ArvadosR Documentation

Arvados

Description

Arvados

Arvados

Details

This class implements a full REST client to the Arvados API.

Methods

Public methods

Method new()

Create a new Arvados API client.

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

Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.

hostName

Host name. If not specified ARVADOS_API_HOST environment variable will be used.

numRetries

Number which specifies how many times to retry failed service requests.

Returns

A new Arvados object.

Method api_client_authorizations_get()

Get a ApiClientAuthorization record by UUID.

Usage
Arvados$api_client_authorizations_get(uuid, select = NULL)
Arguments
uuid

The UUID of the ApiClientAuthorization to return.

select

An array of names of attributes to return in the response.

Returns

ApiClientAuthorization object.

Method api_client_authorizations_list()

Retrieve a ApiClientAuthorizationList.

Usage
Arvados$api_client_authorizations_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

Returns

ApiClientAuthorizationList object.

Method api_client_authorizations_create()

Create a new ApiClientAuthorization.

Usage
Arvados$api_client_authorizations_create(
  apiClientAuthorization,
  select = NULL,
  ensureUniqueName = NULL,
  clusterID = NULL
)
Arguments
apiClientAuthorization

ApiClientAuthorization object.

select

An array of names of attributes to return in the response.

ensureUniqueName

If the given name is already used by this owner, adjust the name to ensure uniqueness instead of returning an error.

clusterID

Cluster ID of a federated cluster where this object should be created.

Returns

ApiClientAuthorization object.

Method api_client_authorizations_update()

Update attributes of an existing ApiClientAuthorization.

Usage
Arvados$api_client_authorizations_update(
  apiClientAuthorization,
  uuid,
  select = NULL
)
Arguments
apiClientAuthorization

ApiClientAuthorization object.

uuid

The UUID of the ApiClientAuthorization to update.

select

An array of names of attributes to return in the response.

Returns

ApiClientAuthorization object.

Method api_client_authorizations_delete()

Delete an existing ApiClientAuthorization.

Usage
Arvados$api_client_authorizations_delete(uuid)
Arguments
uuid

The UUID of the ApiClientAuthorization to delete.

Returns

ApiClientAuthorization object.

Method api_client_authorizations_create_system_auth()

Create a token for the system ("root") user.

Usage
Arvados$api_client_authorizations_create_system_auth(scopes = NULL)
Arguments
scopes

An array of strings defining the scope of resources this token will be allowed to access. Refer to the scopes reference for details.

Returns

ApiClientAuthorization object.

Method api_client_authorizations_current()

Return all metadata for the token used to authorize this request.

Usage
Arvados$api_client_authorizations_current()
Returns

ApiClientAuthorization object.

Method authorized_keys_get()

Get a AuthorizedKey record by UUID.

Usage
Arvados$authorized_keys_get(uuid, select = NULL)
Arguments
uuid

The UUID of the AuthorizedKey to return.

select

An array of names of attributes to return in the response.

Returns

AuthorizedKey object.

Method authorized_keys_list()

Retrieve a AuthorizedKeyList.

Usage
Arvados$authorized_keys_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

Returns

AuthorizedKeyList object.

Method authorized_keys_create()

Create a new AuthorizedKey.

Usage
Arvados$authorized_keys_create(
  authorizedKey,
  select = NULL,
  ensureUniqueName = NULL,
  clusterID = NULL
)
Arguments
authorizedKey

AuthorizedKey object.

select

An array of names of attributes to return in the response.

ensureUniqueName

If the given name is already used by this owner, adjust the name to ensure uniqueness instead of returning an error.

clusterID

Cluster ID of a federated cluster where this object should be created.

Returns

AuthorizedKey object.

Method authorized_keys_update()

Update attributes of an existing AuthorizedKey.

Usage
Arvados$authorized_keys_update(authorizedKey, uuid, select = NULL)
Arguments
authorizedKey

AuthorizedKey object.

uuid

The UUID of the AuthorizedKey to update.

select

An array of names of attributes to return in the response.

Returns

AuthorizedKey object.

Method authorized_keys_delete()

Delete an existing AuthorizedKey.

Usage
Arvados$authorized_keys_delete(uuid)
Arguments
uuid

The UUID of the AuthorizedKey to delete.

Returns

AuthorizedKey object.

