This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.tool_util.deps.container_volumes

import shlex
from abc import (

[docs]class ContainerVolume(metaclass=ABCMeta): valid_modes = frozenset({"ro", "rw"})
[docs] def __init__(self, path, host_path=None, mode=None): self.path = path self.host_path = host_path self.mode = mode if mode and not self.mode_is_valid: raise ValueError(f"Invalid container volume mode: {mode}")
[docs] @abstractmethod def from_str(cls, as_str): """Classmethod to convert from this container type's string representation. :param as_str: string representation of volume :type as_str: str """
@abstractmethod def __str__(self): """Return this container type's string representation of the volume.""" @property def mode_is_valid(self): return self.mode in self.valid_modes
[docs]class DockerVolume(ContainerVolume):
[docs] @classmethod def from_str(cls, as_str): """Construct an instance from a string as would be passed to `docker run --volume`. A string in the format ``<host_path>:<mode>`` is supported for legacy purposes even though it is not valid Docker volume syntax. """ if not as_str: raise ValueError(f"Failed to parse Docker volume from {as_str}") parts = as_str.split(":", 2) kwds = dict(host_path=parts[0]) if len(parts) == 1: # auto-generated volume kwds["path"] = kwds["host_path"] elif len(parts) == 2: # /host_path:mode is not (or is no longer?) valid Docker volume syntax if parts[1] in DockerVolume.valid_modes: kwds["mode"] = parts[1] kwds["path"] = kwds["host_path"] else: kwds["path"] = parts[1] elif len(parts) == 3: kwds["path"] = parts[1] kwds["mode"] = parts[2] return cls(**kwds)
def __str__(self): volume_str = ":".join(filter(lambda x: x is not None, (self.host_path, self.path, self.mode))) if "$" not in volume_str: volume_for_cmd_line = shlex.quote(volume_str) else: # e.g. $_GALAXY_JOB_TMP_DIR:$_GALAXY_JOB_TMP_DIR:rw so don't single quote. volume_for_cmd_line = f'"{volume_str}"' return volume_for_cmd_line