springsuite: planemo/lib/python3.7/site-packages/galaxy/containers/docker.py comparison

comparison planemo/lib/python3.7/site-packages/galaxy/containers/docker.py @ 0:d30785e31577 draft

"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"

author	guerler
date	Fri, 31 Jul 2020 00:18:57 -0400
parents
children

comparison

equal deleted inserted replaced

--1:000000000000
+:d30785e31577
+"""
+Interface to Docker
+"""
+from __future__ import absolute_import
+import logging
+import os
+from functools import partial
+from itertools import cycle, repeat
+from time import sleep
+try:
+import docker
+except ImportError:
+docker = None
+try:
+from requests.exceptions import ConnectionError, ReadTimeout
+except ImportError:
+ConnectionError = None
+ReadTimeout = None
+from six import string_types
+from six.moves import shlex_quote
+from galaxy.containers import ContainerInterface
+from galaxy.containers.docker_decorators import (
+docker_columns,
+docker_json
+)
+from galaxy.containers.docker_model import (
+DockerContainer,
+DockerVolume
+)
+from galaxy.exceptions import (
+ContainerCLIError,
+ContainerImageNotFound,
+ContainerNotFound
+)
+from galaxy.util.json import safe_dumps_formatted
+log = logging.getLogger(__name__)
+class DockerInterface(ContainerInterface):
+container_class = DockerContainer
+volume_class = DockerVolume
+conf_defaults = {
+'host': None,
+'tls': False,
+'force_tlsverify': False,
+'auto_remove': True,
+'image': None,
+'cpus': None,
+'memory': None,
+}
+# These values are inserted into kwopts for run commands
+conf_run_kwopts = (
+'cpus',
+'memory',
+)
+def validate_config(self):
+super(DockerInterface, self).validate_config()
+self.__host_iter = None
+if self._conf.host is None or isinstance(self._conf.host, string_types):
+self.__host_iter = repeat(self._conf.host)
+else:
+self.__host_iter = cycle(self._conf.host)
+@property
+def _default_image(self):
+assert self._conf.image is not None, "No default image for this docker interface"
+return self._conf.image
+def run_in_container(self, command, image=None, **kwopts):
+for opt in self.conf_run_kwopts:
+if self._conf[opt]:
+kwopts[opt] = self._conf[opt]
+self.set_kwopts_name(kwopts)
+return self.run(command, image=image, **kwopts)
+def image_repodigest(self, image):
+"""Get the digest image string for an image.
+:type image: str
+:param image: image id or image name and optionally, tag
+:returns: digest string, having the format `<name>@<hash_alg>:<digest>`, e.g.:
+`'bgruening/docker-jupyter-notebook@sha256:3ec0bc9abc9d511aa602ee4fff2534d80dd9b1564482de52cb5de36cce6debae'`
+or, the original image name if the digest cannot be
+determined (the image has not been pulled)
+"""
+try:
+inspect = self.image_inspect(image)
+return inspect['RepoDigests'][0]
+except ContainerImageNotFound:
+return image
+@property
+def host(self):
+return next(self.__host_iter)
+@property
+def host_iter(self):
+return self.__host_iter
+class DockerCLIInterface(DockerInterface):
+container_type = 'docker_cli'
+conf_defaults = {
+'command_template': '{executable} {global_kwopts} {subcommand} {args}',
+'executable': 'docker',
+}
+option_map = {
+# `run` options
+'environment': {'flag': '--env', 'type': 'list_of_kvpairs'},
+'volumes': {'flag': '--volume', 'type': 'docker_volumes'},
+'name': {'flag': '--name', 'type': 'string'},
+'detach': {'flag': '--detach', 'type': 'boolean'},
