ArvadosR 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


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)