R: R6 Class Representing a Arvados

Arvados

R Documentation

R6 Class Representing a Arvados

Description

Arvados class gives users ability to access Arvados REST API. It also allowes user to manipulate collections (and projects?)

Methods

Public methods

Arvados$new()
Arvados$project_exist()
Arvados$project_get()
Arvados$project_create()
Arvados$project_properties_set()
Arvados$project_properties_append()
Arvados$project_properties_get()
Arvados$project_properties_delete()
Arvados$project_update()
Arvados$project_list()
Arvados$project_delete()
Arvados$api_clients_get()
Arvados$api_clients_create()
Arvados$api_clients_update()
Arvados$api_clients_delete()
Arvados$api_clients_list()
Arvados$api_client_authorizations_get()
Arvados$api_client_authorizations_create()
Arvados$api_client_authorizations_update()
Arvados$api_client_authorizations_delete()
Arvados$api_client_authorizations_create_system_auth()
Arvados$api_client_authorizations_current()
Arvados$api_client_authorizations_list()
Arvados$authorized_keys_get()
Arvados$authorized_keys_create()
Arvados$authorized_keys_update()
Arvados$authorized_keys_delete()
Arvados$authorized_keys_list()
Arvados$collections_get()
Arvados$collections_create()
Arvados$collections_update()
Arvados$collections_delete()
Arvados$collections_provenance()
Arvados$collections_used_by()
Arvados$collections_trash()
Arvados$collections_untrash()
Arvados$collections_list()
Arvados$containers_get()
Arvados$containers_create()
Arvados$containers_update()
Arvados$containers_delete()
Arvados$containers_auth()
Arvados$containers_lock()
Arvados$containers_unlock()
Arvados$containers_secret_mounts()
Arvados$containers_current()
Arvados$containers_list()
Arvados$container_requests_get()
Arvados$container_requests_create()
Arvados$container_requests_update()
Arvados$container_requests_delete()
Arvados$container_requests_list()
Arvados$groups_get()
Arvados$groups_create()
Arvados$groups_update()
Arvados$groups_delete()
Arvados$groups_contents()
Arvados$groups_shared()
Arvados$groups_trash()
Arvados$groups_untrash()
Arvados$groups_list()
Arvados$keep_services_get()
Arvados$keep_services_create()
Arvados$keep_services_update()
Arvados$keep_services_delete()
Arvados$keep_services_accessible()
Arvados$keep_services_list()
Arvados$project_permission_give()
Arvados$project_permission_refuse()
Arvados$project_permission_update()
Arvados$project_permission_check()
Arvados$links_get()
Arvados$links_create()
Arvados$links_update()
Arvados$links_delete()
Arvados$links_list()
Arvados$links_get_permissions()
Arvados$logs_get()
Arvados$logs_create()
Arvados$logs_update()
Arvados$logs_delete()
Arvados$logs_list()
Arvados$users_get()
Arvados$users_create()
Arvados$users_update()
Arvados$users_delete()
Arvados$users_current()
Arvados$users_system()
Arvados$users_activate()
Arvados$users_setup()
Arvados$users_unsetup()
Arvados$users_merge()
Arvados$users_list()
Arvados$repositories_get()
Arvados$repositories_create()
Arvados$repositories_update()
Arvados$repositories_delete()
Arvados$repositories_get_all_permissions()
Arvados$repositories_list()
Arvados$virtual_machines_get()
Arvados$virtual_machines_create()
Arvados$virtual_machines_update()
Arvados$virtual_machines_delete()
Arvados$virtual_machines_logins()
Arvados$virtual_machines_get_all_logins()
Arvados$virtual_machines_list()
Arvados$workflows_get()
Arvados$workflows_create()
Arvados$workflows_update()
Arvados$workflows_delete()
Arvados$workflows_list()
Arvados$user_agreements_get()
Arvados$user_agreements_create()
Arvados$user_agreements_update()
Arvados$user_agreements_delete()
Arvados$user_agreements_signatures()
Arvados$user_agreements_sign()
Arvados$user_agreements_list()
Arvados$user_agreements_new()
Arvados$configs_get()
Arvados$getHostName()
Arvados$getToken()
Arvados$setRESTService()
Arvados$getRESTService()

Method `new()`

Initialize new enviroment.

Usage

Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)

Arguments

authToken: ARVADOS_API_TOKEN from 'Get API Token' on Arvados.
hostName: ARVADOS_API_HOST from 'Get API Token' on Arvados.
numRetries: Specify number of times to retry failed service requests.

Returns

A new 'Arvados' object.

Examples

arv <- Arvados$new(authToken = "ARVADOS_API_TOKEN", hostName = "ARVADOS_API_HOST", numRetries = 3)

Method `project_exist()`

project_exist enables checking if the project with such a UUID exist.

Usage

Arvados$project_exist(uuid)

Arguments

uuid: The UUID of a project or a file.

Examples

arv$project_exist(uuid = projectUUID)

Method `project_get()`

project_get returns the demanded project.

