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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 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_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[ $? -ne 0 ] && %s > /dev/null 2>&1\n" % (inspect_image_command, pull_image_command)
return cache_command
[docs]def build_docker_images_command(truncate=True, **kwds):
args = ["--no-trunc"] if not truncate else[]
return command_shell("images", args, **kwds)
[docs]def build_docker_run_command(
container_command,
image,
interactive=False,
terminal=False,
tag=None,
volumes=[],
volumes_from=DEFAULT_VOLUMES_FROM,
memory=DEFAULT_MEMORY,
env_directives=[],
working_directory=DEFAULT_WORKING_DIRECTORY,
name=None,
net=DEFAULT_NET,
run_extra_arguments=DEFAULT_RUN_EXTRA_ARGUMENTS,
docker_cmd=DEFAULT_DOCKER_COMMAND,
sudo=DEFAULT_SUDO,
sudo_cmd=DEFAULT_SUDO_COMMAND,
auto_rm=DEFAULT_AUTO_REMOVE,
set_user=DEFAULT_SET_USER,
host=DEFAULT_HOST,
):
command_parts = _docker_prefix(
docker_cmd=docker_cmd,
sudo=sudo,
sudo_cmd=sudo_cmd,
host=host
)
command_parts.append("run")
if interactive:
command_parts.append("-i")
if terminal:
command_parts.append("-t")
for env_directive in env_directives:
# e.g. -e "GALAXY_SLOTS=$GALAXY_SLOTS"
# These are environment variable expansions so we don't quote these.
command_parts.extend(["-e", 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:
# If future-us is ever in here and fixing this for docker-machine just
# use cwltool.docker_id - it takes care of this default nicely.
euid = os.geteuid()
egid = os.getgid()
user = "%d:%d" % (euid, egid)
command_parts.extend(["--user", 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