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Source code for galaxy.tool_util.deps.container_classes
import os
import string
from abc import (
ABCMeta,
abstractmethod
)
from logging import getLogger
from uuid import uuid4
from galaxy.containers.docker_model import DockerVolume
from galaxy.util import (
asbool,
in_directory
)
from . import (
docker_util,
singularity_util
)
from .requirements import (
DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES,
DEFAULT_CONTAINER_SHELL,
)
log = getLogger(__name__)
DOCKER_CONTAINER_TYPE = "docker"
SINGULARITY_CONTAINER_TYPE = "singularity"
TRAP_KILL_CONTAINER = "trap _on_exit EXIT"
LOAD_CACHED_IMAGE_COMMAND_TEMPLATE = r'''
python << EOF
from __future__ import print_function
import json
import re
import subprocess
import tarfile
t = tarfile.TarFile("${cached_image_file}")
meta_str = t.extractfile('repositories').read()
meta = json.loads(meta_str)
tag, tag_value = next(iter(meta.items()))
rev, rev_value = next(iter(tag_value.items()))
cmd = "${images_cmd}"
proc = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
stdo, stde = proc.communicate()
found = False
for line in stdo.split("\n"):
tmp = re.split(r'\s+', line)
if tmp[0] == tag and tmp[1] == rev and tmp[2] == rev_value:
found = True
if not found:
print("Loading image")
cmd = "cat ${cached_image_file} | ${load_cmd}"
subprocess.check_call(cmd, shell=True)
EOF
'''
SOURCE_CONDA_ACTIVATE = """
# Check if container was created by installing conda packages,
# and if so, source scripts to populate environment variables
# that would be set by activating the conda environment.
if [ -d /usr/local/etc/conda/activate.d ]; then
export CONDA_PREFIX=/usr/local
for f in /usr/local/etc/conda/activate.d/*.sh; do
case "$f" in
"/usr/local/etc/conda/activate.d/activate-"*) :;;
*) . "$f" ;;
esac;
done
fi
"""
[docs]class Container(metaclass=ABCMeta):
[docs] def __init__(self, container_id, app_info, tool_info, destination_info, job_info, container_description, container_name=None):
self.container_id = container_id
self.app_info = app_info
self.tool_info = tool_info
self.destination_info = destination_info
self.job_info = job_info
self.container_description = container_description
self.container_name = container_name or uuid4().hex
self.container_info = {}
[docs] def prop(self, name, default):
destination_name = f"{self.container_type}_{name}"
return self.destination_info.get(destination_name, default)
@property
def resolve_dependencies(self):
return DEFAULT_CONTAINER_RESOLVE_DEPENDENCIES if not self.container_description else self.container_description.resolve_dependencies
@property
def shell(self):
return DEFAULT_CONTAINER_SHELL if not self.container_description else self.container_description.shell
@property
def source_environment(self):
if self.container_description and not self.container_description.explicit:
return SOURCE_CONDA_ACTIVATE
return ""
[docs] @abstractmethod
def containerize_command(self, command):
"""
Use destination supplied container configuration parameters,
container_id, and command to build a new command that runs
input command in container.
"""
[docs]def preprocess_volumes(volumes_raw_str, container_type):
"""Process Galaxy volume specification string to either Docker or Singularity specification.
Galaxy allows the mount try "default_ro" which translates to ro for Docker and
ro for Singularity iff no subdirectories are rw (Singularity does not allow ro
parent directories with rw subdirectories).