Usage

Arvados$project_get(uuid)

Arguments

uuid: The UUID of the Group in question.

Examples

project <- arv$project_get(uuid = projectUUID)

Method `project_create()`

project_create creates a new project of a given name and description.

Usage

Arvados$project_create(
  name,
  description,
  ownerUUID,
  properties = NULL,
  ensureUniqueName = "false"
)

Arguments

name: Name of the project.
description: Description of the project.
ownerUUID: The UUID of the maternal project to created one.
properties: List of the properties of the project.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.

Examples

Properties <- list() # should contain a list of new properties to be added
new_project <- arv$project_create(name = "project name", description = "project description", owner_uuid = "project UUID", properties = NULL, ensureUniqueName = "false")

Method `project_properties_set()`

project_properties_set is a method defined in Arvados class that enables setting properties. Allows to set or overwrite the properties. In case there are set already it overwrites them.

Usage

Arvados$project_properties_set(listProperties, uuid)

Arguments

listProperties: List of new properties.
uuid: The UUID of a project or a file.

Examples

Properties <- list() # should contain a list of new properties to be added
arv$project_properties_set(Properties, uuid)

Method `project_properties_append()`

project_properties_append is a method defined in Arvados class that enables appending properties. Allows to add new properties.

Usage

Arvados$project_properties_append(properties, uuid)

Arguments

uuid: The UUID of a project or a file.
listOfNewProperties: List of new properties.

Examples

newProperties <- list() # should contain a list of new properties to be added
arv$project_properties_append(properties = newProperties, uuid)

Method `project_properties_get()`

project_properties_get is a method defined in Arvados class that returns properties.

Usage

Arvados$project_properties_get(uuid)

Arguments

uuid: The UUID of a project or a file.

Examples

arv$project_properties_get(projectUUID)

Method `project_properties_delete()`

project_properties_delete is a method defined in Arvados class that deletes list of properties.

Usage

Arvados$project_properties_delete(oneProp, uuid)

Arguments

oneProp: Property to be deleted.
uuid: The UUID of a project or a file.

Examples

Properties <- list() # should contain a list of new properties to be added
arv$project_properties_delete(Properties,  projectUUID)

Method `project_update()`

project_update enables updating project. New name, description and properties may be given.

Usage

Arvados$project_update(..., uuid)

Arguments

...: Feature to be updated (name, description, properties).
uuid: The UUID of a project in question.

Examples

newProperties <- list() # should contain a list of new properties to be added
arv$project_update(name = "new project name", properties = newProperties, uuid = projectUUID)

Method `project_list()`

project_list enables listing project by its name, uuid, properties, permissions.

Usage

Arvados$project_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  includeTrash = NULL
)

Arguments

includeTrash: Include items whose is_trashed attribute is true.
uuid: The UUID of a project in question.
recursive: Include contents from child groups recursively.

Examples

listOfprojects <- arv$project_list(list(list("owner_uuid", "=", projectUUID))) # Sample query which show projects within the project of a given UUID

Method `project_delete()`

project_delete trashes project of a given uuid. It can be restored from trash or deleted permanently.

Usage

Arvados$project_delete(uuid)

Arguments

uuid: The UUID of the Group in question.

Method `api_clients_get()`

api_clients_get is a method defined in Arvados class.

Usage

Arvados$api_clients_get(uuid)

Arguments

uuid: The UUID of the apiClient in question.

Method `api_clients_create()`

api_clients_create is a method defined in Arvados class.

Usage

Arvados$api_clients_create(
  apiClient,
  ensureUniqueName = "false",
  clusterID = NULL
)

Arguments

apiClient: apiClient object.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.
clusterID: Create object on a remote federated cluster instead of the current one.

Method `api_clients_update()`

api_clients_update is a method defined in Arvados class.

Usage

Arvados$api_clients_update(apiClient, uuid)

Arguments

apiClient: apiClient object.
uuid: The UUID of the apiClient in question.

Method `api_clients_delete()`

api_clients_delete is a method defined in Arvados class.

Usage

Arvados$api_clients_delete(uuid)

Arguments

uuid: The UUID of the apiClient in question.

Method `api_clients_list()`

api_clients_list is a method defined in Arvados class.

Usage

Arvados$api_clients_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.

Method `api_client_authorizations_get()`

api_client_authorizations_get is a method defined in Arvados class.

Usage

Arvados$api_client_authorizations_get(uuid)

Arguments

uuid: The UUID of the apiClientAuthorization in question.

Method `api_client_authorizations_create()`

api_client_authorizations_create is a method defined in Arvados class.

Usage

Arvados$api_client_authorizations_create(
  apiClientAuthorization,
  ensureUniqueName = "false",
  clusterID = NULL
)

Arguments

apiClientAuthorization: apiClientAuthorization object.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error on (ownerUUID, name) collision_
clusterID: Create object on a remote federated cluster instead of the current one.

Method `api_client_authorizations_update()`

api_client_authorizations_update is a method defined in Arvados class.