Method collections_get()

Get a Collection record by UUID.

Usage
Arvados$collections_get(uuid, select = NULL, includeTrash = NULL)
Arguments
uuid

The UUID of the Collection to return.

select

An array of names of attributes to return in the response.

includeTrash

Show collection even if its is_trashed attribute is true.

Returns

Collection object.

Method collections_list()

Retrieve a CollectionList.

Usage
Arvados$collections_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL,
  includeTrash = NULL,
  includeOldVersions = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

includeTrash

Include collections whose is_trashed attribute is true.

includeOldVersions

Include past collection versions.

Returns

CollectionList object.

Method collections_create()

Create a new Collection.

Usage
Arvados$collections_create(
  collection,
  select = NULL,
  ensureUniqueName = NULL,
  clusterID = NULL,
  replaceFiles = NULL,
  replaceSegments = NULL
)
Arguments
collection

Collection object.

select

An array of names of attributes to return in the response.

ensureUniqueName

If the given name is already used by this owner, adjust the name to ensure uniqueness instead of returning an error.

clusterID

Cluster ID of a federated cluster where this object should be created.

replaceFiles

Add, delete, and replace files and directories with new content and/or content from other collections. Refer to the replace_files reference for details.

replaceSegments

Replace existing block segments in the collection with new segments. Refer to the replace_segments reference for details.

Returns

Collection object.

Method collections_update()

Update attributes of an existing Collection.

Usage
Arvados$collections_update(
  collection,
  uuid,
  select = NULL,
  replaceFiles = NULL,
  replaceSegments = NULL
)
Arguments
collection

Collection object.

uuid

The UUID of the Collection to update.

select

An array of names of attributes to return in the response.

replaceFiles

Add, delete, and replace files and directories with new content and/or content from other collections. Refer to the replace_files reference for details.

replaceSegments

Replace existing block segments in the collection with new segments. Refer to the replace_segments reference for details.

Returns

Collection object.

Method collections_delete()

Delete an existing Collection.

Usage
Arvados$collections_delete(uuid)
Arguments
uuid

The UUID of the Collection to delete.

Returns

Collection object.

Method collections_provenance()

Detail the provenance of a given collection.

Usage
Arvados$collections_provenance(uuid)
Arguments
uuid

The UUID of the Collection to query.

Returns

Collection object.

Method collections_used_by()

Detail where a given collection has been used.

Usage
Arvados$collections_used_by(uuid)
Arguments
uuid

The UUID of the Collection to query.

Returns

Collection object.

Method collections_trash()

Trash a collection.

Usage
Arvados$collections_trash(uuid)
Arguments
uuid

The UUID of the Collection to update.

Returns

Collection object.

Method collections_untrash()

Untrash a collection.

Usage
Arvados$collections_untrash(uuid)
Arguments
uuid

The UUID of the Collection to update.

Returns

Collection object.

Method computed_permissions_list()

Retrieve a ComputedPermissionList.

Usage
Arvados$computed_permissions_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  count = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

Returns

ComputedPermissionList object.

Method containers_get()

Get a Container record by UUID.

Usage
Arvados$containers_get(uuid, select = NULL)
Arguments
uuid

The UUID of the Container to return.

select

An array of names of attributes to return in the response.

Returns

Container object.

Method containers_list()

Retrieve a ContainerList.

Usage
Arvados$containers_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

Returns

ContainerList object.

Method containers_create()

Create a new Container.

Usage
Arvados$containers_create(
  container,
  select = NULL,
  ensureUniqueName = NULL,
  clusterID = NULL
)
Arguments
container

Container object.

select

An array of names of attributes to return in the response.

ensureUniqueName

If the given name is already used by this owner, adjust the name to ensure uniqueness instead of returning an error.

clusterID

Cluster ID of a federated cluster where this object should be created.

Returns

Container object.

Method containers_update()

Update attributes of an existing Container.

Usage
Arvados$containers_update(container, uuid, select = NULL)
Arguments
container

Container object.

uuid

The UUID of the Container to update.

select

An array of names of attributes to return in the response.

Returns

Container object.

Method containers_delete()

Delete an existing Container.

Usage
Arvados$containers_delete(uuid)
Arguments
uuid

The UUID of the Container to delete.

Returns

Container object.

