args, list) or script_args is None
         command = (
             ["python", "execute.py"]
             + (["--batch"] if run_batch else [])
@@ -391,6 +394,9 @@ def run(
                 else []
             )
             + (["--from-saved"] if from_saved else [])
+            + script_args
+            if script_args is not None
+            else []
         )
         run_args: dict[str, Any] = dict(
             image=self.image, command=command, remove=False, detach=True
@@ -400,10 +406,14 @@ def run(
         container: Container = self.client.containers.run(**run_args)
         LOGGER.info(f"Waiting for container {container.short_id} to complete.")
         default_sigint_handler = signal.getsignal(signal.SIGINT)
+
         def signal_hander(signum, frame):
             signal.signal(signal.SIGINT, default_sigint_handler)
-            LOGGER.info(f"Caught SIGINT. Stopping container {container.short_id}")
+            LOGGER.info(
+                f"Caught SIGINT. Stopping container {container.short_id}"
+            )
             container.stop()
+
         signal.signal(signal.SIGINT, signal_hander)
         while container.status in {"created", "running"}:
             LOGGER.debug(