docker_cmd.py

WORKER_DATA_LOCATION = "/wf_pipeline_data/userdata"


def get_dockercmd(params: dict, location):
    """A task which runs in the docker worker and spins up a docker container with the an image and giver parameters.

        Args:
            image(str): contianer image
            stageout_args (list): a list of files which are results from the execution
            job_args (str): a string of further arguments which might be needed for the task execution
            entrypoint (str): specify or overwrite the docker entrypoint
            command(str): you can specify or override the command to be executed
            args_to_dockerrun(str): docker options
            
        """

    image = params.get(
        "image"
    )  # {"image": 'ghcr.io/helmholtz-analytics/heat:1.1.1-alpha'}
    # stagein_args = params.get('stagein_args', []) # {"stagein_args": ["demo_knn.py", "iris.h5"]}
    job_args = params.get("job_args", "")
    entrypoint = params.get("entrypoint", "")  # {"entrypoint": "/bin/bash"}
    command = params.get("command", "")  # {"command": "python"}
    args_to_dockerrun = params.get("args_to_docker", "")

    user_id = "id -u"
    entrypoint_part = f"--entrypoint={entrypoint}" if entrypoint else ""

    working_dir = "/data"
    # file_args = stagein_args + stageout_args
    # args = " "
    # args = args.join(file_args)
    # args = args + string_args
    # cmd_part = f"-c \"{command} {args}\"" if command else args
    cmd_part = f'-c "{command}"' if command else ""
    volumes = f"-v {location}:{working_dir} -w={working_dir}"

    cmd = f'userid=$({user_id}) ; docker run {args_to_dockerrun} --user=$userid --rm --name="test" {volumes} {entrypoint_part} {image} {cmd_part} {job_args} > {location}/stdout.txt'

    return cmd