Method containers_auth()

Get the API client authorization token associated with this container.

Usage
Arvados$containers_auth(uuid)
Arguments
uuid

The UUID of the Container to query.

Returns

Container object.

Method containers_lock()

Lock a container (for a dispatcher to begin running it).

Usage
Arvados$containers_lock(uuid)
Arguments
uuid

The UUID of the Container to update.

Returns

Container object.

Method containers_unlock()

Unlock a container (for a dispatcher to stop running it).

Usage
Arvados$containers_unlock(uuid)
Arguments
uuid

The UUID of the Container to update.

Returns

Container object.

Method containers_update_priority()

Recalculate and return the priority of a given container.

Usage
Arvados$containers_update_priority(uuid)
Arguments
uuid

The UUID of the Container to update.

Returns

Container object.

Method containers_secret_mounts()

Return secret mount information for the container associated with the API token authorizing this request.

Usage
Arvados$containers_secret_mounts(uuid)
Arguments
uuid

The UUID of the Container to query.

Returns

Container object.

Method containers_current()

Return the container record associated with the API token authorizing this request.

Usage
Arvados$containers_current()
Returns

Container object.

Method container_requests_get()

Get a ContainerRequest record by UUID.

Usage
Arvados$container_requests_get(uuid, select = NULL, includeTrash = NULL)
Arguments
uuid

The UUID of the ContainerRequest to return.

select

An array of names of attributes to return in the response.

includeTrash

Show container request even if its owner project is trashed.

Returns

ContainerRequest object.

Method container_requests_list()

Retrieve a ContainerRequestList.

Usage
Arvados$container_requests_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL,
  includeTrash = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

includeTrash

Include container requests whose owner project is trashed.

Returns

ContainerRequestList object.

Method container_requests_create()

Create a new ContainerRequest.

Usage
Arvados$container_requests_create(
  containerRequest,
  select = NULL,
  ensureUniqueName = NULL,
  clusterID = NULL
)
Arguments
containerRequest

ContainerRequest object.

select

An array of names of attributes to return in the response.

ensureUniqueName

If the given name is already used by this owner, adjust the name to ensure uniqueness instead of returning an error.

clusterID

Cluster ID of a federated cluster where this object should be created.

Returns

ContainerRequest object.

Method container_requests_update()

Update attributes of an existing ContainerRequest.

Usage
Arvados$container_requests_update(containerRequest, uuid, select = NULL)
Arguments
containerRequest

ContainerRequest object.

uuid

The UUID of the ContainerRequest to update.

select

An array of names of attributes to return in the response.

Returns

ContainerRequest object.

Method container_requests_delete()

Delete an existing ContainerRequest.

Usage
Arvados$container_requests_delete(uuid)
Arguments
uuid

The UUID of the ContainerRequest to delete.

Returns

ContainerRequest object.

Method container_requests_container_status()

Return scheduling details for a container request.

Usage
Arvados$container_requests_container_status(uuid)
Arguments
uuid

The UUID of the container request to query.

Returns

ContainerRequest object.

Method groups_get()

Get a Group record by UUID.

Usage
Arvados$groups_get(uuid, select = NULL, includeTrash = NULL)
Arguments
uuid

The UUID of the Group to return.

select

An array of names of attributes to return in the response.

includeTrash

Return group/project even if its is_trashed attribute is true.

Returns

Group object.

Method groups_list()

Retrieve a GroupList.

Usage
Arvados$groups_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL,
  includeTrash = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

includeTrash

Include items whose is_trashed attribute is true.

Returns

GroupList object.

Method groups_create()

Create a new Group.

Usage
Arvados$groups_create(
  group,
  select = NULL,
  ensureUniqueName = NULL,
  clusterID = NULL,
  async = NULL
)
Arguments
group

Group object.

select

An array of names of attributes to return in the response.

ensureUniqueName

If the given name is already used by this owner, adjust the name to ensure uniqueness instead of returning an error.

clusterID

Cluster ID of a federated cluster where this object should be created.

async

If true, cluster permission will not be updated immediately, but instead at the next configured update interval.

Returns

Group object.

Method groups_update()

Update attributes of an existing Group.

Usage
Arvados$groups_update(group, uuid, select = NULL, async = NULL)
Arguments
group

Group object.

uuid

The UUID of the Group to update.

select

An array of names of attributes to return in the response.

async

If true, cluster permission will not be updated immediately, but instead at the next configured update interval.

