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.docker_util

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

...using common defaults and configuration mechanisms.

import os
import shlex
import sys
from typing import (

    from .container_volumes import DockerVolume

from galaxy.util.commands import argv_to_str

DEFAULT_SET_USER = None if sys.platform == "darwin" else "$UID"

[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 ->") >>> slurm_ports[8888]['host'] '' >>> 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