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Source code for galaxy.tool_util.deps.docker_util
"""Utilities for building up Docker commands...
...using common defaults and configuration mechanisms.
"""
import os
from six.moves import shlex_quote
from galaxy.util.commands import argv_to_str
DEFAULT_DOCKER_COMMAND = "docker"
DEFAULT_SUDO = False
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]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[ $? -ne 0 ] && %s > /dev/null 2>&1\n" % (inspect_image_command, pull_image_command)
return cache_command
[docs]def build_docker_images_command(truncate=True, **kwds):
args = ["--no-trunc"] if not truncate else[]
return command_shell("images", args, **kwds)
[docs]def build_docker_simple_command(
command,
docker_cmd=DEFAULT_DOCKER_COMMAND,
sudo=DEFAULT_SUDO,
sudo_cmd=DEFAULT_SUDO_COMMAND,
container_name=None,
**kwd
):
command_parts = _docker_prefix(
docker_cmd=docker_cmd,
sudo=sudo,
sudo_cmd=sudo_cmd,
)
command_parts.append(command)
command_parts.append(container_name or '{CONTAINER_NAME}')
return " ".join(command_parts)
[docs]def build_docker_run_command(
container_command,
image,
interactive=False,
terminal=False,
tag=None,
volumes=[],
volumes_from=DEFAULT_VOLUMES_FROM,
memory=DEFAULT_MEMORY,
env_directives=[],
working_directory=DEFAULT_WORKING_DIRECTORY,
name=None,
net=DEFAULT_NET,
run_extra_arguments=DEFAULT_RUN_EXTRA_ARGUMENTS,
docker_cmd=DEFAULT_DOCKER_COMMAND,
sudo=DEFAULT_SUDO,
sudo_cmd=DEFAULT_SUDO_COMMAND,
auto_rm=DEFAULT_AUTO_REMOVE,
set_user=DEFAULT_SET_USER,
host=DEFAULT_HOST,
guest_ports=False,
container_name=None
):
command_parts = _docker_prefix(
docker_cmd=docker_cmd,
sudo=sudo,
sudo_cmd=sudo_cmd,
host=host
)
command_parts.append("run")
if interactive:
command_parts.append("-i")
if terminal:
command_parts.append("-t")
for env_directive in env_directives:
# e.g. -e "GALAXY_SLOTS=$GALAXY_SLOTS"
# These are environment variable expansions so we don't quote these.
command_parts.extend(["-e", env_directive])
if guest_ports is True:
# When is True, expose all ports
command_parts.append("-P")
elif guest_ports:
if not isinstance(guest_ports, list):
guest_ports = [guest_ports]
for guest_port in guest_ports:
command_parts.extend(["-p", guest_port])
if container_name:
command_parts.extend(["--name", container_name])
for volume in volumes:
command_parts.extend(["-v", 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
[docs]def parse_port_text(port_text):
"""
>>> slurm_ports = parse_port_text("8888/tcp -> 0.0.0.0:32769")
>>> slurm_ports[8888]['host']
'0.0.0.0'
"""
ports = None
if port_text is not None:
ports = {}
for line in port_text.strip().split('\n'):
if " -> " not in line:
raise Exception("Cannot parse host and port from line [%s]" % line)
tool, host = line.split(" -> ", 1)
hostname, port = host.split(':')
port = int(port)
tool_p, tool_prot = tool.split("/")
tool_p = int(tool_p)
ports[tool_p] = dict(tool_port=tool_p, host=hostname, port=port, protocol=tool_prot)
return ports