Usage

Arvados$api_client_authorizations_update(apiClientAuthorization, uuid)

Arguments

apiClientAuthorization: apiClientAuthorization object.
uuid: The UUID of the apiClientAuthorization in question.

Method `api_client_authorizations_delete()`

api_client_authorizations_delete is a method defined in Arvados class.

Usage

Arvados$api_client_authorizations_delete(uuid)

Arguments

uuid: The UUID of the apiClientAuthorization in question.

Method `api_client_authorizations_create_system_auth()`

api_client_authorizations_create_system_auth is a method defined in Arvados class.

Usage

Arvados$api_client_authorizations_create_system_auth(
  apiClientID = NULL,
  scopes = NULL
)

Method `api_client_authorizations_current()`

api_client_authorizations_current is a method defined in Arvados class.

Usage

Arvados$api_client_authorizations_current()

Method `api_client_authorizations_list()`

api_client_authorizations_list is a method defined in Arvados class.

Usage

Arvados$api_client_authorizations_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.

Method `authorized_keys_get()`

authorized_keys_get is a method defined in Arvados class.

Usage

Arvados$authorized_keys_get(uuid)

Arguments

uuid: The UUID of the authorizedKey in question.

Method `authorized_keys_create()`

authorized_keys_create is a method defined in Arvados class.

Usage

Arvados$authorized_keys_create(
  authorizedKey,
  ensureUniqueName = "false",
  clusterID = NULL
)

Arguments

authorizedKey: authorizedKey object.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.
clusterID: Create object on a remote federated cluster instead of the current one.

Method `authorized_keys_update()`

authorized_keys_update is a method defined in Arvados class.

Usage

Arvados$authorized_keys_update(authorizedKey, uuid)

Arguments

authorizedKey: authorizedKey object.
uuid: The UUID of the authorizedKey in question.

Method `authorized_keys_delete()`

authorized_keys_delete is a method defined in Arvados class.

Usage

Arvados$authorized_keys_delete(uuid)

Arguments

uuid: The UUID of the authorizedKey in question.

Method `authorized_keys_list()`

authorized_keys_list is a method defined in Arvados class.

Usage

Arvados$authorized_keys_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.

Method `collections_get()`

collections_get is a method defined in Arvados class.

Usage

Arvados$collections_get(uuid)

Arguments

uuid: The UUID of the Collection in question. collection <- arv$collections_get(uuid = collectionUUID)

Method `collections_create()`

collections_create is a method defined in Arvados class that enables collections creation.

Usage

Arvados$collections_create(
  name,
  description,
  ownerUUID = NULL,
  properties = NULL,
  ensureUniqueName = "false",
  clusterID = NULL
)

Arguments

name: Name of the collection.
description: Description of the collection.
ownerUUID: UUID of the maternal project to created one.
properties: Properties of the collection.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.
clusterID: Create object on a remote federated cluster instead of the current one.

Examples

Properties <- list() # should contain a list of new properties to be added
arv$collections_create(name = "collectionTitle", description = "collectionDescription", ownerUUID = "collectionOwner", properties = Properties)

Method `collections_update()`

collections_update is a method defined in Arvados class.

Usage

Arvados$collections_update(
  name,
  description,
  ownerUUID = NULL,
  properties = NULL,
  uuid
)

Arguments

name: New name of the collection.
description: New description of the collection.
ownerUUID: UUID of the maternal project to created one.
properties: New list of properties of the collection.
uuid: The UUID of the Collection in question.

Examples

collection <- arv$collections_create(name = "newCollectionTitle", description = "newCollectionDescription", ownerUUID = "collectionOwner", properties = NULL)

Method `collections_delete()`

collections_delete is a method defined in Arvados class.

Usage

Arvados$collections_delete(uuid)

Arguments

uuid: The UUID of the Collection in question.

Examples

arv$collection_delete(collectionUUID)

Method `collections_provenance()`

collections_provenance is a method defined in Arvados class, it returns the collection by uuid.

Usage

Arvados$collections_provenance(uuid)

Arguments

uuid: The UUID of the Collection in question.

Examples

collection <- arv$collections_provenance(collectionUUID)

Method `collections_used_by()`

collections_used_by is a method defined in Arvados class, it returns collection by portable_data_hash.

Usage

Arvados$collections_used_by(uuid)

Arguments

uuid: The UUID of the Collection in question.

Method `collections_trash()`

collections_trash is a method defined in Arvados class, it moves collection to trash.

Usage

Arvados$collections_trash(uuid)

Arguments

uuid: The UUID of the Collection in question.

Examples

arv$collections_trash(collectionUUID)

Method `collections_untrash()`

collections_untrash is a method defined in Arvados class, it moves collection from trash to project.

Usage

Arvados$collections_untrash(uuid)

Arguments

uuid: The UUID of the Collection in question.

Examples

arv$collections_untrash(collectionUUID)

Method `collections_list()`

collections_list is a method defined in Arvados class.