Returns

Group object.

Method groups_delete()

Delete an existing Group.

Usage
Arvados$groups_delete(uuid)
Arguments
uuid

The UUID of the Group to delete.

Returns

Group object.

Method groups_contents()

List objects that belong to a group.

Usage
Arvados$groups_contents(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL,
  includeTrash = NULL,
  uuid = NULL,
  recursive = NULL,
  include = NULL,
  includeOldVersions = NULL,
  excludeHomeProject = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

includeTrash

Include items whose is_trashed attribute is true.

uuid

If given, limit the listing to objects owned by the user or group with this UUID.

recursive

If true, include contents from child groups recursively.

include

An array of referenced objects to include in the included field of the response. Supported values in the array are:

  • "container_uuid"

  • "owner_uuid"

includeOldVersions

If true, include past versions of collections in the listing.

excludeHomeProject

If true, exclude contents of the user's home project from the listing. Calling this method with this flag set is how clients enumerate objects shared with the current user.

Returns

Group object.

Method groups_shared()

List groups that the current user can access via permission links.

Usage
Arvados$groups_shared(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL,
  includeTrash = NULL,
  include = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

includeTrash

Include items whose is_trashed attribute is true.

include

A string naming referenced objects to include in the included field of the response. Supported values are:

  • "owner_uuid"

Returns

Group object.

Method groups_trash()

Trash a group.

Usage
Arvados$groups_trash(uuid)
Arguments
uuid

The UUID of the Group to update.

Returns

Group object.

Method groups_untrash()

Untrash a group.

Usage
Arvados$groups_untrash(uuid)
Arguments
uuid

The UUID of the Group to update.

Returns

Group object.

Method keep_services_get()

Get a KeepService record by UUID.

Usage
Arvados$keep_services_get(uuid, select = NULL)
Arguments
uuid

The UUID of the KeepService to return.

select

An array of names of attributes to return in the response.

Returns

KeepService object.

Method keep_services_list()

Retrieve a KeepServiceList.

Usage
Arvados$keep_services_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

Returns

KeepServiceList object.

Method keep_services_create()

Create a new KeepService.

Usage
Arvados$keep_services_create(
  keepService,
  select = NULL,
  ensureUniqueName = NULL,
  clusterID = NULL
)
Arguments
keepService

KeepService object.

select

An array of names of attributes to return in the response.

ensureUniqueName

If the given name is already used by this owner, adjust the name to ensure uniqueness instead of returning an error.

clusterID

Cluster ID of a federated cluster where this object should be created.

Returns

KeepService object.

Method keep_services_update()

Update attributes of an existing KeepService.

Usage
Arvados$keep_services_update(keepService, uuid, select = NULL)
Arguments
keepService

KeepService object.

uuid

The UUID of the KeepService to update.

select

An array of names of attributes to return in the response.

Returns

KeepService object.

Method keep_services_delete()

Delete an existing KeepService.

Usage
Arvados$keep_services_delete(uuid)
Arguments
uuid

The UUID of the KeepService to delete.

Returns

KeepService object.

Method keep_services_accessible()

List Keep services that the current client can access.

Usage
Arvados$keep_services_accessible()
Returns

KeepService object.

Method links_get()

Get a Link record by UUID.

Usage
Arvados$links_get(uuid, select = NULL)
Arguments
uuid

The UUID of the Link to return.

select

An array of names of attributes to return in the response.

Returns

Link object.

Method links_list()

Retrieve a LinkList.

Usage
Arvados$links_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

Returns

LinkList object.

Method links_create()

Create a new Link.

Usage
Arvados$links_create(
  link,
  select = NULL,
  ensureUniqueName = NULL,
  clusterID = NULL
)
Arguments
link

Link object.

select

An array of names of attributes to return in the response.

ensureUniqueName

If the given name is already used by this owner, adjust the name to ensure uniqueness instead of returning an error.

clusterID

Cluster ID of a federated cluster where this object should be created.

Returns

Link object.

Method links_update()

Update attributes of an existing Link.

Usage
Arvados$links_update(link, uuid, select = NULL)
Arguments
link

Link object.

uuid

The UUID of the Link to update.

select

An array of names of attributes to return in the response.

