diff env/lib/python3.9/site-packages/galaxy/containers/docker.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/galaxy/containers/docker.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,599 @@
+"""
+Interface to Docker
+"""
+
+import logging
+import os
+import shlex
+from functools import partial
+from itertools import cycle, repeat
+from time import sleep
+from typing import Any, Dict, Optional, Type
+
+try:
+    import docker
+except ImportError:
+    docker = None  # type: ignore
+
+try:
+    from requests.exceptions import ConnectionError, ReadTimeout
+except ImportError:
+    ConnectionError = None  # type: ignore
+    ReadTimeout = None  # type: ignore
+
+from galaxy.containers import Container, 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: Type[Container] = DockerContainer
+    volume_class = DockerVolume
+    conf_defaults: Dict[str, Optional[Any]] = {
+        '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().validate_config()
+        self.__host_iter = None
+        if self._conf.host is None or isinstance(self._conf.host, str):
+            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: Dict[str, Optional[Any]] = {
+        '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().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 f'--filter id={id}'
+        elif name:
+            return f'--filter name={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, str):
+                    # {'/host/vol': '/container/vol'}
+                    l.append(f'{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 == f'Error: no such object: {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 == f'Error: no such image: {image}':
+                log.warning(msg, image)
+                return []
+            else:
+                raise ContainerImageNotFound(msg, image=image)
+
+
+class DockerAPIClient:
+    """Wraps a ``docker.APIClient`` to catch exceptions.
+    """
+
+    _exception_retry_time = 5
+    _default_max_tries = 10
+    _host_iter = None
+    _client = None
+    _client_args = ()
+    _client_kwargs: Dict[str, Optional[Any]] = {}
+
+    @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().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)