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galaxy.containers package

Interfaces to containerization software

class galaxy.containers.ContainerPort(port: int, protocol: str, hostaddr: str, hostport: int)[source]

Bases: tuple

Named tuple representing ports published by a container, with attributes

property port

Alias for field number 0

property protocol

Alias for field number 1

property hostaddr

Alias for field number 2

property hostport

Alias for field number 3

class galaxy.containers.ContainerVolume(path, host_path=None, mode=None)[source]

Bases: object

valid_modes = frozenset({'ro', 'rw'})
__init__(path, host_path=None, mode=None)[source]

Initialize self. See help(type(self)) for accurate signature.

abstract from_str(as_str)[source]

Classmethod to convert from this container type’s string representation.

Parameters

as_str (str) – string representation of volume

abstract to_native()[source]

Return this container type’s native representation of the volume.

property mode_is_valid
class galaxy.containers.Container(interface, id, name=None, **kwargs)[source]

Bases: object

__init__(interface, id, name=None, **kwargs)[source]
Parameters
  • interface (ContainerInterface subclass instance) – Container interface for the given container type

  • id (str) – Container identifier

  • name (str) – Container name

property id

The container’s id

property name

The container’s name

abstract from_id(interface, id)[source]

Classmethod to create an instance of Container from the container system’s id for the given container type.

Parameters
  • interface (ContainerInterface subclass instance) – Container insterface for the given id

  • id (str) – Container identifier

Returns

Container object

Return type

Container subclass instance

abstract property ports

Attribute for accessing details of ports published by the container.

Returns

Port details

Return type

list of ContainerPort s

abstract property address

Attribute for accessing the address or hostname where published ports can be accessed.

Returns

Hostname or IP address

Return type

str

abstract is_ready()[source]

Indicate whether or not the container is “ready” (up, available, running).

Returns

True if ready, else False

Rtpe

bool

map_port(port)[source]

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

Parameters

port (int) – Container port to map

Returns

Mapping to host address/port for given container port

Return type

ContainerPort instance

class galaxy.containers.ContainerInterface(conf, key, containers_config_file)[source]

Bases: object

container_type: Optional[str] = None
container_class: Optional[Type[galaxy.containers.Container]] = None
volume_class = typing.Union[typing.Type[galaxy.containers.ContainerVolume], NoneType]
conf_defaults: Dict[str, Optional[Any]] = {'name_prefix': 'galaxy_'}
option_map: Dict[str, Dict] = {}
publish_port_list_required = False
supports_volumes = True
__init__(conf, key, containers_config_file)[source]

Initialize self. See help(type(self)) for accurate signature.

property key
property containers_config_file
get_container(container_id)[source]
set_kwopts_name(kwopts)[source]
validate_config()[source]
abstract run_in_container(command, image=None, **kwopts)[source]
class galaxy.containers.ContainerInterfaceConfig[source]

Bases: dict

get(name, default=None)[source]

Return the value for key if key is in the dictionary, else default.

galaxy.containers.build_container_interfaces(containers_config_file, containers_conf=None)[source]

Build ContainerInterface`s. Pass ``containers_conf` to avoid rereading the config file.

Parameters
  • containers_config_file (str) – Filename of containers_conf.yml

  • containers_conf (dict) – Optional containers conf (as read from containers_conf.yml), will be used in place of containers_config_file

Returns

Instantiated container interfaces with keys corresponding to containers keys

Return type

dict of ContainerInterface subclass instances

galaxy.containers.parse_containers_config(containers_config_file)[source]

Parse a containers_conf.yml and return the contents of its containers dictionary.

Parameters

containers_config_file (str) – Filename of containers_conf.yml

Returns

Contents of the dictionary under the containers key

Return type

dict

Submodules

galaxy.containers.docker module

Interface to Docker

class galaxy.containers.docker.DockerInterface(conf, key, containers_config_file)[source]

Bases: galaxy.containers.ContainerInterface

container_class

alias of galaxy.containers.docker_model.DockerContainer

volume_class

alias of galaxy.containers.docker_model.DockerVolume

conf_defaults: Dict[str, Optional[Any]] = {'auto_remove': True, 'cpus': None, 'force_tlsverify': False, 'host': None, 'image': None, 'memory': None, 'tls': False}
conf_run_kwopts = ('cpus', 'memory')
validate_config()[source]
run_in_container(command, image=None, **kwopts)[source]
image_repodigest(image)[source]

Get the digest image string for an image.

