[arvados] created: 2.1.0-3085-gde8cd4c6a
git repository hosting
git at public.arvados.org
Thu Dec 1 18:29:46 UTC 2022
at de8cd4c6a56cac85dbcf7fe1fcb29abe98fe9f18 (commit)
commit de8cd4c6a56cac85dbcf7fe1fcb29abe98fe9f18
Author: AnetaSta22 <107112384+AnetaSta22 at users.noreply.github.com>
Date: Tue Aug 16 12:34:07 2022 +0200
19704: Merge contributed updates to R SDK
* Add roxygen documentation
* Add readArvFile() function
* Add files via upload
* New README
* Add parameter relativePath in getCollectionContent()
Contributed by Aneta Stanczyk <aneta.stanczyk at contractors.roche.com>
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/R/DESCRIPTION b/sdk/R/DESCRIPTION
index 9c682412a..6ea78ceec 100644
--- a/sdk/R/DESCRIPTION
+++ b/sdk/R/DESCRIPTION
@@ -3,13 +3,15 @@ Type: Package
Title: Arvados R SDK
Version: 2.4.0
Authors at R: c(person("Fuad", "Muhic", role = c("aut", "ctr"), email = "fmuhic at capeannenterprises.com"),
- person("Peter", "Amstutz", role = c("cre"), email = "peter.amstutz at curii.com"))
+ person("Peter", "Amstutz", role = c("cre"), email = "peter.amstutz at curii.com"),
+ person("Piotr", "Nowosielski", role = c("aut"), email = "piotr.nowosielski at contractors.roche.com"),
+ person("Aneta", "Stanczyk", role = c("aut"), email = "aneta.stanczyk at contractors.roche.com"))
Description: This is the Arvados R SDK
URL: http://doc.arvados.org
License: Apache-2.0
Encoding: UTF-8
LazyData: true
-RoxygenNote: 6.0.1.9000
+RoxygenNote: 7.1.1
Imports:
R6,
httr,
diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R
index 52d6c95f5..882e272c3 100644
--- a/sdk/R/R/Arvados.R
+++ b/sdk/R/R/Arvados.R
@@ -2,4012 +2,3274 @@
#
# SPDX-License-Identifier: Apache-2.0
-#' api_clients.get
+#' R6 Class Representing a Arvados
#'
-#' api_clients.get is a method defined in Arvados class.
-#'
-#' @usage arv$api_clients.get(uuid)
-#' @param uuid The UUID of the ApiClient in question.
-#' @return ApiClient object.
-#' @name api_clients.get
-NULL
-
-#' api_clients.create
-#'
-#' api_clients.create is a method defined in Arvados class.
-#'
-#' @usage arv$api_clients.create(apiclient,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param apiClient ApiClient object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return ApiClient object.
-#' @name api_clients.create
-NULL
-
-#' api_clients.update
-#'
-#' api_clients.update is a method defined in Arvados class.
-#'
-#' @usage arv$api_clients.update(apiclient,
-#' uuid)
-#' @param apiClient ApiClient object.
-#' @param uuid The UUID of the ApiClient in question.
-#' @return ApiClient object.
-#' @name api_clients.update
-NULL
-
-#' api_clients.delete
-#'
-#' api_clients.delete is a method defined in Arvados class.
-#'
-#' @usage arv$api_clients.delete(uuid)
-#' @param uuid The UUID of the ApiClient in question.
-#' @return ApiClient object.
-#' @name api_clients.delete
-NULL
-
-#' api_clients.list
-#'
-#' api_clients.list is a method defined in Arvados class.
-#'
-#' @usage arv$api_clients.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return ApiClientList object.
-#' @name api_clients.list
-NULL
-
-#' api_client_authorizations.get
-#'
-#' api_client_authorizations.get is a method defined in Arvados class.
-#'
-#' @usage arv$api_client_authorizations.get(uuid)
-#' @param uuid The UUID of the ApiClientAuthorization in question.
-#' @return ApiClientAuthorization object.
-#' @name api_client_authorizations.get
-NULL
-
-#' api_client_authorizations.create
-#'
-#' api_client_authorizations.create is a method defined in Arvados class.
-#'
-#' @usage arv$api_client_authorizations.create(apiclientauthorization,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param apiClientAuthorization ApiClientAuthorization object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return ApiClientAuthorization object.
-#' @name api_client_authorizations.create
-NULL
-
-#' api_client_authorizations.update
-#'
-#' api_client_authorizations.update is a method defined in Arvados class.
-#'
-#' @usage arv$api_client_authorizations.update(apiclientauthorization,
-#' uuid)
-#' @param apiClientAuthorization ApiClientAuthorization object.
-#' @param uuid The UUID of the ApiClientAuthorization in question.
-#' @return ApiClientAuthorization object.
-#' @name api_client_authorizations.update
-NULL
-
-#' api_client_authorizations.delete
-#'
-#' api_client_authorizations.delete is a method defined in Arvados class.
-#'
-#' @usage arv$api_client_authorizations.delete(uuid)
-#' @param uuid The UUID of the ApiClientAuthorization in question.
-#' @return ApiClientAuthorization object.
-#' @name api_client_authorizations.delete
-NULL
-
-#' api_client_authorizations.create_system_auth
-#'
-#' api_client_authorizations.create_system_auth is a method defined in Arvados class.
-#'
-#' @usage arv$api_client_authorizations.create_system_auth(api_client_id = NULL,
-#' scopes = NULL)
-#' @param api_client_id
-#' @param scopes
-#' @return ApiClientAuthorization object.