>>> preprocess_volumes(None, DOCKER_CONTAINER_TYPE)
[]
>>> preprocess_volumes("", DOCKER_CONTAINER_TYPE)
[]
>>> preprocess_volumes("/a/b", DOCKER_CONTAINER_TYPE)
['/a/b:rw']
>>> preprocess_volumes("/a/b:ro,/a/b/c:rw", DOCKER_CONTAINER_TYPE)
['/a/b:ro', '/a/b/c:rw']
>>> preprocess_volumes("/a/b:/a:ro,/a/b/c:/a/b:rw", DOCKER_CONTAINER_TYPE)
['/a/b:/a:ro', '/a/b/c:/a/b:rw']
>>> preprocess_volumes("/a/b:default_ro,/a/b/c:rw", DOCKER_CONTAINER_TYPE)
['/a/b:ro', '/a/b/c:rw']
>>> preprocess_volumes("/a/b:default_ro,/a/b/c:ro", SINGULARITY_CONTAINER_TYPE)
['/a/b:ro', '/a/b/c:ro']
>>> preprocess_volumes("/a/b:default_ro,/a/b/c:rw", SINGULARITY_CONTAINER_TYPE)
['/a/b', '/a/b/c']
"""
if not volumes_raw_str:
return []
volumes_raw_strs = [v.strip() for v in volumes_raw_str.split(",")]
volumes = []
rw_paths = []
for volume_raw_str in volumes_raw_strs:
volume_parts = volume_raw_str.split(":")
if len(volume_parts) > 3:
raise Exception(f"Unparsable volumes string in configuration [{volumes_raw_str}]")
if len(volume_parts) == 3:
volume_parts = [f"{volume_parts[0]}:{volume_parts[1]}", volume_parts[2]]
if len(volume_parts) == 2 and volume_parts[1] not in ("rw", "ro", "default_ro"):
volume_parts = [f"{volume_parts[0]}:{volume_parts[1]}", "rw"]
if len(volume_parts) == 1:
volume_parts.append("rw")
volumes.append(volume_parts)
if volume_parts[1] == "rw":
rw_paths.append(volume_parts[0])
for volume in volumes:
path = volume[0]
how = volume[1]
if how == "default_ro":
how = "ro"
if container_type == SINGULARITY_CONTAINER_TYPE:
for rw_path in rw_paths:
if in_directory(rw_path, path):
how = "rw"
volume[1] = how
# for a while singularity did not allow to specify the bind type rw
# (which is the default). so we omit this default
# see https://github.com/hpcng/singularity/pull/5487
if container_type == SINGULARITY_CONTAINER_TYPE and volume[1] == 'rw':
del volume[1]
return [":".join(v) for v in volumes]
[docs]class HasDockerLikeVolumes:
"""Mixin to share functionality related to Docker volume handling.
Singularity seems to have a fairly compatible syntax for volume handling.
"""
def _expand_volume_str(self, value):
if not value:
return value
template = string.Template(value)
variables = dict()
def add_var(name, value):
if value:
if not value.startswith("$"):
value = os.path.abspath(value)
variables[name] = value
add_var("working_directory", self.job_info.working_directory)
add_var("tmp_directory", self.job_info.tmp_directory)
add_var("job_directory", self.job_info.job_directory)
add_var("tool_directory", self.job_info.tool_directory)
add_var("home_directory", self.job_info.home_directory)
add_var("galaxy_root", self.app_info.galaxy_root_dir)
add_var("default_file_path", self.app_info.default_file_path)
add_var("library_import_dir", self.app_info.library_import_dir)
add_var('tool_data_path', self.app_info.tool_data_path)
add_var('shed_tool_data_path', self.app_info.shed_tool_data_path)
if self.job_info.job_directory and self.job_info.job_directory_type == "pulsar":
# We have a Pulsar job directory, so everything needed (excluding index
# files) should be available in job_directory...
defaults = "$job_directory:default_ro"
if self.job_info.tool_directory:
defaults += ",$tool_directory:default_ro"
defaults += ",$job_directory/outputs:rw,$working_directory:rw"
else:
defaults = "$galaxy_root:default_ro"
if self.job_info.tool_directory:
defaults += ",$tool_directory:default_ro"
if self.job_info.job_directory:
defaults += ",$job_directory:default_ro,$job_directory/outputs:rw"
if self.tool_info.profile <= 19.09:
defaults += ",$job_directory/configs:rw"
if self.job_info.tmp_directory is not None:
defaults += ",$tmp_directory:rw"