Returns

Link object.

Method links_delete()

Delete an existing Link.

Usage
Arvados$links_delete(uuid)
Arguments
uuid

The UUID of the Link to delete.

Returns

Link object.

Method links_get_permissions()

List permissions granted on an Arvados object.

Usage
Arvados$links_get_permissions(uuid)
Arguments
uuid

The UUID of the Link to query.

Returns

Link object.

Method logs_get()

Get a Log record by UUID.

Usage
Arvados$logs_get(uuid, select = NULL)
Arguments
uuid

The UUID of the Log to return.

select

An array of names of attributes to return in the response.

Returns

Log object.

Method logs_list()

Retrieve a LogList.

Usage
Arvados$logs_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

Returns

LogList object.

Method logs_create()

Create a new Log.

Usage
Arvados$logs_create(
  log,
  select = NULL,
  ensureUniqueName = NULL,
  clusterID = NULL
)
Arguments
log

Log object.

select

An array of names of attributes to return in the response.

ensureUniqueName

If the given name is already used by this owner, adjust the name to ensure uniqueness instead of returning an error.

clusterID

Cluster ID of a federated cluster where this object should be created.

Returns

Log object.

Method logs_update()

Update attributes of an existing Log.

Usage
Arvados$logs_update(log, uuid, select = NULL)
Arguments
log

Log object.

uuid

The UUID of the Log to update.

select

An array of names of attributes to return in the response.

Returns

Log object.

Method logs_delete()

Delete an existing Log.

Usage
Arvados$logs_delete(uuid)
Arguments
uuid

The UUID of the Log to delete.

Returns

Log object.

Method users_get()

Get a User record by UUID.

Usage
Arvados$users_get(uuid, select = NULL)
Arguments
uuid

The UUID of the User to return.

select

An array of names of attributes to return in the response.

Returns

User object.

Method users_list()

Retrieve a UserList.

Usage
Arvados$users_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

Returns

UserList object.

Method users_create()

Create a new User.

Usage
Arvados$users_create(
  user,
  select = NULL,
  ensureUniqueName = NULL,
  clusterID = NULL
)
Arguments
user

User object.

select

An array of names of attributes to return in the response.

ensureUniqueName

If the given name is already used by this owner, adjust the name to ensure uniqueness instead of returning an error.

clusterID

Cluster ID of a federated cluster where this object should be created.

Returns

User object.

Method users_update()

Update attributes of an existing User.

Usage
Arvados$users_update(user, uuid, select = NULL, bypassFederation = NULL)
Arguments
user

User object.

uuid

The UUID of the User to update.

select

An array of names of attributes to return in the response.

bypassFederation

If true, do not try to update the user on any other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

Returns

User object.

Method users_delete()

Delete an existing User.

Usage
Arvados$users_delete(uuid)
Arguments
uuid

The UUID of the User to delete.

Returns

User object.

Method users_current()

Return the user record associated with the API token authorizing this request.

Usage
Arvados$users_current()
Returns

User object.

Method users_system()

Return this cluster's system ("root") user record.

Usage
Arvados$users_system()
Returns

User object.

Method users_activate()

Set the is_active flag on a user record.

Usage
Arvados$users_activate(uuid)
Arguments
uuid

The UUID of the User to update.

Returns

User object.

Method users_setup()

Convenience method to "fully" set up a user record with a virtual machine login and notification email.

Usage
Arvados$users_setup(
  uuid = NULL,
  user = NULL,
  repoName = NULL,
  vmUUID = NULL,
  sendNotificationEmail = NULL
)
Arguments
uuid

UUID of an existing user record to set up.

user

Attributes of a new user record to set up.

repoName

This parameter is obsolete and ignored.

vmUUID

If given, setup creates a login link to allow this user to access the Arvados virtual machine with this UUID.

sendNotificationEmail

If true, send an email to the user notifying them they can now access this Arvados cluster.

Returns

User object.

Method users_unsetup()

Unset a user's active flag and delete associated records.

Usage
Arvados$users_unsetup(uuid)
Arguments
uuid

The UUID of the User to update.

Returns

User object.

Method users_merge()

Transfer ownership of one user's data to another.

