Warning
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.containers
"""
Interfaces to containerization software
"""
from __future__ import absolute_import
import errno
import inspect
import logging
import shlex
import subprocess
import sys
import uuid
from abc import (
ABCMeta,
abstractmethod,
abstractproperty
)
from collections import namedtuple
import yaml
from six import string_types, with_metaclass
from six.moves import shlex_quote
from galaxy.exceptions import ContainerCLIError
from galaxy.util.submodules import import_submodules
DEFAULT_CONTAINER_TYPE = 'docker'
DEFAULT_CONF = {'_default_': {'type': DEFAULT_CONTAINER_TYPE}}
log = logging.getLogger(__name__)
[docs]class ContainerPort(namedtuple('ContainerPort', ('port', 'protocol', 'hostaddr', 'hostport'))):
"""Named tuple representing ports published by a container, with attributes:
:ivar port: Port number (inside the container)
:vartype port: int
:ivar protocol: Port protocol, either ``tcp`` or ``udp``
:vartype protocol: str
:ivar hostaddr: Address or hostname where the published port can be accessed
:vartype hostaddr: str
:ivar hostport: Published port number on which the container can be accessed
:vartype hostport: int
"""
[docs]class ContainerVolume(with_metaclass(ABCMeta, object)):
valid_modes = frozenset(["ro", "rw"])
[docs] def __init__(self, path, host_path=None, mode=None):
self.path = path
self.host_path = host_path
self.mode = mode
if mode and not self.mode_is_valid:
raise ValueError("Invalid container volume mode: %s" % mode)
[docs] @abstractmethod
def from_str(cls, as_str):
"""Classmethod to convert from this container type's string representation.
:param as_str: string representation of volume
:type as_str: str
"""
@abstractmethod
def __str__(self):
"""Return this container type's string representation of the volume.
"""
[docs] @abstractmethod
def to_native(self):
"""Return this container type's native representation of the volume.
"""
@property
def mode_is_valid(self):
return self.mode in self.valid_modes
[docs]class Container(with_metaclass(ABCMeta, object)):
[docs] def __init__(self, interface, id, name=None, **kwargs):
""":param interface: Container interface for the given container type
:type interface: :class:`ContainerInterface` subclass instance
:param id: Container identifier
:type id: str
:param name: Container name
:type name: str
"""
self._interface = interface
self._id = id
self._name = name
@property
def id(self):
"""The container's id"""
return self._id
@property
def name(self):
"""The container's name"""
return self._name
[docs] @abstractmethod
def from_id(cls, interface, id):
"""Classmethod to create an instance of Container from the container system's id for the given container type.
:param interface: Container insterface for the given id
:type interface: :class:`ContainerInterface` subclass instance
:param id: Container identifier
:type id: str
:returns: Container object
:rtype: :class:`Container` subclass instance
"""
@abstractproperty
def ports(self):
"""Attribute for accessing details of ports published by the container.
:returns: Port details
:rtype: list of :class:`ContainerPort`s
"""
@abstractproperty
def address(self):
"""Attribute for accessing the address or hostname where published ports can be accessed.
:returns: Hostname or IP address
:rtype: str
"""
[docs] @abstractmethod
def is_ready(self):
"""Indicate whether or not the container is "ready" (up, available, running).
:returns: True if ready, else False
:rtpe: bool
"""
[docs] def map_port(self, port):
"""Map a given container port to a host address/port.
For legacy reasons, if port is ``None``, the first port (if any) will be returned
:param port: Container port to map
:type port: int
:returns: Mapping to host address/port for given container port
:rtype: :class:`ContainerPort` instance
"""
mapping = None
ports = self.ports or []
for mapping in ports:
if port == mapping.port:
return mapping
if port is None:
log.warning("Container %s (%s): Don't know how to map ports to containers with multiple exposed ports "
"when a specific port is not requested. Arbitrarily choosing first: %s",
self.name, self.id, mapping)
return mapping
else:
if port is None:
log.warning("Container %s (%s): No exposed ports found!", self.name, self.id)
else:
log.warning("Container %s (%s): No mapping found for port: %s", self.name, self.id, port)
return None
[docs]class ContainerInterface(with_metaclass(ABCMeta, object)):
container_type = None
container_class = None
volume_class = None
conf_defaults = {
'name_prefix': 'galaxy_',
}
option_map = {}
publish_port_list_required = False
supports_volumes = True
[docs] def __init__(self, conf, key, containers_config_file):
self._key = key
self._containers_config_file = containers_config_file
mro = reversed(self.__class__.__mro__)
next(mro)
self._conf = ContainerInterfaceConfig()
for c in mro:
self._conf.update(c.conf_defaults)
self._conf.update(conf)
self.validate_config()
def _normalize_command(self, command):
if isinstance(command, string_types):
command = shlex.split(command)
return command
def _guess_kwopt_type(self, val):
opttype = 'string'
if isinstance(val, bool):
opttype = 'boolean'