# If a tool definitely has a temp directory available set it to /tmp in container for compat.
# with CWL. This is part of that spec and should make it easier to share containers between CWL
# and Galaxy.
defaults += ",$tmp_directory:/tmp:rw"
else:
defaults += ",$_GALAXY_JOB_TMP_DIR:rw"
if self.job_info.home_directory is not None:
defaults += ",$home_directory:rw"
if self.app_info.outputs_to_working_directory:
# Should need default_file_path (which is of course an estimate given
# object stores anyway).
defaults += ",$working_directory:rw,$default_file_path:default_ro"
else:
defaults += ",$working_directory:rw,$default_file_path:rw"
if self.app_info.library_import_dir:
defaults += ",$library_import_dir:default_ro"
if self.app_info.tool_data_path:
defaults += ",$tool_data_path:default_ro"
if self.app_info.shed_tool_data_path:
defaults += ",$shed_tool_data_path:default_ro"
# Define $defaults that can easily be extended with external library and
# index data without deployer worrying about above details.
variables["defaults"] = string.Template(defaults).safe_substitute(variables)
volumes_str = template.safe_substitute(variables)
# Not all tools have a tool_directory - strip this out if supplied by
# job_conf.
tool_directory_index = volumes_str.find("$tool_directory")
if tool_directory_index > 0:
end_index = volumes_str.find(",", tool_directory_index)
if end_index < 0:
end_index = len(volumes_str)
volumes_str = volumes_str[0:tool_directory_index] + volumes_str[end_index:len(volumes_str)]
return volumes_str
[docs]class DockerContainer(Container, HasDockerLikeVolumes):
container_type = DOCKER_CONTAINER_TYPE
@property
def docker_host_props(self):
docker_host_props = dict(
docker_cmd=self.prop("cmd", docker_util.DEFAULT_DOCKER_COMMAND),
sudo=asbool(self.prop("sudo", docker_util.DEFAULT_SUDO)),
sudo_cmd=self.prop("sudo_cmd", docker_util.DEFAULT_SUDO_COMMAND),
host=self.prop("host", docker_util.DEFAULT_HOST),
)
return docker_host_props
@property
def connection_configuration(self):
return self.docker_host_props
[docs] def build_pull_command(self):
return docker_util.build_pull_command(self.container_id, **self.docker_host_props)
[docs] def containerize_command(self, command):
env_directives = []
for pass_through_var in self.tool_info.env_pass_through:
env_directives.append(f'"{pass_through_var}=${pass_through_var}"')
# Allow destinations to explicitly set environment variables just for
# docker container. Better approach is to set for destination and then
# pass through only what tool needs however. (See todo in ToolInfo.)
for key, value in self.destination_info.items():
if key.startswith("docker_env_"):
env = key[len("docker_env_"):]
env_directives.append(f'"{env}={value}"')
working_directory = self.job_info.working_directory
if not working_directory:
raise Exception(f"Cannot containerize command [{working_directory}] without defined working directory.")
volumes_raw = self._expand_volume_str(self.destination_info.get("docker_volumes", "$defaults"))
preprocessed_volumes_list = preprocess_volumes(volumes_raw, self.container_type)
# TODO: Remove redundant volumes...
volumes = [DockerVolume.from_str(v) for v in preprocessed_volumes_list]
volumes_from = self.destination_info.get("docker_volumes_from", docker_util.DEFAULT_VOLUMES_FROM)
docker_host_props = self.docker_host_props
cached_image_file = self.__get_cached_image_file()
if not cached_image_file:
# TODO: Add option to cache it once here and create cached_image_file.
cache_command = docker_util.build_docker_cache_command(self.container_id, **docker_host_props)
else:
cache_command = self.__cache_from_file_command(cached_image_file, docker_host_props)
run_command = docker_util.build_docker_run_command(
command,
self.container_id,
volumes=volumes,
volumes_from=volumes_from,
env_directives=env_directives,
working_directory=working_directory,
net=self.prop("net", None), # By default, docker instance has networking disabled
auto_rm=asbool(self.prop("auto_rm", docker_util.DEFAULT_AUTO_REMOVE)),
set_user=self.prop("set_user", docker_util.DEFAULT_SET_USER),
run_extra_arguments=self.prop("run_extra_arguments", docker_util.DEFAULT_RUN_EXTRA_ARGUMENTS),
guest_ports=self.tool_info.guest_ports,
container_name=self.container_name,
**docker_host_props
)
kill_command = docker_util.build_docker_simple_command("kill", container_name=self.container_name, **docker_host_props)
