nipoppy.container.ContainerHandler

class nipoppy.container.ContainerHandler(args=None)

Abstract class for container handlers.

Parameters:

args (Iterable[str])

add_bind_arg(path_src, path_dest=None, mode='rw')

Add a bind path to the container args.

Parameters:

  • path_src (nipoppy.env.StrOrPathLike) – Path on disk. If this is a relative path or contains symlinks, it will be resolved

  • path_dest (Optional[nipoppy.env.StrOrPathLike], optional) – Path inside the container (if None, will be the same as the local path), by default None

  • mode (str, optional) – Read/write permissions, by default “rw”

add_env_arg(key, value)

Set environment variables for the container.

Parameters:
check_command_exists()

Check that the command is available (i.e. in PATH).

fix_bind_args()

Fix bind flags in args.

abstractmethod get_pull_command(uri, fpath_container)

Get the command to pull a container image to a specified location.

Parameters:

  • uri (Optional[str]) – URI of the container image (e.g. docker://…)

  • fpath_container (Optional[nipoppy.env.StrOrPathLike]) – Path where the container image should be saved

Returns:

The command string

Return type:

str

abstractmethod get_pull_confirmation_prompt(fpath_container)

Get the confirmation prompt for pulling the container image.

Parameters:

fpath_container (nipoppy.env.StrOrPathLike) – Path where the container image will be saved

Returns:

The confirmation prompt string

Return type:

str

get_shell_command(subcommand='run')

Get the shell command for running the container.

Parameters:

subcommand (str, optional) – Subcommand to use (e.g. “run”, “exec”), by default “run”

Returns:

The command string

Return type:

str

abstractmethod is_image_downloaded(uri, fpath_container)

Check if a container image has been downloaded.

Parameters:

  • uri (Optional[str]) – URI of the container image (e.g. docker://…)

  • fpath_container (Optional[nipoppy.env.StrOrPathLike]) – Path to the container image

Returns:

True if the container image exists at the specified path

Return type:

bool

args
property bind_flags: tuple[str]
Abstractmethod:

Return type:

tuple[str]

Flag for binding paths.

property command: str
Abstractmethod:

Return type:

str

Container executable name.

env_flag = '--env'