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

UUID of the user or group that will take ownership of data owned by the old user.

newUserToken

Valid API token for the user receiving ownership. If you use this option, it takes ownership of data owned by the user making the request.

redirectToNewUser

If true, authorization attempts for the old user will be redirected to the new user.

oldUserUUID

UUID of the user whose ownership is being transferred to new_owner_uuid. You must be an admin to use this option.

newUserUUID

UUID of the user receiving ownership. You must be an admin to use this option.

Returns

User object.

Method user_agreements_get()

Get a UserAgreement record by UUID.

Usage
Arvados$user_agreements_get(uuid, select = NULL)
Arguments
uuid

The UUID of the UserAgreement to return.

select

An array of names of attributes to return in the response.

Returns

UserAgreement object.

Method user_agreements_list()

Retrieve a UserAgreementList.

Usage
Arvados$user_agreements_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

Returns

UserAgreementList object.

Method user_agreements_create()

Create a new UserAgreement.

Usage
Arvados$user_agreements_create(
  userAgreement,
  select = NULL,
  ensureUniqueName = NULL,
  clusterID = NULL
)
Arguments
userAgreement

UserAgreement object.

select

An array of names of attributes to return in the response.

ensureUniqueName

If the given name is already used by this owner, adjust the name to ensure uniqueness instead of returning an error.

clusterID

Cluster ID of a federated cluster where this object should be created.

Returns

UserAgreement object.

Method user_agreements_update()

Update attributes of an existing UserAgreement.

Usage
Arvados$user_agreements_update(userAgreement, uuid, select = NULL)
Arguments
userAgreement

UserAgreement object.

uuid

The UUID of the UserAgreement to update.

select

An array of names of attributes to return in the response.

Returns

UserAgreement object.

Method user_agreements_delete()

Delete an existing UserAgreement.

Usage
Arvados$user_agreements_delete(uuid)
Arguments
uuid

The UUID of the UserAgreement to delete.

Returns

UserAgreement object.

Method user_agreements_signatures()

List all user agreement signature links from a user.

Usage
Arvados$user_agreements_signatures()
Returns

UserAgreement object.

Method user_agreements_sign()

Create a signature link from the current user for a given user agreement.

Usage
Arvados$user_agreements_sign()
Returns

UserAgreement object.

Method virtual_machines_get()

Get a VirtualMachine record by UUID.

Usage
Arvados$virtual_machines_get(uuid, select = NULL)
Arguments
uuid

The UUID of the VirtualMachine to return.

select

An array of names of attributes to return in the response.

Returns

VirtualMachine object.

Method virtual_machines_list()

Retrieve a VirtualMachineList.

Usage
Arvados$virtual_machines_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

Returns

VirtualMachineList object.

Method virtual_machines_create()

Create a new VirtualMachine.

Usage
Arvados$virtual_machines_create(
  virtualMachine,
  select = NULL,
  ensureUniqueName = NULL,
  clusterID = NULL
)
Arguments
virtualMachine

VirtualMachine object.

select

An array of names of attributes to return in the response.

ensureUniqueName

If the given name is already used by this owner, adjust the name to ensure uniqueness instead of returning an error.

clusterID

Cluster ID of a federated cluster where this object should be created.

Returns

VirtualMachine object.

Method virtual_machines_update()

Update attributes of an existing VirtualMachine.

Usage
Arvados$virtual_machines_update(virtualMachine, uuid, select = NULL)
Arguments
virtualMachine

VirtualMachine object.

uuid

The UUID of the VirtualMachine to update.

select

An array of names of attributes to return in the response.

Returns

VirtualMachine object.

Method virtual_machines_delete()

Delete an existing VirtualMachine.

Usage
Arvados$virtual_machines_delete(uuid)
Arguments
uuid

The UUID of the VirtualMachine to delete.

Returns

VirtualMachine object.

Method virtual_machines_logins()

List login permission links for a given virtual machine.

Usage
Arvados$virtual_machines_logins(uuid)
Arguments
uuid

The UUID of the VirtualMachine to query.

Returns

VirtualMachine object.

Method virtual_machines_get_all_logins()

List login permission links for all virtual machines.

Usage
Arvados$virtual_machines_get_all_logins()
Returns

VirtualMachine object.

Method workflows_get()

Get a Workflow record by UUID.