+'publish_all_ports': {'flag': '--publish-all', 'type': 'boolean'},
+'publish_port_random': {'flag': '--publish', 'type': 'string'},
+'auto_remove': {'flag': '--rm', 'type': 'boolean'},
+'cpus': {'flag': '--cpus', 'type': 'string'},
+'memory': {'flag': '--memory', 'type': 'string'},
+}
+def validate_config(self):
+log.warning('The `docker_cli` interface is deprecated and will be removed in Galaxy 18.09, please use `docker`')
+super(DockerCLIInterface, self).validate_config()
+global_kwopts = []
+if self._conf.host:
+global_kwopts.append('--host')
+global_kwopts.append(shlex_quote(self._conf.host))
+if self._conf.force_tlsverify:
+global_kwopts.append('--tlsverify')
+self._docker_command = self._conf['command_template'].format(
+executable=self._conf['executable'],
+global_kwopts=' '.join(global_kwopts),
+subcommand='{subcommand}',
+args='{args}'
+)
+def _filter_by_id_or_name(self, id, name):
+if id:
+return '--filter id={}'.format(id)
+elif name:
+return '--filter name={}'.format(name)
+return None
+def _stringify_kwopt_docker_volumes(self, flag, val):
+"""The docker API will take a volumes argument in many formats, try to
+deal with that for the command line
+"""
+l = []
+if isinstance(val, list):
+# ['/host/vol']
+l = val
+else:
+for hostvol, guestopts in val.items():
+if isinstance(guestopts, string_types):
+# {'/host/vol': '/container/vol'}
+l.append('{}:{}'.format(hostvol, guestopts))
+else:
+# {'/host/vol': {'bind': '/container/vol'}}
+# {'/host/vol': {'bind': '/container/vol', 'mode': 'rw'}}
+mode = guestopts.get('mode', '')
+l.append('{vol}:{bind}{mode}'.format(
+vol=hostvol,
+bind=guestopts['bind'],
+mode=':' + mode if mode else ''
+))
+return self._stringify_kwopt_list(flag, l)
+def _run_docker(self, subcommand, args=None, verbose=False):
+command = self._docker_command.format(subcommand=subcommand, args=args or '')
+return self._run_command(command, verbose=verbose)
+#
+# docker subcommands
+#
+@docker_columns
+def ps(self, id=None, name=None):
+return self._run_docker(subcommand='ps', args=self._filter_by_id_or_name(id, name))
+def run(self, command, image=None, **kwopts):
+args = '{kwopts} {image} {command}'.format(
+kwopts=self._stringify_kwopts(kwopts),
+image=image or self._default_image,
+command=command if command else ''
+).strip()
+container_id = self._run_docker(subcommand='run', args=args, verbose=True)
+return DockerContainer.from_id(self, container_id)
+@docker_json
+def inspect(self, container_id):
+try:
+return self._run_docker(subcommand='inspect', args=container_id)[0]
+except (IndexError, ContainerCLIError) as exc:
+msg = "Invalid container id: %s" % container_id
+if exc.stdout == '[]' and exc.stderr == 'Error: no such object: {container_id}'.format(container_id=container_id):
+log.warning(msg)
+return []
+else:
+raise ContainerNotFound(msg, container_id=container_id)
+@docker_json
+def image_inspect(self, image):
+try:
+return self._run_docker(subcommand='image inspect', args=image)[0]
+except (IndexError, ContainerCLIError) as exc:
+msg = "%s not pulled, cannot get digest" % image
+if exc.stdout == '[]' and exc.stderr == 'Error: no such image: {image}'.format(image=image):
+log.warning(msg, image)
+return []
+else:
+raise ContainerImageNotFound(msg, image=image)
+class DockerAPIClient(object):
+"""Wraps a ``docker.APIClient`` to catch exceptions.