Usage

Arvados$collections_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL,
  includeTrash = NULL,
  includeOldVersions = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.
includeTrash: Include collections whose is_trashed attribute is true.
includeOldVersions: Include past collection versions.

Examples

collectionList <- arv$collections.list(list(list("name", "=", "Example")))

Method `containers_get()`

containers_get is a method defined in Arvados class.

Usage

Arvados$containers_get(uuid)

Arguments

uuid: The UUID of the Container in question.

Method `containers_create()`

containers_create is a method defined in Arvados class.

Usage

Arvados$containers_create(
  container,
  ensureUniqueName = "false",
  clusterID = NULL
)

Arguments

container: Container object.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.
clusterID: Create object on a remote federated cluster instead of the current one.

Method `containers_update()`

containers_update is a method defined in Arvados class.

Usage

Arvados$containers_update(container, uuid)

Arguments

container: Container object.
uuid: The UUID of the Container in question.

Method `containers_delete()`

containers_delete is a method defined in Arvados class.

Usage

Arvados$containers_delete(uuid)

Arguments

uuid: The UUID of the Container in question.

Method `containers_auth()`

containers_auth is a method defined in Arvados class.

Usage

Arvados$containers_auth(uuid)

Arguments

uuid: The UUID of the Container in question.

Method `containers_lock()`

containers_lock is a method defined in Arvados class.

Usage

Arvados$containers_lock(uuid)

Arguments

uuid: The UUID of the Container in question.

Method `containers_unlock()`

containers_unlock is a method defined in Arvados class.

Usage

Arvados$containers_unlock(uuid)

Arguments

uuid: The UUID of the Container in question.

Method `containers_secret_mounts()`

containers_secret_mounts is a method defined in Arvados class.

Usage

Arvados$containers_secret_mounts(uuid)

Arguments

uuid: The UUID of the Container in question.

Method `containers_current()`

containers_current is a method defined in Arvados class.

Usage

Arvados$containers_current()

Method `containers_list()`

containers_list is a method defined in Arvados class.

Usage

Arvados$containers_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.

Method `container_requests_get()`

container_requests_get is a method defined in Arvados class.

Usage

Arvados$container_requests_get(uuid)

Arguments

uuid: The UUID of the containerRequest in question.

Method `container_requests_create()`

container_requests_create is a method defined in Arvados class.

Usage

Arvados$container_requests_create(
  containerRequest,
  ensureUniqueName = "false",
  clusterID = NULL
)

Arguments

containerRequest: containerRequest object.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.
clusterID: Create object on a remote federated cluster instead of the current one.

Method `container_requests_update()`

container_requests_update is a method defined in Arvados class.

Usage

Arvados$container_requests_update(containerRequest, uuid)

Arguments

containerRequest: containerRequest object.
uuid: The UUID of the containerRequest in question.

Method `container_requests_delete()`

container_requests_delete is a method defined in Arvados class.

Usage

Arvados$container_requests_delete(uuid)

Arguments

uuid: The UUID of the containerRequest in question.

Method `container_requests_list()`

container_requests_list is a method defined in Arvados class.

Usage

Arvados$container_requests_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL,
  includeTrash = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: bypass federation behavior, list items from local instance database only
includeTrash: Include container requests whose owner project is trashed.

Method `groups_get()`

groups_get is a method defined in Arvados class.

Usage

Arvados$groups_get(uuid)

Arguments

uuid: The UUID of the Group in question.

Method `groups_create()`

groups_create is a method defined in Arvados class that supports project creation.

Usage

Arvados$groups_create(
  group,
  ensureUniqueName = "false",
  clusterID = NULL,
  async = "false"
)

Arguments

group: Group object.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.
clusterID: Create object on a remote federated cluster instead of the current one.
async: Defer permissions update.

Method `groups_update()`

groups_update is a method defined in Arvados class.

Usage

Arvados$groups_update(group, uuid, async = "false")

Arguments

group: Group object.
uuid: The UUID of the Group in question.
async: Defer permissions update.

Method `groups_delete()`

groups_delete is a method defined in Arvados class.

Usage

Arvados$groups_delete(uuid)

Arguments

uuid: The UUID of the Group in question.

Method `groups_contents()`

groups_contents is a method defined in Arvados class.

Usage

Arvados$groups_contents(
  filters = NULL,
  where = NULL,
  order = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL,
  includeTrash = NULL,
  uuid = NULL,
  recursive = NULL,
  include = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.
includeTrash: Include items whose is_trashed attribute is true.
recursive: Include contents from child groups recursively.
include: Include objects referred to by listed field in "included" (only ownerUUID).

Method `groups_shared()`

groups_shared is a method defined in Arvados class.

Usage

Arvados$groups_shared(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL,
  includeTrash = NULL,
  include = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.
includeTrash: Include items whose is_trashed attribute is true.

Method `groups_trash()`

groups_trash is a method defined in Arvados class.

Usage

Arvados$groups_trash(uuid)

Arguments

uuid: The UUID of the Group in question.