Parameters

image (str) – 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)

property host
property host_iter
class galaxy.containers.docker.DockerCLIInterface(conf, key, containers_config_file)[source]

Bases: galaxy.containers.docker.DockerInterface

container_type: Optional[str] = 'docker_cli'
conf_defaults: Dict[str, Optional[Any]] = {'command_template': '{executable} {global_kwopts} {subcommand} {args}', 'executable': 'docker'}
option_map: Dict[str, Dict] = {'auto_remove': {'flag': '--rm', 'type': 'boolean'}, 'cpus': {'flag': '--cpus', 'type': 'string'}, 'detach': {'flag': '--detach', 'type': 'boolean'}, 'environment': {'flag': '--env', 'type': 'list_of_kvpairs'}, 'memory': {'flag': '--memory', 'type': 'string'}, 'name': {'flag': '--name', 'type': 'string'}, 'publish_all_ports': {'flag': '--publish-all', 'type': 'boolean'}, 'publish_port_random': {'flag': '--publish', 'type': 'string'}, 'volumes': {'flag': '--volume', 'type': 'docker_volumes'}}
validate_config()[source]
ps(id=None, name=None)[source]
run(command, image=None, **kwopts)[source]
inspect(container_id)[source]
image_inspect(image)[source]
class galaxy.containers.docker.DockerAPIClient(*args, **kwargs)[source]

Bases: object

Wraps a docker.APIClient to catch exceptions.

__init__(*args, **kwargs)[source]

Initialize self. See help(type(self)) for accurate signature.

class galaxy.containers.docker.DockerAPIInterface(conf, key, containers_config_file)[source]

Bases: galaxy.containers.docker.DockerInterface

container_type: Optional[str] = 'docker'
host_config_option_map = {'auto_remove': {}, 'binds': {}, 'cpus': {'map': <function DockerAPIInterface.<lambda>>, 'param': 'nano_cpus'}, 'memory': {'param': 'mem_limit'}, 'port_bindings': {}, 'publish_all_ports': {}}
validate_config()[source]
ps(id=None, name=None, running=True)[source]
run(command, image=None, **kwopts)[source]
inspect(container_id)[source]
image_inspect(image)[source]

galaxy.containers.docker_decorators module

Decorators for docker

galaxy.containers.docker_decorators.docker_columns(f)[source]
galaxy.containers.docker_decorators.docker_json(f)[source]

galaxy.containers.docker_model module

Model objects for docker objects

class galaxy.containers.docker_model.DockerAttributeContainer(members=None)[source]

Bases: object

__init__(members=None)[source]

Initialize self. See help(type(self)) for accurate signature.

property members
hash()[source]
get(name, default)[source]
class galaxy.containers.docker_model.DockerVolume(path, host_path=None, mode=None)[source]

Bases: galaxy.containers.ContainerVolume

classmethod from_str(as_str)[source]

Construct an instance from a string as would be passed to docker run –volume.

A string in the format <host_path>:<mode> is supported for legacy purposes even though it is not valid Docker volume syntax.

to_native()[source]

Return this container type’s native representation of the volume.

class galaxy.containers.docker_model.DockerContainer(interface, id, name=None, inspect=None)[source]

Bases: galaxy.containers.Container

__init__(interface, id, name=None, inspect=None)[source]
Parameters
  • interface (ContainerInterface subclass instance) – Container interface for the given container type

  • id (str) – Container identifier

  • name (str) – Container name

classmethod from_id(interface, id)[source]

Classmethod to create an instance of Container from the container system’s id for the given container type.

Parameters
  • interface (ContainerInterface subclass instance) – Container insterface for the given id

  • id (str) – Container identifier

Returns

Container object

Return type

Container subclass instance

property ports

Attribute for accessing details of ports published by the container.

Returns

Port details

Return type

list of ContainerPort s

property address

Attribute for accessing the address or hostname where published ports can be accessed.

Returns

Hostname or IP address

Return type

str

is_ready()[source]

Indicate whether or not the container is “ready” (up, available, running).

Returns

True if ready, else False

Rtpe

bool

property inspect
class galaxy.containers.docker_model.DockerService(interface, id, name=None, image=None, inspect=None)[source]

Bases: galaxy.containers.Container

__init__(interface, id, name=None, image=None, inspect=None)[source]
Parameters
  • interface (ContainerInterface subclass instance) – Container interface for the given container type

  • id (str) – Container identifier

  • name (str) – Container name

classmethod from_cli(interface, s, task_list)[source]
classmethod from_id(interface, id)[source]

Classmethod to create an instance of Container from the container system’s id for the given container type.

