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galaxy.containers package

Interfaces to containerization software

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

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)

Bases: object

valid_modes = frozenset({'ro', 'rw'})

__init__(path, host_path=None, mode=None)

abstract from_str(as_str)

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

Parameters

as_str (str) – string representation of volume

abstract to_native()

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

property mode_is_valid

class galaxy.containers.Container(interface, id, name=None, **kwargs)

Bases: object

__init__(interface, id, name=None, **kwargs)

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)

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()

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

Returns

True if ready, else False

Rtpe

bool

map_port(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

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)

Bases: object

container_type: Optional[str] = None

container_class: Optional[Type[galaxy.containers.Container]] = None

volume_class

alias of Optional[Type[galaxy.containers.ContainerVolume]]

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)

property key

property containers_config_file

get_container(container_id)

set_kwopts_name(kwopts)

validate_config()

abstract run_in_container(command, image=None, **kwopts)

class galaxy.containers.ContainerInterfaceConfig

Bases: dict

get(name, default=None)

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

galaxy.containers.build_container_interfaces(containers_config_file, containers_conf=None)

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)

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)

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()

run_in_container(command, image=None, **kwopts)

image_repodigest(image)

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)

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()

ps(id=None, name=None)

run(command, image=None, **kwopts)

inspect(container_id)

image_inspect(image)

class galaxy.containers.docker.DockerAPIClient(*args, **kwargs)

Bases: object

Wraps a docker.APIClient to catch exceptions.

__init__(*args, **kwargs)

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

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()

ps(id=None, name=None, running=True)

run(command, image=None, **kwopts)

inspect(container_id)

image_inspect(image)

galaxy.containers.docker_decorators module

Decorators for docker

galaxy.containers.docker_decorators.docker_columns(f)

galaxy.containers.docker_decorators.docker_json(f)

galaxy.containers.docker_model module

Model objects for docker objects

class galaxy.containers.docker_model.DockerAttributeContainer(members=None)

Bases: object

__init__(members=None)

property members

hash()

get(name, default)

class galaxy.containers.docker_model.DockerVolume(path, host_path=None, mode=None)

Bases: galaxy.containers.ContainerVolume

classmethod from_str(as_str)

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()

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

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

Bases: galaxy.containers.Container

__init__(interface, id, name=None, inspect=None)

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)

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()

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)

Bases: galaxy.containers.Container

__init__(interface, id, name=None, image=None, inspect=None)

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)

classmethod from_id(interface, id)

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()

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

Returns

True if ready, else False

Rtpe

bool

task_add(task)

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')

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

constraint_add(name, op, value)

set_cpus()

set_image()

class galaxy.containers.docker_model.DockerServiceConstraint(name=None, op=None, value=None)

Bases: object

__init__(name=None, op=None, value=None)

static split_constraint_string(constraint_str)

classmethod from_str(constraint_str)

property name

property op

property value

property label

class galaxy.containers.docker_model.DockerServiceConstraints(members=None)

Bases: galaxy.containers.docker_model.DockerAttributeContainer

member_class

alias of galaxy.containers.docker_model.DockerServiceConstraint

classmethod from_constraint_string_list(inspect)

property labels

class galaxy.containers.docker_model.DockerNode(interface, id=None, name=None, status=None, availability=None, manager=False, inspect=None)

Bases: object

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

classmethod from_cli(interface, n, task_list)

classmethod from_id(interface, id)

task_add(task)

property id

property name

property version

property inspect

property state

property cpus

property labels

label_add(label, value)

property labels_as_constraints

set_labels_for_constraints(constraints)

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)

is_ok()

is_managed()

destroyable()

drain()

class galaxy.containers.docker_model.DockerNodeLabel(name=None, value=None)

Bases: object

__init__(name=None, value=None)

property name

property value

property constraint_string

property constraint

class galaxy.containers.docker_model.DockerNodeLabels(members=None)

Bases: galaxy.containers.docker_model.DockerAttributeContainer

member_class

alias of galaxy.containers.docker_model.DockerNodeLabel

classmethod from_label_dictionary(inspect)

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)

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)

classmethod from_cli(interface, t, service=None, node=None)

classmethod from_api(interface, t, service=None, node=None)

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)

galaxy.containers.docker_swarm module

Docker Swarm mode interface

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

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()

run_in_container(command, image=None, **kwopts)

Run a service like a detached container

services(id=None, name=None)

service(id=None, name=None)

services_in_state(desired, current, tasks='any')

service_tasks(service)

nodes(id=None, name=None)

node(id=None, name=None)

nodes_in_state(status, availability)

node_tasks(node)

services_waiting()

services_waiting_by_constraints()

services_completed()

services_terminal()

nodes_active()

nodes_active_by_constraints()

services_clean()

class galaxy.containers.docker_swarm.DockerSwarmCLIInterface(conf, key, containers_config_file)

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)

service_tasks(service)

nodes(id=None, name=None)

service_create(command, image=None, **kwopts)

service_inspect(service_id)

service_ls(id=None, name=None)

service_ps(service_id)

service_rm(service_ids)

node_inspect(node_id)

node_ls(id=None, name=None)

node_ps(node_id)

node_update(node_id, **kwopts)

task_inspect(task_id)

class galaxy.containers.docker_swarm.DockerSwarmAPIInterface(conf, key, containers_config_file)

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)

service_create(command, image=None, **kwopts)

service_inspect(service_id)

service_ls(id=None, name=None)

service_ps(service_id)

service_rm(service_ids)

node_inspect(node_id)

node_ls(id=None, name=None)

node_ps(node_id)

node_update(node_id, **kwopts)

task_inspect(task_id)

task_ls(filters=None)