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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
import shlex
import sys
from typing import (
List,
Optional,
TYPE_CHECKING,
Union,
)
if TYPE_CHECKING:
from .container_volumes import DockerVolume
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 = None if sys.platform == "darwin" else "$UID"
DEFAULT_RUN_EXTRA_ARGUMENTS = None
[docs]def kill_command(container: str, signal: Optional[str] = None, **kwds) -> List[str]:
args = (["-s", signal] if signal else []) + [container]
return command_list("kill", args, **kwds)
[docs]def logs_command(container: str, **kwds) -> List[str]:
return command_list("logs", [container], **kwds)
[docs]def build_command(image: str, docker_build_path: str, **kwds) -> List[str]:
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: str, destination: str, **kwds) -> List[str]:
return command_list("save", ["-o", destination, image], **kwds)
[docs]def build_pull_command(tag: str, **kwds) -> List[str]:
return command_list("pull", [tag], **kwds)
[docs]def build_docker_cache_command(image: str, **kwds) -> str:
assert kwds.get("to_str", True)
inspect_image_command = command_shell("inspect", [image], **kwds)
pull_image_command = command_shell("pull", [image], **kwds)
cache_command = f"{inspect_image_command} > /dev/null 2>&1\n[ $? -ne 0 ] && {pull_image_command} > /dev/null 2>&1\n"
return cache_command
[docs]def build_docker_images_command(truncate=True, **kwds) -> Union[str, List[str]]:
args = ["--no-trunc"] if not truncate else []
return command_shell("images", args, **kwds)
[docs]def build_docker_load_command(**kwds) -> Union[str, List[str]]:
return command_shell("load", [])
[docs]def build_docker_simple_command(
command: str,
docker_cmd: str = DEFAULT_DOCKER_COMMAND,
sudo: bool = DEFAULT_SUDO,
sudo_cmd: str = DEFAULT_SUDO_COMMAND,
container_name: Optional[str] = None,
**kwd,
) -> str:
command_parts = _docker_prefix(
docker_cmd=docker_cmd,
sudo=sudo,
sudo_cmd=sudo_cmd,
)
command_parts.append(command)
command_parts.append(container_name or "{CONTAINER_NAME}")
return " ".join(command_parts)
[docs]def build_docker_run_command(
container_command: str,
image: str,
interactive: bool = False,
terminal: bool = False,
tag: Optional[str] = None,
volumes: Optional[List["DockerVolume"]] = None,
volumes_from: Optional[str] = DEFAULT_VOLUMES_FROM,
memory: Optional[str] = DEFAULT_MEMORY,
env_directives: Optional[List[str]] = None,
working_directory: Optional[str] = DEFAULT_WORKING_DIRECTORY,
name: Optional[str] = None,
net: Optional[str] = DEFAULT_NET,
run_extra_arguments: Optional[str] = DEFAULT_RUN_EXTRA_ARGUMENTS,
docker_cmd: str = DEFAULT_DOCKER_COMMAND,
sudo: bool = DEFAULT_SUDO,
sudo_cmd: str = DEFAULT_SUDO_COMMAND,
auto_rm: bool = DEFAULT_AUTO_REMOVE,
set_user: Optional[str] = DEFAULT_SET_USER,
host: Optional[str] = DEFAULT_HOST,
guest_ports: Union[bool, str, List[str]] = False,
container_name: Optional[str] = None,
) -> str:
env_directives = env_directives or []
volumes = volumes or []
command_parts = _docker_prefix(docker_cmd=docker_cmd, sudo=sudo, sudo_cmd=sudo_cmd, host=host)
command_parts.append("run")
if interactive:
command_parts.append("-i")
if terminal:
command_parts.append("-t")
for env_directive in env_directives:
# e.g. -e "GALAXY_SLOTS=$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)])
command_parts.extend(["--cpus", "${GALAXY_SLOTS:-1}"])
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 = f"{full_image}:{tag}"
command_parts.append(shlex.quote(full_image))
command_parts.append(container_command)
return " ".join(command_parts)
[docs]def command_list(command: str, command_args: Optional[List[str]] = None, **kwds) -> List[str]:
"""Return Docker command as an argv list."""
command_args = command_args or []
command_parts = _docker_prefix(**kwds)
command_parts.append(command)
command_parts.extend(command_args)
return command_parts
[docs]def command_shell(command: str, command_args: Optional[List[str]] = None, **kwds) -> Union[str, List[str]]:
"""Return Docker command as a string for a shell or command-list."""
command_args = command_args or []
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: str = DEFAULT_DOCKER_COMMAND,
sudo: bool = DEFAULT_SUDO,
sudo_cmd: str = DEFAULT_SUDO_COMMAND,
host: Optional[str] = DEFAULT_HOST,
**kwds,
) -> List[str]:
"""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 = parse_port_text("5432/tcp -> :::5432")
>>> len(ports)
0
>>> ports_new = parse_port_text("5432/tcp -> [::]:5432")
>>> len(ports_new)
0
"""
ports = None
if port_text is not None:
ports = {}
for line in port_text.strip().split("\n"):
if " -> " not in line:
raise Exception(f"Cannot parse host and port from line [{line}]")
tool, host = line.split(" -> ", 1)
hostname, port = host.rsplit(":", 1)
if hostname in ["::", "[::]"]:
# Skip unspecified IPv6 address, which is also specified as 0:0:0:0 in another line.
# This is brittle of course, but so is parsing the container ports like this.
continue
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