+"""
+_exception_retry_time = 5
+_default_max_tries = 10
+_host_iter = None
+_client = None
+_client_args = ()
+_client_kwargs = {}
+@staticmethod
+def _qualname(f):
+if isinstance(f, partial):
+f = f.func
+try:
+return getattr(f, '__qualname__', f.im_class.__name__ + '.' + f.__name__)
+except AttributeError:
+return f.__name__
+@staticmethod
+def _should_retry_request(response_code):
+return response_code >= 500 or response_code in (404, 408, 409, 429)
+@staticmethod
+def _nonfatal_error(response_code):
+return response_code in (404,)
+@staticmethod
+def _unwrapped_attr(attr):
+return getattr(DockerAPIClient._client, attr)
+@staticmethod
+def _init_client():
+kwargs = DockerAPIClient._client_kwargs.copy()
+if DockerAPIClient._host_iter is not None and 'base_url' not in kwargs:
+kwargs['base_url'] = next(DockerAPIClient._host_iter)
+DockerAPIClient._client = docker.APIClient(*DockerAPIClient._client_args, **kwargs)
+log.info('Initialized Docker API client for server: %s', kwargs.get('base_url', 'localhost'))
+@staticmethod
+def _default_client_handler(fname, *args, **kwargs):
+success_test = kwargs.pop('success_test', None)
+max_tries = kwargs.pop('max_tries', DockerAPIClient._default_max_tries)
+for tries in range(1, max_tries + 1):
+retry_time = DockerAPIClient._exception_retry_time
+reinit = False
+exc = None
+# re-get the APIClient method every time as a different caller (such as the success test function) may have
+# already reinitialized the client, and we always want to use the current client
+f = DockerAPIClient._unwrapped_attr(fname)
+qualname = DockerAPIClient._qualname(f)
+try:
+r = f(*args, **kwargs)
+if tries > 1:
+log.info('%s() succeeded on attempt %s', qualname, tries)
+return r
+except ConnectionError:
+reinit = True
+except docker.errors.APIError as exc:
+if not DockerAPIClient._should_retry_request(exc.response.status_code):
+raise
+except ReadTimeout:
+reinit = True
+retry_time = 0
+finally:
+# this is inside the finally context so we can do a bare raise when we give up (so the real stack for
+# the exception is raised)
+if exc is not None:
+log.warning("Caught exception on %s(): %s: %s",
+DockerAPIClient._qualname(f), exc.__class__.__name__, exc)
+if reinit:
+log.warning("Reinitializing Docker API client due to connection-oriented failure")
+DockerAPIClient._init_client()
+f = DockerAPIClient._unwrapped_attr(fname)
+qualname = DockerAPIClient._qualname(f)
+r = None
+if success_test is not None:
+log.info("Testing if %s() succeeded despite the exception", qualname)
+r = success_test()
+if r:
+log.warning("The request appears to have succeeded, will not retry. Response is: %s", str(r))
+return r
+elif tries >= max_tries:
+log.error("Maximum number of attempts (%s) exceeded", max_tries)
+if 'response' in exc and DockerAPIClient._nonfatal_error(exc.response.status_code):
+return None
+else:
+raise
+else:
+log.error("Retrying %s() in %s seconds (attempt: %s of %s)", qualname, retry_time, tries,
+max_tries)
+sleep(retry_time)
+def __init__(self, *args, **kwargs):
+# Only initialize the host iterator once
+host_iter = kwargs.pop('host_iter', None)
+DockerAPIClient._host_iter = DockerAPIClient._host_iter or host_iter
+DockerAPIClient._client_args = args
+DockerAPIClient._client_kwargs = kwargs
+DockerAPIClient._init_client()
+def __getattr__(self, attr):
+"""Allow the calling of methods on this class as if it were a docker.APIClient instance.
+"""
+cattr = DockerAPIClient._unwrapped_attr(attr)
+if callable(cattr):
+return partial(DockerAPIClient._default_client_handler, attr)
+else:
+return cattr
+class DockerAPIInterface(DockerInterface):
+container_type = 'docker'
+# 'publish_port_random' and 'volumes' are special cases handled in _create_host_config()
+host_config_option_map = {
+'auto_remove': {},
+'publish_all_ports': {},
+'cpus': {'param': 'nano_cpus', 'map': lambda x: int(x * 1000000000)},
+'memory': {'param': 'mem_limit'},
+'binds': {},
+'port_bindings': {},
+}
+def validate_config(self):
+assert docker is not None, "Docker module could not be imported, DockerAPIInterface unavailable"
+super(DockerAPIInterface, self).validate_config()
+self.__client = None
+@property
+def _client(self):
+# TODO: add cert options to containers conf
+cert_path = os.environ.get('DOCKER_CERT_PATH') or None
+if not cert_path:
+cert_path = os.path.join(os.path.expanduser('~'), '.docker')
+if self._conf.force_tlsverify or self._conf.tls:
+tls_config = docker.tls.TLSConfig(
+client_cert=(os.path.join(cert_path, 'cert.pem'),
+os.path.join(cert_path, 'key.pem')),
+ca_cert=os.path.join(cert_path, 'ca.pem'),
+verify=self._conf.force_tlsverify,
+)
+else:
+tls_config = False
+if not self.__client:
+self.__client = DockerAPIClient(
+host_iter=self.host_iter,
+tls=tls_config,
+)
+return self.__client
+@staticmethod
+def _first(f, *args, **kwargs):
+try:
+return f(*args, **kwargs)[0]
+except IndexError:
+return None
+@staticmethod
+def _filter_by_id_or_name(id, name):
+if id:
+return {'id': id}
+elif name:
+return {'name': name}
+return None
+@staticmethod
+def _kwopt_to_param_names(map_spec, key):
+"""For a given containers lib method parameter name, return the matching docker-py parameter name(s).