Usage
Arvados$workflows_get(uuid, select = NULL)
Arguments
uuid

The UUID of the Workflow to return.

select

An array of names of attributes to return in the response.

Returns

Workflow object.

Method workflows_list()

Retrieve a WorkflowList.

Usage
Arvados$workflows_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

Returns

WorkflowList object.

Method workflows_create()

Create a new Workflow.

Usage
Arvados$workflows_create(
  workflow,
  select = NULL,
  ensureUniqueName = NULL,
  clusterID = NULL
)
Arguments
workflow

Workflow object.

select

An array of names of attributes to return in the response.

ensureUniqueName

If the given name is already used by this owner, adjust the name to ensure uniqueness instead of returning an error.

clusterID

Cluster ID of a federated cluster where this object should be created.

Returns

Workflow object.

Method workflows_update()

Update attributes of an existing Workflow.

Usage
Arvados$workflows_update(workflow, uuid, select = NULL)
Arguments
workflow

Workflow object.

uuid

The UUID of the Workflow to update.

select

An array of names of attributes to return in the response.

Returns

Workflow object.

Method workflows_delete()

Delete an existing Workflow.

Usage
Arvados$workflows_delete(uuid)
Arguments
uuid

The UUID of the Workflow to delete.

Returns

Workflow object.

Method configs_get()

Get this cluster's public configuration settings.

Usage
Arvados$configs_get()
Returns

object.

Method vocabularies_get()

Get this cluster's configured vocabulary definition.

Refer to metadata vocabulary documentation for details.

Usage
Arvados$vocabularies_get()
Returns

object.

Method sys_get()

Run scheduled data trash and sweep operations across this cluster's Keep services.

Usage
Arvados$sys_get()
Returns

object.

Method project_get()

An alias for groups_get.

Usage
Arvados$project_get(uuid, select = NULL, includeTrash = NULL)
Arguments
uuid

The UUID of the Group to return.

select

An array of names of attributes to return in the response.

includeTrash

Return group/project even if its is_trashed attribute is true.

Returns

A Group object.

Method project_create()

A wrapper for groups_create that sets group_class="project".

Usage
Arvados$project_create(
  group,
  select = NULL,
  ensureUniqueName = NULL,
  clusterID = NULL,
  async = NULL
)
Arguments
group

Group object.

select

An array of names of attributes to return in the response.

ensureUniqueName

If the given name is already used by this owner, adjust the name to ensure uniqueness instead of returning an error.

clusterID

Cluster ID of a federated cluster where this object should be created.

async

If true, cluster permission will not be updated immediately, but instead at the next configured update interval.

Returns

A Group object.

Method project_update()

A wrapper for groups_update that sets group_class="project".

Usage
Arvados$project_update(group, uuid, select = NULL, async = NULL)
Arguments
group

Group object.

uuid

The UUID of the Group to update.

select

An array of names of attributes to return in the response.

async

If true, cluster permission will not be updated immediately, but instead at the next configured update interval.

Returns

A Group object.

Method project_list()

A wrapper for groups_list that adds a filter for group_class="project".

Usage
Arvados$project_list(
  filters = NULL,
  where = NULL,
  order = NULL,
  select = NULL,
  distinct = NULL,
  limit = NULL,
  offset = NULL,
  count = NULL,
  clusterID = NULL,
  bypassFederation = NULL,
  includeTrash = NULL
)
Arguments
filters

Filters to limit which objects are returned by their attributes. Refer to the filters reference for more information about how to write filters.

where

An object to limit which objects are returned by their attributes. The keys of this object are attribute names. Each value is either a single matching value or an array of matching values for that attribute. The filters parameter is more flexible and preferred.

order

An array of strings to set the order in which matching objects are returned. Each string has the format <ATTRIBUTE> <DIRECTION>. DIRECTION can be asc or omitted for ascending, or desc for descending.

select

An array of names of attributes to return from each matching object.

distinct

If this is true, and multiple objects have the same values for the attributes that you specify in the select parameter, then each unique set of values will only be returned once in the result set.

limit

The maximum number of objects to return in the result. Note that the API may return fewer results than this if your request hits other limits set by the administrator.

offset

Return matching objects starting from this index. Note that result indexes may change if objects are modified in between a series of list calls.

count

A string to determine result counting behavior. Supported values are:

  • "exact": The response will include an items_available field that counts the number of objects that matched this search criteria, including ones not included in items.