# Suppress standard error below in the kill command because it can cause jobs that otherwise would work
# to fail. Likely, in these cases the container has been stopped normally and so cannot be stopped again.
# A less hacky approach might be to check if the container is running first before trying to kill.
# https://stackoverflow.com/questions/34228864/stop-and-delete-docker-container-if-its-running
# Standard error is:
# Error response from daemon: Cannot kill container: 2b0b961527574ebc873256b481bbe72e: No such container: 2b0b961527574ebc873256b481bbe72e
return f"""
_on_exit() {{
{kill_command} &> /dev/null
}}
{TRAP_KILL_CONTAINER}
{cache_command}
{run_command}"""
def __cache_from_file_command(self, cached_image_file, docker_host_props):
images_cmd = docker_util.build_docker_images_command(truncate=False, **docker_host_props)
load_cmd = docker_util.build_docker_load_command(**docker_host_props)
return string.Template(LOAD_CACHED_IMAGE_COMMAND_TEMPLATE).safe_substitute(
cached_image_file=cached_image_file,
images_cmd=images_cmd,
load_cmd=load_cmd
)
def __get_cached_image_file(self):
container_id = self.container_id
cache_directory = os.path.abspath(self.__get_destination_overridable_property("container_image_cache_path"))
cache_path = docker_cache_path(cache_directory, container_id)
return cache_path if os.path.exists(cache_path) else None
def __get_destination_overridable_property(self, name):
prop_name = f"docker_{name}"
if prop_name in self.destination_info:
return self.destination_info[prop_name]
else:
return getattr(self.app_info, name)
[docs]def docker_cache_path(cache_directory, container_id):
file_container_id = container_id.replace("/", "_slash_")
cache_file_name = f"docker_{file_container_id}.tar"
return os.path.join(cache_directory, cache_file_name)
[docs]class SingularityContainer(Container, HasDockerLikeVolumes):
container_type = SINGULARITY_CONTAINER_TYPE
[docs] def get_singularity_target_kwds(self):
return dict(
singularity_cmd=self.prop("cmd", singularity_util.DEFAULT_SINGULARITY_COMMAND),
sudo=asbool(self.prop("sudo", singularity_util.DEFAULT_SUDO)),
sudo_cmd=self.prop("sudo_cmd", singularity_util.DEFAULT_SUDO_COMMAND),
)
@property
def connection_configuration(self):
return self.get_singularity_target_kwds()
[docs] def build_mulled_singularity_pull_command(self, cache_directory, namespace="biocontainers"):
return singularity_util.pull_mulled_singularity_command(
docker_image_identifier=self.container_id,
cache_directory=cache_directory,
namespace=namespace,
**self.get_singularity_target_kwds()
)
[docs] def build_singularity_pull_command(self, cache_path):
return singularity_util.pull_singularity_command(
image_identifier=self.container_id,
cache_path=cache_path,
**self.get_singularity_target_kwds()
)
[docs] def containerize_command(self, command):
env = []
for pass_through_var in self.tool_info.env_pass_through:
env.append((pass_through_var, f"${pass_through_var}"))
# Allow destinations to explicitly set environment variables just for
# docker container. Better approach is to set for destination and then
# pass through only what tool needs however. (See todo in ToolInfo.)
for key, value in self.destination_info.items():
if key.startswith("singularity_env_"):
real_key = key[len("singularity_env_"):]
env.append((real_key, value))
working_directory = self.job_info.working_directory
if not working_directory:
raise Exception(f"Cannot containerize command [{working_directory}] without defined working directory.")
volumes_raw = self._expand_volume_str(self.destination_info.get("singularity_volumes", "$defaults"))
preprocessed_volumes_list = preprocess_volumes(volumes_raw, self.container_type)
volumes = [DockerVolume.from_str(v) for v in preprocessed_volumes_list]
run_command = singularity_util.build_singularity_run_command(
command,
self.container_id,
volumes=volumes,
env=env,
working_directory=working_directory,
run_extra_arguments=self.prop("run_extra_arguments", singularity_util.DEFAULT_RUN_EXTRA_ARGUMENTS),
guest_ports=self.tool_info.guest_ports,
container_name=self.container_name,
**self.get_singularity_target_kwds()
)
return run_command
CONTAINER_CLASSES = dict(
docker=DockerContainer,
singularity=SingularityContainer,
)
NULL_CONTAINER = NullContainer()