+See :meth:`_create_docker_api_spec`.
+"""
+params = []
+if 'param' not in map_spec and 'params' not in map_spec:
+params.append(key)
+elif 'param' in map_spec:
+params.append(map_spec['param'])
+params.extend(map_spec.get('params', ()))
+return params
+@staticmethod
+def _kwopt_to_params(map_spec, key, value):
+"""For a given containers lib method parameter name and value, return the matching docker-py parameters with
+values set (including transformation with an optional map function).
+See :meth:`_create_docker_api_spec`.
+"""
+params = {}
+if 'map' in map_spec:
+value = map_spec['map'](value)
+for param in DockerAPIInterface._kwopt_to_param_names(map_spec, key):
+params[param] = value
+return params
+def _create_docker_api_spec(self, option_map_name, spec_class, kwopts):
+"""Create docker-py objects used as arguments to docker-py methods.
+This method modifies ``kwopts`` by removing options that match the spec.
+An option map is a class-level variable with name ``<map_name>_option_map`` and is a dict with format:
+.. code-block:: python
+sample_option_map = {
+'containers_lib_option_name': {
+'param': docker_lib_positional_argument_int or 'docker_lib_keyword_argument_name',
+'params': like 'param' but an iterable containing multiple docker lib params to set,
+'default': default value,
+'map': function with with to transform the value,
+'required': True if this param is required, else False (default),
+},
+'_spec_param': {
+'spec_class': class of param value,
+}
+}
+All members of the mapping value are optional.
+For example, a spec map for (some of) the possible values of the :class:`docker.types.TaskTemplate`, which is
+used as the ``task_template`` argument to :meth:`docker.APIClient.create_service`, and the possible values of
+the :class`:docker.types.ContainerSpec`, which is used as the ``container_spec`` argument to the
+``TaskTemplate``  would be:
+.. code-block:: python
+task_template_option_map = {
+# TaskTemplate's 'container_spec' param is a ContainerSpec
+'_container_spec': {
+'spec_class': docker.types.ContainerSpec,
+'required': True
+}
+}
+container_spec_option_map = {
+'image': {'param': 0},      # positional argument 0 to ContainerSpec()
+'command': {},              # 'command' keyword argument to ContainerSpec()
+'environment': {            # 'env' keyword argument to ContainerSpec(), 'environment' keyword argument
+'param': 'env'          #   to ContainerInterface.run_in_container()
+},
+}
+Thus, calling ``DockerInterface.run_in_contaner('true', image='busybox', environment={'FOO': 'foo'}`` will
+essentially do this (for example, if using Docker Swarm mode):
+.. code-block:: python
+container_spec = docker.types.ContainerSpec('busybox', command='true', env={'FOO': 'foo'})
+task_template = docker.types.TaskTemplate(container_spec=container_spec)
+docker.APIClient().create_service(task_template)
+:param  option_map_name:    Name of option map class variable (``_option_map`` is automatically appended)
+:type   option_map_name:    str
+:param  spec_class:         docker-py specification class or callable returning an instance
+:type   spec_class:         :class:`docker.types.Resources`, :class:`docker.types.ContainerSpec`, etc. or
+callable
+:param  kwopts:             Keyword options passed to calling method (e.g.