  • "none": The response will not include an items_avaliable field. This improves performance by returning a result as soon as enough items have been loaded for this result.

clusterID

Cluster ID of a federated cluster to return objects from

bypassFederation

If true, do not return results from other clusters in the federation, only the cluster that received the request. You must be an administrator to use this flag.

includeTrash

Include items whose is_trashed attribute is true.

Returns

A GroupList object.

Method project_delete()

An alias for groups_delete.

Usage
Arvados$project_delete(uuid)
Arguments
uuid

The UUID of the Group to delete.

Returns

A Group object.

Method project_exist()

Test whether or not a project exists.

Usage
Arvados$project_exist(uuid, select = NULL, includeTrash = NULL)
Arguments
uuid

The UUID of the Group to return.

select

An array of names of attributes to return in the response.

includeTrash

Return group/project even if its is_trashed attribute is true.

Method project_properties_set()

A convenience wrapper for project_update to set project metadata properties.

Usage
Arvados$project_properties_set(listProperties, uuid)
Arguments
listProperties

List of new properties.

uuid

UUID of the project to update.

Returns

A Group object.

Method project_properties_append()

Get a project and update it with additional properties.

Usage
Arvados$project_properties_append(properties, uuid)
Arguments
properties

List of new properties.

uuid

UUID of the project to update.

Returns

A Group object.

Method project_properties_get()

Get properties of a project.

Usage
Arvados$project_properties_get(uuid)
Arguments
uuid

The UUID of the project to query.

Method project_properties_delete()

Delete one property from a project by name.

Usage
Arvados$project_properties_delete(oneProp, uuid)
Arguments
oneProp

Name of the property to delete.

uuid

The UUID of the project to update.

Returns

A Group object.

Method project_permission_give()

Convenience wrapper of links_list to create a permission link.

Usage
Arvados$project_permission_give(type, uuid, user)
Arguments
type

The type of permission: one of 'can_read', 'can_write', or 'can_manage'.

uuid

The UUID of the object to grant permission to.

user

The UUID of the user or group who receives this permission.

Returns

A Link object if one was updated, else NULL.

Method project_permission_update()

Find an existing permission link and update its level.

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

The type of permission to find: one of 'can_read', 'can_write', or 'can_manage'.

typeNew

The type of permission to set: one of 'can_read', 'can_write', or 'can_manage'.

uuid

The UUID of the object to grant permission to.

user

The UUID of the user or group who receives this permission.

Returns

A Link object if one was updated, else NULL.

Method project_permission_delete()

Delete an existing permission link.

Usage
Arvados$project_permission_delete(type, uuid, user)
Arguments
type

The type of permission to delete: one of 'can_read', 'can_write', or 'can_manage'.

uuid

The UUID of the object to grant permission to.

user

The UUID of the user or group who receives this permission.

Returns

A Link object if one was deleted, else NULL.

Method project_permission_check()

Check for an existing permission link.

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

The UUID of the object to check permission on.

user

The UUID of the user or group to check permission for.

type

The type of permission to check: one of 'can_read', 'can_write', 'can_manage', or NULL (the default).

Returns

If type is NULL, the list of matching permission links. Otherwise, prints and invisibly returns the level of the found permission link.

Method getHostName()

Return the host name of this client's Arvados API server.

Usage
Arvados$getHostName()
Returns

Hostname string.

Method getToken()

Return the Arvados API token used by this client.

Usage
Arvados$getToken()
Returns

API token string.

Method setRESTService()

Set the RESTService object used by this client.

Usage
Arvados$setRESTService(newREST)

Method getRESTService()

Return the RESTService object used by this client.

Usage
Arvados$getRESTService()
Returns

RESTService object.

Examples

## Not run: 
arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")

collection <- arv$collections.get("uuid")

collectionList <- arv$collections.list(list(list("name", "like", "Test%")))
collectionList <- listAll(arv$collections.list, list(list("name", "like", "Test%")))

deletedCollection <- arv$collections.delete("uuid")

updatedCollection <- arv$collections.update(list(name = "New name", description = "New description"),
                                            "uuid")

createdCollection <- arv$collections.create(list(name = "Example",
                                                 description = "This is a test collection"))

## End(Not run)