Method `groups_untrash()`

groups_untrash is a method defined in Arvados class.

Usage

Arvados$groups_untrash(uuid)

Arguments

uuid: The UUID of the Group in question.

Method `groups_list()`

groups_list is a method defined in Arvados class.

Usage

Arvados$groups_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL,
  includeTrash = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.
includeTrash: Include items whose is_trashed attribute is true.

Method `keep_services_get()`

keep_services_get is a method defined in Arvados class.

Usage

Arvados$keep_services_get(uuid)

Arguments

uuid: The UUID of the keepService in question.

Method `keep_services_create()`

keep_services_create is a method defined in Arvados class.

Usage

Arvados$keep_services_create(
  keepService,
  ensureUniqueName = "false",
  clusterID = NULL
)

Arguments

keepService: keepService object.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.
clusterID: Create object on a remote federated cluster instead of the current one.

Method `keep_services_update()`

keep_services_update is a method defined in Arvados class.

Usage

Arvados$keep_services_update(keepService, uuid)

Arguments

keepService: keepService object.
uuid: The UUID of the keepService in question.

Method `keep_services_delete()`

keep_services_delete is a method defined in Arvados class.

Usage

Arvados$keep_services_delete(uuid)

Arguments

uuid: The UUID of the keepService in question.

Method `keep_services_accessible()`

keep_services_accessible is a method defined in Arvados class.

Usage

Arvados$keep_services_accessible()

Method `keep_services_list()`

keep_services_list is a method defined in Arvados class.

Usage

Arvados$keep_services_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.

Method `project_permission_give()`

project_permission_give is a method defined in Arvados class that enables sharing files with another users.

Usage

Arvados$project_permission_give(type, uuid, user)

Arguments

type: Possible options are can_read or can_write or can_manage.
uuid: The UUID of a project or a file.
user: The UUID of the person that gets the permission.

Examples

arv$project_permission_give(type = "can_read", uuid = objectUUID, user = userUUID)

Method `project_permission_refuse()`

project_permission_refuse is a method defined in Arvados class that unables sharing files with another users.

Usage

Arvados$project_permission_refuse(type, uuid, user)

Arguments

type: Possible options are can_read or can_write or can_manage.
uuid: The UUID of a project or a file.
user: The UUID of a person that permissions are taken from.

Examples

arv$project_permission_refuse(type = "can_read", uuid = objectUUID, user = userUUID)

Method `project_permission_update()`

project_permission_update is a method defined in Arvados class that enables updating permissions.

Usage

Arvados$project_permission_update(typeOld, typeNew, uuid, user)

Arguments

typeOld: Old option.
typeNew: New option like can_read or can_write or can_manage.
uuid: The UUID of a project or a file.
user: The UUID of the person that the permission is being updated.

Examples

arv$project_permission_update(typeOld = "can_read", typeNew = "can_write", uuid = objectUUID, user = userUUID)

Method `project_permission_check()`

project_permission_check is a method defined in Arvados class that enables checking file permissions.

Usage

Arvados$project_permission_check(uuid, user, type = NULL)

Arguments

uuid: The UUID of a project or a file.
user: The UUID of the person that the permission is being updated.
type: Possible options are can_read or can_write or can_manage.

Examples

arv$project_permission_check(type = "can_read", uuid = objectUUID, user = userUUID)

Method `links_get()`

links_get is a method defined in Arvados class.

Usage

Arvados$links_get(uuid)

Arguments

uuid: The UUID of the Link in question.

Method `links_create()`

links_create is a method defined in Arvados class.

Usage

Arvados$links_create(link, ensureUniqueName = "false", clusterID = NULL)

Arguments

link: Link object.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.
clusterID: Create object on a remote federated cluster instead of the current one.

Method `links_update()`

links_update is a method defined in Arvados class.

Usage

Arvados$links_update(link, uuid, async = "false")

Arguments

link: Link object.
uuid: The UUID of the Link in question.

Method `links_delete()`

links_delete is a method defined in Arvados class.

Usage

Arvados$links_delete(uuid)

Arguments

uuid: The UUID of the Link in question.

Method `links_list()`

links_list is a method defined in Arvados class.

Usage

Arvados$links_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.

Method `links_get_permissions()`

links_get_permissions is a method defined in Arvados class.

Usage

Arvados$links_get_permissions(uuid)

Arguments

uuid: The UUID of the Log in question.

Method `logs_get()`

logs_get is a method defined in Arvados class.

Usage

Arvados$logs_get(uuid)

Arguments

uuid: The UUID of the Log in question.

Method `logs_create()`

logs_create is a method defined in Arvados class.

Usage

Arvados$logs_create(log, ensureUniqueName = "false", clusterID = NULL)

Arguments

log: Log object.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.
clusterID: Create object on a remote federated cluster instead of the current one.

Method `logs_update()`

logs_update is a method defined in Arvados class.

Usage

Arvados$logs_update(log, uuid)

Arguments

log: Log object.
uuid: The UUID of the Log in question.