Parameters
  • interface (ContainerInterface subclass instance) – Container insterface for the given id

  • id (str) – Container identifier

Returns

Container object

Return type

Container subclass instance

property ports

Attribute for accessing details of ports published by the container.

Returns

Port details

Return type

list of ContainerPort s

property address

Attribute for accessing the address or hostname where published ports can be accessed.

Returns

Hostname or IP address

Return type

str

is_ready()[source]

Indicate whether or not the container is “ready” (up, available, running).

Returns

True if ready, else False

Rtpe

bool

task_add(task)[source]
property inspect
property state

If one of this service’s tasks desired state is running, return that task state, otherwise, return the state of a non-running task.

This is imperfect because it doesn’t attempt to provide useful information for replicas > 1 tasks, but it suits our purposes for now.

property env
property terminal

Same caveats as state().

property node

Same caveats as state().

property image
property cpus
property constraints
property tasks

A list of all tasks, including terminal ones.

property task_count

A count of all tasks, including terminal ones.

in_state(desired, current, tasks='any')[source]

Indicate if one of this service’s tasks matches the desired state.

constraint_add(name, op, value)[source]
set_cpus()[source]
set_image()[source]
class galaxy.containers.docker_model.DockerServiceConstraint(name=None, op=None, value=None)[source]

Bases: object

__init__(name=None, op=None, value=None)[source]

Initialize self. See help(type(self)) for accurate signature.

static split_constraint_string(constraint_str)[source]
classmethod from_str(constraint_str)[source]
property name
property op
property value
property label
class galaxy.containers.docker_model.DockerServiceConstraints(members=None)[source]

Bases: galaxy.containers.docker_model.DockerAttributeContainer

member_class

alias of DockerServiceConstraint

classmethod from_constraint_string_list(inspect)[source]
property labels
class galaxy.containers.docker_model.DockerNode(interface, id=None, name=None, status=None, availability=None, manager=False, inspect=None)[source]

Bases: object

__init__(interface, id=None, name=None, status=None, availability=None, manager=False, inspect=None)[source]

Initialize self. See help(type(self)) for accurate signature.

classmethod from_cli(interface, n, task_list)[source]
classmethod from_id(interface, id)[source]
task_add(task)[source]
property id
property name
property version
property inspect
property state
property cpus
property labels
label_add(label, value)[source]
property labels_as_constraints
set_labels_for_constraints(constraints)[source]
property tasks

A list of all tasks, including terminal ones.

property non_terminal_tasks
property task_count

A count of all tasks, including terminal ones.

in_state(status, availability)[source]
is_ok()[source]
is_managed()[source]
destroyable()[source]
drain()[source]
class galaxy.containers.docker_model.DockerNodeLabel(name=None, value=None)[source]

Bases: object

__init__(name=None, value=None)[source]

Initialize self. See help(type(self)) for accurate signature.

property name
property value
property constraint_string
property constraint
class galaxy.containers.docker_model.DockerNodeLabels(members=None)[source]

Bases: galaxy.containers.docker_model.DockerAttributeContainer

member_class

alias of DockerNodeLabel

classmethod from_label_dictionary(inspect)[source]
property constraints
class galaxy.containers.docker_model.DockerTask(interface, id=None, name=None, image=None, desired_state=None, state=None, error=None, ports=None, service=None, node=None)[source]

Bases: object

terminal_states = ('shutdown', 'complete', 'failed', 'rejected', 'orphaned')
__init__(interface, id=None, name=None, image=None, desired_state=None, state=None, error=None, ports=None, service=None, node=None)[source]

Initialize self. See help(type(self)) for accurate signature.

classmethod from_cli(interface, t, service=None, node=None)[source]
classmethod from_api(interface, t, service=None, node=None)[source]
property id
property name
property inspect
property slot
property node
property service
property cpus
property state
property current_state
property current_state_time
property desired_state
property terminal
in_state(desired, current)[source]

galaxy.containers.docker_swarm module

Docker Swarm mode interface

class galaxy.containers.docker_swarm.DockerSwarmInterface(conf, key, containers_config_file)[source]

Bases: galaxy.containers.docker.DockerInterface

container_class

alias of galaxy.containers.docker_model.DockerService

conf_defaults: Dict[str, Optional[Any]] = {'ignore_volumes': False, 'managed': True, 'manager_autostart': True, 'node_prefix': None, 'resolve_image_digest': False, 'service_create_cpus_constraint': False, 'service_create_image_constraint': False}
publish_port_list_required = True
supports_volumes = False
validate_config()[source]
run_in_container(command, image=None, **kwopts)[source]

