Merge pull request #74 from aCLImatise/auto-docker-image

Automatically store docker images produced by docker executor

aclimatise/execution/docker.py

@@ -8,6 +8,7 @@
 from docker.utils.socket import consume_socket_output, demux_adaptor, frames_iter
 
 from aclimatise.execution.help import CliHelpExecutor
+from aclimatise.model import Command
 
 
 def read_socket(sock, timeout: int = None) -> Tuple[bytes, bytes]:
@@ -40,9 +41,27 @@ class DockerExecutor(CliHelpExecutor):
     An executor that runs the commands on an already-running docker Container (not an Image!)
     """
 
-    def __init__(self, container: "docker.models.containers.Container", **kwargs):
+    def __init__(
+        self, container: "docker.models.containers.Container", save_image=True, **kwargs
+    ):
+        """
+        :param container: The object from the Docker API that represents the running container to run inside
+        :param save_image: If true (default), save the image name on the command, meaning that the resulting tool
+            definitions also use this Docker image
+        """
         super().__init__(**kwargs)
         self.container = container
+        self.save_image = save_image
+
+    def convert(
+        self,
+        cmd: List[str],
+    ) -> Command:
+        # Use the existing function, but patch in the docker image
+        cmd = super().convert(cmd)
+        if self.save_image:
+            cmd.docker_image = self.container.image.tags[0]
+        return cmd
 
     def execute(self, command: List[str]) -> str:
         _, sock = self.container.exec_run(

docs/changes.rst

@@ -14,6 +14,7 @@ Breaking Changes
 New Features
 ************
 * Add ``docker_image`` field to ``Command``
+* The ``DockerExecutor`` has been updated to automatically set this field based on the Docker image being used by it
 * Add `Janis <https://janis.readthedocs.io/en/latest/index.html>`_ converter (`#73 <https://github.com/aCLImatise/CliHelpParser/issues/73>`_)
 
 Bug Fixes

test/executors/test_docker.py

@@ -4,6 +4,20 @@
 from aclimatise.execution.docker import DockerExecutor
 
 
+@pytest.mark.timeout(360)
+def test_docker_image_saved(bwamem_help):
+    client = docker.from_env()
+    container = client.containers.run(
+        "biocontainers/bwa:v0.7.17_cv1",
+        entrypoint=["sleep", "999999999"],
+        detach=True,
+    )
+
+    exec = DockerExecutor(container)
+    cmd = exec.convert(["bwa", "mem"])
+    assert cmd.docker_image == "biocontainers/bwa:v0.7.17_cv1"
+
+
 def test_docker(bwamem_help):
     client = docker.from_env()
     container = client.containers.run(