Method `logs_delete()`

logs_delete is a method defined in Arvados class.

Usage

Arvados$logs_delete(uuid)

Arguments

uuid: The UUID of the Log in question.

Method `logs_list()`

logs_list is a method defined in Arvados class.

Usage

Arvados$logs_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.

Method `users_get()`

users_get is a method defined in Arvados class.

Usage

Arvados$users_get(uuid)

Arguments

uuid: The UUID of the User in question.

Method `users_create()`

users_create is a method defined in Arvados class.

Usage

Arvados$users_create(user, ensureUniqueName = "false", clusterID = NULL)

Arguments

user: User object.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.
clusterID: Create object on a remote federated cluster instead of the current one.

Method `users_update()`

users_update is a method defined in Arvados class.

Usage

Arvados$users_update(user, uuid, bypassFederation = NULL)

Arguments

user: User object.
uuid: The UUID of the User in question.

Method `users_delete()`

users_delete is a method defined in Arvados class.

Usage

Arvados$users_delete(uuid)

Arguments

uuid: The UUID of the User in question.

Method `users_current()`

users_current is a method defined in Arvados class.

Usage

Arvados$users_current()

Method `users_system()`

users_system is a method defined in Arvados class.

Usage

Arvados$users_system()

Method `users_activate()`

users_activate is a method defined in Arvados class.

Usage

Arvados$users_activate(uuid)

Arguments

uuid: The UUID of the User in question.

Method `users_setup()`

users_setup is a method defined in Arvados class.

Usage

Arvados$users_setup(
  uuid = NULL,
  user = NULL,
  repo_name = NULL,
  vm_uuid = NULL,
  send_notification_email = "false"
)

Method `users_unsetup()`

users_unsetup is a method defined in Arvados class.

Usage

Arvados$users_unsetup(uuid)

Arguments

uuid: The UUID of the User in question.

Method `users_merge()`

users_merge is a method defined in Arvados class.

Usage

Arvados$users_merge(
  newOwnerUUID,
  newUserToken = NULL,
  redirectToNewUser = NULL,
  oldUserUUID = NULL,
  newUserUUID = NULL
)

Method `users_list()`

users_list is a method defined in Arvados class.

Usage

Arvados$users_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.

Method `repositories_get()`

repositories_get is a method defined in Arvados class.

Usage

Arvados$repositories_get(uuid)

Arguments

uuid: The UUID of the Repository in question.

Method `repositories_create()`

repositories_create is a method defined in Arvados class.

Usage

Arvados$repositories_create(
  repository,
  ensureUniqueName = "false",
  clusterID = NULL
)

Arguments

repository: Repository object.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.
clusterID: Create object on a remote federated cluster instead of the current one.

Method `repositories_update()`

repositories_update is a method defined in Arvados class.

Usage

Arvados$repositories_update(repository, uuid)

Arguments

repository: Repository object.
uuid: The UUID of the Repository in question.

Method `repositories_delete()`

repositories_delete is a method defined in Arvados class.

Usage

Arvados$repositories_delete(uuid)

Arguments

uuid: The UUID of the Repository in question.

Method `repositories_get_all_permissions()`

repositories_get_all_permissions is a method defined in Arvados class.

Usage

Arvados$repositories_get_all_permissions()

Method `repositories_list()`

repositories_list is a method defined in Arvados class.

Usage

Arvados$repositories_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.

Method `virtual_machines_get()`

virtual_machines_get is a method defined in Arvados class.

Usage

Arvados$virtual_machines_get(uuid)

Arguments

uuid: The UUID of the virtualMachine in question.

Method `virtual_machines_create()`

virtual_machines_create is a method defined in Arvados class.

Usage

Arvados$virtual_machines_create(
  virtualMachine,
  ensureUniqueName = "false",
  clusterID = NULL
)

Arguments

virtualMachine: virtualMachine object.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.
clusterID: Create object on a remote federated cluster instead of the current one.

Method `virtual_machines_update()`

virtual_machines_update is a method defined in Arvados class.

Usage

Arvados$virtual_machines_update(virtualMachine, uuid)

Arguments

virtualMachine: virtualMachine object.
uuid: The UUID of the virtualMachine in question.

Method `virtual_machines_delete()`

virtual_machines_delete is a method defined in Arvados class.

Usage

Arvados$virtual_machines_delete(uuid)

Arguments

uuid: The UUID of the virtualMachine in question.

Method `virtual_machines_logins()`

virtual_machines_logins is a method defined in Arvados class.

Usage

Arvados$virtual_machines_logins(uuid)

Arguments

uuid: The UUID of the virtualMachine in question.

Method `virtual_machines_get_all_logins()`

virtual_machines_get_all_logins is a method defined in Arvados class.

Usage

Arvados$virtual_machines_get_all_logins()

Method `virtual_machines_list()`

virtual_machines_list is a method defined in Arvados class.

