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galaxy.containers package

Interfaces to containerization software

class galaxy.containers.ContainerPort

Bases: galaxy.containers.ContainerPort

Named tuple representing ports published by a container, with attributes:

Variables:

• port (int) – Port number (inside the container)
• protocol (str) – Port protocol, either tcp or udp
• hostaddr (str) – Address or hostname where the published port can be accessed
• hostport (int) – Published port number on which the container can be accessed

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

Bases: object

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

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

from_str(as_str)

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

Parameters:as_str (str) – string representation of volume

to_native()

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

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

id

The container’s id

name

The container’s name

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

ports

Attribute for accessing details of ports published by the container.

Returns:Port details Return type:list of :class:`ContainerPort`s

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

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 = None

container_class = None

volume_class = None

conf_defaults = {'name_prefix': 'galaxy_'}

option_map = {}

publish_port_list_required = False

supports_volumes = True

__init__(conf, key, containers_config_file)

key

containers_config_file

get_container(container_id)

set_kwopts_name(kwopts)

validate_config()

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

class galaxy.containers.ContainerInterfaceConfig

Bases: dict

get(name, default=None)

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 = {'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)

host

host_iter

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

Bases: galaxy.containers.docker.DockerInterface

container_type = 'docker_cli'

conf_defaults = {'command_template': '{executable} {global_kwopts} {subcommand} {args}', 'executable': 'docker'}

option_map = {'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 = 'docker'

host_config_option_map = {'auto_remove': {}, 'binds': {}, 'cpus': {'param': 'nano_cpus', 'map': <function DockerAPIInterface.<lambda> at 0x7fabc06d9730>}, '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)

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()

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

Bases: galaxy.containers.Container

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

classmethod from_id(interface, id)

ports

address

is_ready()

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)

classmethod from_cli(interface, s, task_list)

classmethod from_id(interface, id)

ports

address

is_ready()

task_add(task)

inspect

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.

env

terminal

Same caveats as state().

node

Same caveats as state().

image

cpus

constraints

tasks

A list of all tasks, including terminal ones.

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)

name

op

value

label

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

Bases: galaxy.containers.docker_model.DockerAttributeContainer

member_class

alias of DockerServiceConstraint

classmethod from_constraint_string_list(inspect)

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)

id

name

version

inspect

state

cpus

labels

label_add(label, value)

labels_as_constraints

set_labels_for_constraints(constraints)

tasks

A list of all tasks, including terminal ones.

non_terminal_tasks

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)

name

value

constraint_string

constraint

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

Bases: galaxy.containers.docker_model.DockerAttributeContainer

member_class

alias of DockerNodeLabel

classmethod from_label_dictionary(inspect)

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)

id

name

inspect

slot

node

service

cpus

state

current_state

current_state_time

desired_state

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 = {'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 = 'docker_swarm_cli'

option_map = {'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 = 'docker_swarm'

placement_option_map = {'constraint': {'param': 'constraints'}}

service_mode_option_map = {'replicas': {'default': 1}, 'service_mode': {'param': 0, 'default': 'replicated'}}

endpoint_spec_option_map = {'ports': {}}

resources_option_map = {'cpus': {'params': ('cpu_limit', 'cpu_reservation'), 'map': <function DockerSwarmAPIInterface.<lambda> at 0x7fabc0946bf8>}, 'memory': {'params': ('mem_limit', 'mem_reservation')}}

container_spec_option_map = {'command': {}, 'environment': {'param': 'env'}, 'image': {'param': 0}, 'labels': {}}

restart_policy_option_map = {'restart_condition': {'param': 'condition', 'default': 'none'}, 'restart_delay': {'param': 'delay'}, 'restart_max_attempts': {'param': 'max_attemps'}}

task_template_option_map = {'_container_spec': {'spec_class': None, 'required': True}, '_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)