Run a service like a detached container

services(id=None, name=None)[source]
service(id=None, name=None)[source]
services_in_state(desired, current, tasks='any')[source]
service_tasks(service)[source]
nodes(id=None, name=None)[source]
node(id=None, name=None)[source]
nodes_in_state(status, availability)[source]
node_tasks(node)[source]
services_waiting()[source]
services_waiting_by_constraints()[source]
services_completed()[source]
services_terminal()[source]
nodes_active()[source]
nodes_active_by_constraints()[source]
services_clean()[source]
class galaxy.containers.docker_swarm.DockerSwarmCLIInterface(conf, key, containers_config_file)[source]

Bases: galaxy.containers.docker_swarm.DockerSwarmInterface, galaxy.containers.docker.DockerCLIInterface

container_type: Optional[str] = 'docker_swarm_cli'
option_map: Dict[str, Dict] = {'availability': {'flag': '--availability', 'type': 'string'}, 'constraint': {'flag': '--constraint', 'type': 'list_of_kovtrips'}, 'cpu_limit': {'flag': '--limit-cpu', 'type': 'string'}, 'cpu_reservation': {'flag': '--reserve-cpu', 'type': 'string'}, 'environment': {'flag': '--env', 'type': 'list_of_kvpairs'}, 'label_add': {'flag': '--label-add', 'type': 'list_of_kvpairs'}, 'label_rm': {'flag': '--label-rm', 'type': 'list_of_kvpairs'}, 'mem_limit': {'flag': '--limit-memory', 'type': 'string'}, 'mem_reservation': {'flag': '--reserve-memory', 'type': 'string'}, 'name': {'flag': '--name', 'type': 'string'}, 'publish_port_random': {'flag': '--publish', 'type': 'string'}, 'replicas': {'flag': '--replicas', 'type': 'string'}, 'restart_condition': {'flag': '--restart-condition', 'type': 'string'}}
services(id=None, name=None)[source]
service_tasks(service)[source]
nodes(id=None, name=None)[source]
service_create(command, image=None, **kwopts)[source]
service_inspect(service_id)[source]
service_ls(id=None, name=None)[source]
service_ps(service_id)[source]
service_rm(service_ids)[source]
node_inspect(node_id)[source]
node_ls(id=None, name=None)[source]
node_ps(node_id)[source]
node_update(node_id, **kwopts)[source]
task_inspect(task_id)[source]
class galaxy.containers.docker_swarm.DockerSwarmAPIInterface(conf, key, containers_config_file)[source]

Bases: galaxy.containers.docker_swarm.DockerSwarmInterface, galaxy.containers.docker.DockerAPIInterface

container_type: Optional[str] = 'docker_swarm'
placement_option_map = {'constraint': {'param': 'constraints'}}
service_mode_option_map = {'replicas': {'default': 1}, 'service_mode': {'default': 'replicated', 'param': 0}}
endpoint_spec_option_map: Dict[str, Dict] = {'ports': {}}
resources_option_map = {'cpus': {'map': <function DockerSwarmAPIInterface.<lambda>>, 'params': ('cpu_limit', 'cpu_reservation')}, 'memory': {'params': ('mem_limit', 'mem_reservation')}}
container_spec_option_map = {'command': {}, 'environment': {'param': 'env'}, 'image': {'param': 0}, 'labels': {}}
restart_policy_option_map = {'restart_condition': {'default': 'none', 'param': 'condition'}, 'restart_delay': {'param': 'delay'}, 'restart_max_attempts': {'param': 'max_attemps'}}
task_template_option_map = {'_container_spec': {'required': True, 'spec_class': None}, '_placement': {'spec_class': None}, '_resources': {'spec_class': None}, '_restart_policy': {'spec_class': None}}
node_spec_option_map = {'availability': {'param': 'Availability'}, 'labels': {'param': 'Labels'}, 'name': {'param': 'Name'}, 'role': {'param': 'Role'}}
static create_random_port_spec(port)[source]
service_create(command, image=None, **kwopts)[source]
service_inspect(service_id)[source]
service_ls(id=None, name=None)[source]
service_ps(service_id)[source]
service_rm(service_ids)[source]
node_inspect(node_id)[source]
node_ls(id=None, name=None)[source]
node_ps(node_id)[source]
node_update(node_id, **kwopts)[source]
task_inspect(task_id)[source]
task_ls(filters=None)[source]