Usage

Arvados$virtual_machines_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: bypass federation behavior, list items from local instance database only

Method `workflows_get()`

workflows_get is a method defined in Arvados class.

Usage

Arvados$workflows_get(uuid)

Arguments

uuid: The UUID of the Workflow in question.

Method `workflows_create()`

workflows_create is a method defined in Arvados class.

Usage

Arvados$workflows_create(
  workflow,
  ensureUniqueName = "false",
  clusterID = NULL
)

Arguments

workflow: Workflow object.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.
clusterID: Create object on a remote federated cluster instead of the current one.

Method `workflows_update()`

workflows_update is a method defined in Arvados class.

Usage

Arvados$workflows_update(workflow, uuid)

Arguments

workflow: Workflow object.
uuid: The UUID of the Workflow in question.

Method `workflows_delete()`

workflows_delete is a method defined in Arvados class.

Usage

Arvados$workflows_delete(uuid)

Arguments

uuid: The UUID of the Workflow in question.

Method `workflows_list()`

workflows_list is a method defined in Arvados class.

Usage

Arvados$workflows_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.

Method `user_agreements_get()`

user_agreements_get is a method defined in Arvados class.

Usage

Arvados$user_agreements_get(uuid)

Arguments

uuid: The UUID of the userAgreement in question.

Method `user_agreements_create()`

user_agreements_create is a method defined in Arvados class.

Usage

Arvados$user_agreements_create(
  userAgreement,
  ensureUniqueName = "false",
  clusterID = NULL
)

Arguments

userAgreement: userAgreement object.
ensureUniqueName: Adjust name to ensure uniqueness instead of returning an error.
clusterID: Create object on a remote federated cluster instead of the current one.

Method `user_agreements_update()`

user_agreements_update is a method defined in Arvados class.

Usage

Arvados$user_agreements_update(userAgreement, uuid)

Arguments

userAgreement: userAgreement object.
uuid: The UUID of the userAgreement in question.

Method `user_agreements_delete()`

user_agreements_delete is a method defined in Arvados class.

Usage

Arvados$user_agreements_delete(uuid)

Arguments

uuid: The UUID of the userAgreement in question.

Method `user_agreements_signatures()`

user_agreements_signatures is a method defined in Arvados class.

Usage

Arvados$user_agreements_signatures()

Method `user_agreements_sign()`

user_agreements_sign is a method defined in Arvados class.

Usage

Arvados$user_agreements_sign()

Method `user_agreements_list()`

user_agreements_list is a method defined in Arvados class.

Usage

Arvados$user_agreements_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = "100",
  offset = "0",
  count = "exact",
  clusterID = NULL,
  bypassFederation = NULL
)

Arguments

clusterID: List objects on a remote federated cluster instead of the current one.
bypassFederation: Bypass federation behavior, list items from local instance database only.

Method `user_agreements_new()`

user_agreements_new is a method defined in Arvados class.

Usage

Arvados$user_agreements_new()

Method `configs_get()`

configs_get is a method defined in Arvados class.

Usage

Arvados$configs_get()

Method `getHostName()`

Usage

Arvados$getHostName()

Method `getToken()`

Usage

Arvados$getToken()

Method `setRESTService()`

Usage

Arvados$setRESTService(newREST)

Method `getRESTService()`

Usage

Arvados$getRESTService()

Examples


## ------------------------------------------------
## Method `Arvados$new`
## ------------------------------------------------

arv <- Arvados$new(authToken = "ARVADOS_API_TOKEN", hostName = "ARVADOS_API_HOST", numRetries = 3)

## ------------------------------------------------
## Method `Arvados$project_exist`
## ------------------------------------------------

arv$project_exist(uuid = projectUUID)

## ------------------------------------------------
## Method `Arvados$project_get`
## ------------------------------------------------

project <- arv$project_get(uuid = projectUUID)

## ------------------------------------------------
## Method `Arvados$project_create`
## ------------------------------------------------

Properties <- list() # should contain a list of new properties to be added
new_project <- arv$project_create(name = "project name", description = "project description", owner_uuid = "project UUID", properties = NULL, ensureUniqueName = "false")

## ------------------------------------------------
## Method `Arvados$project_properties_set`
## ------------------------------------------------

Properties <- list() # should contain a list of new properties to be added
arv$project_properties_set(Properties, uuid)

## ------------------------------------------------
## Method `Arvados$project_properties_append`
## ------------------------------------------------

newProperties <- list() # should contain a list of new properties to be added
arv$project_properties_append(properties = newProperties, uuid)

## ------------------------------------------------
## Method `Arvados$project_properties_get`
## ------------------------------------------------

arv$project_properties_get(projectUUID)

## ------------------------------------------------
## Method `Arvados$project_properties_delete`
## ------------------------------------------------

Properties <- list() # should contain a list of new properties to be added
arv$project_properties_delete(Properties,  projectUUID)

## ------------------------------------------------
## Method `Arvados$project_update`
## ------------------------------------------------

newProperties <- list() # should contain a list of new properties to be added
arv$project_update(name = "new project name", properties = newProperties, uuid = projectUUID)