elif isinstance(val, list):
opttype = 'list'
try:
if isinstance(val[0], tuple) and len(val[0]) == 3:
opttype = 'list_of_kovtrips'
except IndexError:
pass
elif isinstance(val, dict):
opttype = 'list_of_kvpairs'
return opttype
def _guess_kwopt_flag(self, opt):
return '--%s' % opt.replace('_', '-')
def _stringify_kwopts(self, kwopts):
opts = []
for opt, val in kwopts.items():
try:
optdef = self.option_map[opt]
except KeyError:
optdef = {
'flag': self._guess_kwopt_flag(opt),
'type': self._guess_kwopt_type(val),
}
log.warning("option '%s' not in %s.option_map, guessing flag '%s' type '%s'",
opt, self.__class__.__name__, optdef['flag'], optdef['type'])
opts.append(getattr(self, '_stringify_kwopt_' + optdef['type'])(optdef['flag'], val))
return ' '.join(opts)
def _stringify_kwopt_boolean(self, flag, val):
"""
"""
return '{flag}={value}'.format(flag=flag, value=str(val).lower())
def _stringify_kwopt_string(self, flag, val):
"""
"""
return '{flag} {value}'.format(flag=flag, value=shlex_quote(str(val)))
def _stringify_kwopt_list(self, flag, val):
"""
"""
if isinstance(val, string_types):
return self._stringify_kwopt_string(flag, val)
return ' '.join(['{flag} {value}'.format(flag=flag, value=shlex_quote(str(v))) for v in val])
def _stringify_kwopt_list_of_kvpairs(self, flag, val):
"""
"""
l = []
if isinstance(val, list):
# ['foo=bar', 'baz=quux']
l = val
else:
# {'foo': 'bar', 'baz': 'quux'}
for k, v in dict(val).items():
l.append('{k}={v}'.format(k=k, v=v))
return self._stringify_kwopt_list(flag, l)
def _stringify_kwopt_list_of_kovtrips(self, flag, val):
"""
"""
if isinstance(val, string_types):
return self._stringify_kwopt_string(flag, val)
l = []
for k, o, v in val:
l.append('{k}{o}{v}'.format(k=k, o=o, v=v))
return self._stringify_kwopt_list(flag, l)
def _run_command(self, command, verbose=False):
if verbose:
log.debug('running command: [%s]', command)
command_list = self._normalize_command(command)
p = subprocess.Popen(command_list, stdout=subprocess.PIPE, stderr=subprocess.PIPE, close_fds=True)
stdout, stderr = p.communicate()
if p.returncode == 0:
return stdout.strip()
else:
msg = "Command '{}' returned non-zero exit status {}".format(command, p.returncode)
log.error(msg + ': ' + stderr.strip())
raise ContainerCLIError(
msg,
stdout=stdout.strip(),
stderr=stderr.strip(),
returncode=p.returncode,
command=command,
subprocess_command=command_list)
@property
def key(self):
return self._key
@property
def containers_config_file(self):
return self._containers_config_file
[docs] def get_container(self, container_id):
return self.container_class.from_id(self, container_id)
[docs] def set_kwopts_name(self, kwopts):
if self._name_prefix is not None:
name = '{prefix}{name}'.format(
prefix=self._name_prefix,
name=kwopts.get('name', uuid.uuid4().hex)
)
kwopts['name'] = name
[docs]class ContainerInterfaceConfig(dict):
def __setattr__(self, name, value):
self[name] = value
def __getattr__(self, name):
try:
return self[name]
except KeyError:
raise AttributeError("'%s' object has no attribute '%s'" % (self.__class__.__name__, name))
[docs]def build_container_interfaces(containers_config_file, containers_conf=None):
"""Build :class:`ContainerInterface`s. Pass ``containers_conf`` to avoid rereading the config file.
:param containers_config_file: Filename of containers_conf.yml
:type containers_config_file: str
:param containers_conf: Optional containers conf (as read from containers_conf.yml), will be used in place
of containers_config_file
:type containers_conf: dict
:returns: Instantiated container interfaces with keys corresponding to ``containers`` keys
:rtype: dict of :class:`ContainerInterface` subclass instances
"""
if not containers_conf:
containers_conf = parse_containers_config(containers_config_file)
interface_classes = _get_interface_modules()
interfaces = {}
for k, conf in containers_conf.items():
container_type = conf.get('type', DEFAULT_CONTAINER_TYPE)
assert container_type in interface_classes, "unknown container interface type: %s" % container_type
interfaces[k] = interface_classes[container_type](conf, k, containers_config_file)
return interfaces
[docs]def parse_containers_config(containers_config_file):
"""Parse a ``containers_conf.yml`` and return the contents of its ``containers`` dictionary.
:param containers_config_file: Filename of containers_conf.yml
:type containers_config_file: str
:returns: Contents of the dictionary under the ``containers`` key
:rtype: dict
"""
conf = DEFAULT_CONF.copy()
try:
with open(containers_config_file) as fh:
c = yaml.safe_load(fh)
conf.update(c.get('containers', {}))
except (OSError, IOError) as exc:
if exc.errno == errno.ENOENT:
log.debug("config file '%s' does not exist, running with default config", containers_config_file)
else:
raise
return conf
def _get_interface_modules():
interfaces = []
modules = import_submodules(sys.modules[__name__])
for module in modules:
module_names = [getattr(module, _) for _ in dir(module)]
classes = [_ for _ in module_names if inspect.isclass(_) and
not _ == ContainerInterface and issubclass(_, ContainerInterface)]
interfaces.extend(classes)
return dict((x.container_type, x) for x in interfaces)