Warning

This document is for an old release 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.tools.deps.docker_util

"""Utilities for building up Docker commands...

...using common defaults and configuration mechanisms.
"""
import os

from six.moves import shlex_quote

from .commands import argv_to_str

DEFAULT_DOCKER_COMMAND = "docker"
DEFAULT_SUDO = True
DEFAULT_SUDO_COMMAND = "sudo"
DEFAULT_HOST = None
DEFAULT_VOLUME_MOUNT_TYPE = "rw"
DEFAULT_WORKING_DIRECTORY = None
DEFAULT_NET = None
DEFAULT_MEMORY = None
DEFAULT_VOLUMES_FROM = None
DEFAULT_AUTO_REMOVE = True
DEFAULT_SET_USER = "$UID"
DEFAULT_RUN_EXTRA_ARGUMENTS = None


[docs]class DockerVolume(object):
[docs] def __init__(self, path, to_path=None, how=DEFAULT_VOLUME_MOUNT_TYPE): self.from_path = path self.to_path = to_path or path if not DockerVolume.__valid_how(how): raise ValueError("Invalid way to specify Docker volume %s" % how) self.how = how
[docs] @staticmethod def volumes_from_str(volumes_as_str): if not volumes_as_str: return [] volume_strs = [v.strip() for v in volumes_as_str.split(",")] return [DockerVolume.volume_from_str(_) for _ in volume_strs]
[docs] @staticmethod def volume_from_str(as_str): if not as_str: raise ValueError("Failed to parse Docker volume from %s" % as_str) parts = as_str.split(":", 2) kwds = dict(path=parts[0]) if len(parts) == 2: if DockerVolume.__valid_how(parts[1]): kwds["how"] = parts[1] else: kwds["to_path"] = parts[1] elif len(parts) == 3: kwds["to_path"] = parts[1] kwds["how"] = parts[2] return DockerVolume(**kwds)
@staticmethod def __valid_how(how): return how in ["ro", "rw"] def __str__(self): return ":".join([self.from_path, self.to_path, self.how])
[docs]def kill_command( container, signal=None, **kwds ): args = (["-s", signal] if signal else []) + [container] return command_list("kill", args, **kwds)
[docs]def logs_command( container, **kwds ): return command_list("logs", **kwds)
[docs]def build_command( image, docker_build_path, **kwds ): if os.path.isfile(docker_build_path): docker_build_path = os.path.dirname(os.path.abspath(docker_build_path)) return command_list("build", ["-t", image, docker_build_path], **kwds)
[docs]def build_save_image_command( image, destination, **kwds ): return command_list("save", ["-o", destination, image], **kwds)
[docs]def build_pull_command( tag, **kwds ): return command_list("pull", [tag], **kwds)
[docs]def build_docker_cache_command( image, **kwds ): inspect_image_command = command_shell("inspect", [image], **kwds) pull_image_command = command_shell("pull", [image], **kwds) cache_command = "%s > /dev/null 2>&1\n[ $? -ne 0 ] && %s > /dev/null 2>&1\n" % (inspect_image_command, pull_image_command) return cache_command
[docs]def build_docker_images_command(truncate=True, **kwds): args = ["--no-trunc"] if not truncate else[] return command_shell("images", args, **kwds)
[docs]def build_docker_load_command(**kwds): return command_shell("load", [])
[docs]def build_docker_run_command( container_command, image, interactive=False, terminal=False, tag=None, volumes=[], volumes_from=DEFAULT_VOLUMES_FROM, memory=DEFAULT_MEMORY, env_directives=[], working_directory=DEFAULT_WORKING_DIRECTORY, name=None, net=DEFAULT_NET, run_extra_arguments=DEFAULT_RUN_EXTRA_ARGUMENTS, docker_cmd=DEFAULT_DOCKER_COMMAND, sudo=DEFAULT_SUDO, sudo_cmd=DEFAULT_SUDO_COMMAND, auto_rm=DEFAULT_AUTO_REMOVE, set_user=DEFAULT_SET_USER, host=DEFAULT_HOST, ): command_parts = _docker_prefix( docker_cmd=docker_cmd, sudo=sudo, sudo_cmd=sudo_cmd, host=host ) command_parts.append("run") if interactive: command_parts.append("-i") if terminal: command_parts.append("-t") for env_directive in env_directives: command_parts.extend(["-e", shlex_quote(env_directive)]) for volume in volumes: command_parts.extend(["-v", shlex_quote(str(volume))]) if volumes_from: command_parts.extend(["--volumes-from", shlex_quote(str(volumes_from))]) if memory: command_parts.extend(["-m", shlex_quote(memory)]) if name: command_parts.extend(["--name", shlex_quote(name)]) if working_directory: command_parts.extend(["-w", shlex_quote(working_directory)]) if net: command_parts.extend(["--net", shlex_quote(net)]) if auto_rm: command_parts.append("--rm") if run_extra_arguments: command_parts.append(run_extra_arguments) if set_user: user = set_user if set_user == DEFAULT_SET_USER: user = str(os.geteuid()) command_parts.extend(["-u", user]) full_image = image if tag: full_image = "%s:%s" % (full_image, tag) command_parts.append(shlex_quote(full_image)) command_parts.append(container_command) return " ".join(command_parts)
[docs]def command_list(command, command_args=[], **kwds): """Return Docker command as an argv list.""" command_parts = _docker_prefix(**kwds) command_parts.append(command) command_parts.extend(command_args) return command_parts
[docs]def command_shell(command, command_args=[], **kwds): """Return Docker command as a string for a shell or command-list.""" cmd = command_list(command, command_args, **kwds) to_str = kwds.get("to_str", True) if to_str: return argv_to_str(cmd) else: return cmd
def _docker_prefix( docker_cmd=DEFAULT_DOCKER_COMMAND, sudo=DEFAULT_SUDO, sudo_cmd=DEFAULT_SUDO_COMMAND, host=DEFAULT_HOST, **kwds ): """Prefix to issue a docker command.""" command_parts = [] if sudo: command_parts.append(sudo_cmd) command_parts.append(docker_cmd) if host: command_parts.extend(["-H", host]) return command_parts