## ------------------------------------------------
## Method `Arvados$project_list`
## ------------------------------------------------

listOfprojects <- arv$project_list(list(list("owner_uuid", "=", projectUUID))) # Sample query which show projects within the project of a given UUID

## ------------------------------------------------
## Method `Arvados$collections_create`
## ------------------------------------------------

Properties <- list() # should contain a list of new properties to be added
arv$collections_create(name = "collectionTitle", description = "collectionDescription", ownerUUID = "collectionOwner", properties = Properties)

## ------------------------------------------------
## Method `Arvados$collections_update`
## ------------------------------------------------

collection <- arv$collections_create(name = "newCollectionTitle", description = "newCollectionDescription", ownerUUID = "collectionOwner", properties = NULL)

## ------------------------------------------------
## Method `Arvados$collections_delete`
## ------------------------------------------------

arv$collection_delete(collectionUUID)

## ------------------------------------------------
## Method `Arvados$collections_provenance`
## ------------------------------------------------

collection <- arv$collections_provenance(collectionUUID)

## ------------------------------------------------
## Method `Arvados$collections_trash`
## ------------------------------------------------

arv$collections_trash(collectionUUID)

## ------------------------------------------------
## Method `Arvados$collections_untrash`
## ------------------------------------------------

arv$collections_untrash(collectionUUID)

## ------------------------------------------------
## Method `Arvados$collections_list`
## ------------------------------------------------

collectionList <- arv$collections.list(list(list("name", "=", "Example")))

## ------------------------------------------------
## Method `Arvados$project_permission_give`
## ------------------------------------------------

arv$project_permission_give(type = "can_read", uuid = objectUUID, user = userUUID)

## ------------------------------------------------
## Method `Arvados$project_permission_refuse`
## ------------------------------------------------

arv$project_permission_refuse(type = "can_read", uuid = objectUUID, user = userUUID)

## ------------------------------------------------
## Method `Arvados$project_permission_update`
## ------------------------------------------------

arv$project_permission_update(typeOld = "can_read", typeNew = "can_write", uuid = objectUUID, user = userUUID)

## ------------------------------------------------
## Method `Arvados$project_permission_check`
## ------------------------------------------------

arv$project_permission_check(type = "can_read", uuid = objectUUID, user = userUUID)

R6 Class Representing a Arvados

Description

Methods

Public methods

Method new()

Usage

Arguments

Returns

Examples

Method project_exist()

Usage

Arguments

Examples

Method project_get()

Usage

Arguments

Examples

Method project_create()

Usage

Arguments

Examples

Method project_properties_set()

Usage

Arguments

Examples

Method project_properties_append()

Usage

Arguments

Examples

Method project_properties_get()

Usage

Arguments

Examples

Method project_properties_delete()

Usage

Arguments

Examples

Method project_update()

Usage

Arguments

Examples

Method project_list()

Usage

Arguments

Examples

Method project_delete()

Usage

Arguments

Method api_clients_get()

Usage

Arguments

Method api_clients_create()

Usage

Arguments

Method api_clients_update()

Usage

Arguments

Method api_clients_delete()

Usage

Arguments

Method api_clients_list()

Usage

Arguments

Method api_client_authorizations_get()

Usage

Arguments

Method api_client_authorizations_create()

Usage

Arguments

Method api_client_authorizations_update()

Usage

Arguments

Method api_client_authorizations_delete()

Usage

Arguments

Method api_client_authorizations_create_system_auth()

Usage

Method api_client_authorizations_current()

Usage

Method api_client_authorizations_list()

Method `new()`

Method `project_exist()`

Method `project_get()`

Method `project_create()`

Method `project_properties_set()`

Method `project_properties_append()`

Method `project_properties_get()`

Method `project_properties_delete()`

Method `project_update()`

Method `project_list()`

Method `project_delete()`

Method `api_clients_get()`

Method `api_clients_create()`

Method `api_clients_update()`

Method `api_clients_delete()`

Method `api_clients_list()`

Method `api_client_authorizations_get()`

Method `api_client_authorizations_create()`

Method `api_client_authorizations_update()`

Method `api_client_authorizations_delete()`

Method `api_client_authorizations_create_system_auth()`

Method `api_client_authorizations_current()`

Method `api_client_authorizations_list()`

Method `authorized_keys_get()`

Method `authorized_keys_create()`

Method `authorized_keys_update()`

Method `authorized_keys_delete()`

Method `authorized_keys_list()`

Method `collections_get()`

Method `collections_create()`

Method `collections_update()`

Method `collections_delete()`

Method `collections_provenance()`

Method `collections_used_by()`

Method `collections_trash()`

Method `collections_untrash()`

Method `collections_list()`

Method `containers_get()`

Method `containers_create()`

Method `containers_update()`

Method `containers_delete()`

Method `containers_auth()`

Method `containers_lock()`

Method `containers_unlock()`