+:meth:`DockerInterface.run_in_container`)
+:type   kwopts:             dict
+:returns:                   Instantiated ``spec_class`` object
+:rtype:                     ``type(spec_class)``
+"""
+def _kwopt_to_arg(map_spec, key, value, param=None):
+# determines whether the given param is a positional or keyword argument in docker-py and adds it to the
+# list of arguments
+if isinstance(map_spec.get('param'), int):
+spec_opts.append((map_spec.get('param'), value))
+elif param is not None:
+spec_kwopts[param] = value
+else:
+spec_kwopts.update(DockerAPIInterface._kwopt_to_params(map_spec, key, value))
+# positional arguments
+spec_opts = []
+# keyword arguments
+spec_kwopts = {}
+# retrieve the option map for the docker-py object we're creating
+option_map = getattr(self, option_map_name + '_option_map')
+# set defaults
+for key in filter(lambda k: option_map[k].get('default'), option_map.keys()):
+map_spec = option_map[key]
+_kwopt_to_arg(map_spec, key, map_spec['default'])
+# don't allow kwopts that start with _, those are reserved for "child" object params
+for kwopt in filter(lambda k: not k.startswith('_') and k in option_map, list(kwopts.keys())):
+map_spec = option_map[kwopt]
+_v = kwopts.pop(kwopt)
+_kwopt_to_arg(map_spec, kwopt, _v)
+# find any child objects that need to be created and recurse to create them
+for _sub_k in filter(lambda k: k.startswith('_') and 'spec_class' in option_map[k], option_map.keys()):
+map_spec = option_map[_sub_k]
+param = _sub_k.lstrip('_')
+_sub_v = self._create_docker_api_spec(param, map_spec['spec_class'], kwopts)
+if _sub_v is not None or map_spec.get('required') or isinstance(map_spec.get('param'), int):
+_kwopt_to_arg(map_spec, None, _sub_v, param=param)
+# sort positional args and make into a flat tuple
+if spec_opts:
+spec_opts = sorted(spec_opts, key=lambda x: x[0])
+spec_opts = [i[1] for i in spec_opts]
+# create spec object
+if spec_opts or spec_kwopts:
+return spec_class(*spec_opts, **spec_kwopts)
+else:
+return None
+def _volumes_to_native(self, volumes):
+"""Convert a list of volume definitions to the docker-py container creation method parameters.
+:param  volumes:    List of volumes to translate
+:type   volumes:    list of :class:`galaxy.containers.docker_model.DockerVolume`s
+"""
+paths = []
+binds = {}
+for v in volumes:
+path, bind = v.to_native()
+paths.append(path)
+binds.update(bind)
+return (paths, binds)
+def _create_host_config(self, kwopts):
+"""Build the host configuration parameter for docker-py container creation.
+This method modifies ``kwopts`` by removing host config options and potentially setting the ``ports`` and
+``volumes`` keys.
+:param  kwopts: Keyword options passed to calling method (e.g. :method:`DockerInterface.run()`)
+:type   kwopts: dict
+:returns:       The return value of `docker.APIClient.create_host_config()`
+:rtype:         dict
+"""
+if 'publish_port_random' in kwopts:
+port = int(kwopts.pop('publish_port_random'))
+kwopts['port_bindings'] = {port: None}
+kwopts['ports'] = [port]
+if 'volumes' in kwopts:
+paths, binds = self._volumes_to_native(kwopts.pop('volumes'))
+kwopts['binds'] = binds
+kwopts['volumes'] = paths
+return self._create_docker_api_spec('host_config', self._client.create_host_config, kwopts)
+#
+# docker subcommands
+#
+def ps(self, id=None, name=None, running=True):
+return self._client.containers(all=not running, filters=self._filter_by_id_or_name(id, name))
+def run(self, command, image=None, **kwopts):
+image = image or self._default_image
+command = command or None
+log.debug("Creating docker container with image '%s' for command: %s", image, command)
+host_config = self._create_host_config(kwopts)
+log.debug("Docker container host configuration:\n%s", safe_dumps_formatted(host_config))
+log.debug("Docker container creation parameters:\n%s", safe_dumps_formatted(kwopts))
+success_test = partial(self._first, self.ps, name=kwopts['name'], running=False)
+# this can raise exceptions, if necessary we could wrap them in a more generic "creation failed" exception class
+container = self._client.create_container(
+image,
+command=command if command else None,
+host_config=host_config,
+success_test=success_test,
+max_tries=5,
+**kwopts
+)
+container_id = container.get('Id')
+log.debug("Starting container: %s (%s)", kwopts['name'], str(container_id))
+# start can safely be run more than once
+self._client.start(container=container_id)
+return DockerContainer.from_id(self, container_id)
+def inspect(self, container_id):
+try:
+return self._client.inspect_container(container_id)
+except docker.errors.NotFound:
+raise ContainerNotFound("Invalid container id: %s" % container_id, container_id=container_id)
+def image_inspect(self, image):
+try:
+return self._client.inspect_image(image)
+except docker.errors.NotFound:
+raise ContainerImageNotFound("%s not pulled, cannot get digest" % image, image=image)

Mercurial > repos > guerler > springsuite

comparison planemo/lib/python3.7/site-packages/galaxy/containers/docker.py @ 0:d30785e31577 draft