-#' @name api_client_authorizations.create_system_auth
-NULL
-
-#' api_client_authorizations.current
-#'
-#' api_client_authorizations.current is a method defined in Arvados class.
-#'
-#' @usage arv$api_client_authorizations.current(NULL)
-#' @return ApiClientAuthorization object.
-#' @name api_client_authorizations.current
-NULL
-
-#' api_client_authorizations.list
-#'
-#' api_client_authorizations.list is a method defined in Arvados class.
-#'
-#' @usage arv$api_client_authorizations.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return ApiClientAuthorizationList object.
-#' @name api_client_authorizations.list
-NULL
-
-#' authorized_keys.get
-#'
-#' authorized_keys.get is a method defined in Arvados class.
-#'
-#' @usage arv$authorized_keys.get(uuid)
-#' @param uuid The UUID of the AuthorizedKey in question.
-#' @return AuthorizedKey object.
-#' @name authorized_keys.get
-NULL
-
-#' authorized_keys.create
-#'
-#' authorized_keys.create is a method defined in Arvados class.
-#'
-#' @usage arv$authorized_keys.create(authorizedkey,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param authorizedKey AuthorizedKey object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return AuthorizedKey object.
-#' @name authorized_keys.create
-NULL
-
-#' authorized_keys.update
-#'
-#' authorized_keys.update is a method defined in Arvados class.
-#'
-#' @usage arv$authorized_keys.update(authorizedkey,
-#' uuid)
-#' @param authorizedKey AuthorizedKey object.
-#' @param uuid The UUID of the AuthorizedKey in question.
-#' @return AuthorizedKey object.
-#' @name authorized_keys.update
-NULL
-
-#' authorized_keys.delete
-#'
-#' authorized_keys.delete is a method defined in Arvados class.
-#'
-#' @usage arv$authorized_keys.delete(uuid)
-#' @param uuid The UUID of the AuthorizedKey in question.
-#' @return AuthorizedKey object.
-#' @name authorized_keys.delete
-NULL
-
-#' authorized_keys.list
-#'
-#' authorized_keys.list is a method defined in Arvados class.
-#'
-#' @usage arv$authorized_keys.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return AuthorizedKeyList object.
-#' @name authorized_keys.list
-NULL
-
-#' collections.get
-#'
-#' collections.get is a method defined in Arvados class.
-#'
-#' @usage arv$collections.get(uuid)
-#' @param uuid The UUID of the Collection in question.
-#' @return Collection object.
-#' @name collections.get
-NULL
-
-#' collections.create
-#'
-#' collections.create is a method defined in Arvados class.
-#'
-#' @usage arv$collections.create(collection,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param collection Collection object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return Collection object.
-#' @name collections.create
-NULL
-
-#' collections.update
-#'
-#' collections.update is a method defined in Arvados class.
-#'
-#' @usage arv$collections.update(collection,
-#' uuid)
-#' @param collection Collection object.
-#' @param uuid The UUID of the Collection in question.
-#' @return Collection object.
-#' @name collections.update
-NULL
-
-#' collections.delete
-#'
-#' collections.delete is a method defined in Arvados class.
-#'
-#' @usage arv$collections.delete(uuid)
-#' @param uuid The UUID of the Collection in question.
-#' @return Collection object.
-#' @name collections.delete
-NULL
-
-#' collections.provenance
-#'
-#' collections.provenance is a method defined in Arvados class.
-#'
-#' @usage arv$collections.provenance(uuid)
-#' @param uuid
-#' @return Collection object.
-#' @name collections.provenance
-NULL
-
-#' collections.used_by
-#'
-#' collections.used_by is a method defined in Arvados class.
-#'
-#' @usage arv$collections.used_by(uuid)
-#' @param uuid
-#' @return Collection object.
-#' @name collections.used_by
-NULL
-
-#' collections.trash
-#'
-#' collections.trash is a method defined in Arvados class.
-#'
-#' @usage arv$collections.trash(uuid)
-#' @param uuid
-#' @return Collection object.
-#' @name collections.trash
-NULL
-
-#' collections.untrash
-#'
-#' collections.untrash is a method defined in Arvados class.
-#'
-#' @usage arv$collections.untrash(uuid)
-#' @param uuid
-#' @return Collection object.
-#' @name collections.untrash
-NULL
-
-#' collections.list
-#'
-#' collections.list is a method defined in Arvados class.
-#'
-#' @usage arv$collections.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL,
-#' include_trash = NULL, include_old_versions = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @param include_trash Include collections whose is_trashed attribute is true.
-#' @param include_old_versions Include past collection versions.
-#' @return CollectionList object.
-#' @name collections.list
-NULL
-
-#' containers.get
-#'
-#' containers.get is a method defined in Arvados class.
-#'
-#' @usage arv$containers.get(uuid)
-#' @param uuid The UUID of the Container in question.
-#' @return Container object.
-#' @name containers.get
-NULL
-
-#' containers.create
-#'
-#' containers.create is a method defined in Arvados class.
-#'
-#' @usage arv$containers.create(container,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param container Container object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return Container object.
-#' @name containers.create
-NULL
-
-#' containers.update
-#'
-#' containers.update is a method defined in Arvados class.
-#'
-#' @usage arv$containers.update(container,
-#' uuid)
-#' @param container Container object.
-#' @param uuid The UUID of the Container in question.
-#' @return Container object.
-#' @name containers.update
-NULL
-
-#' containers.delete
-#'
-#' containers.delete is a method defined in Arvados class.
-#'
-#' @usage arv$containers.delete(uuid)
-#' @param uuid The UUID of the Container in question.
-#' @return Container object.
-#' @name containers.delete
-NULL
-
-#' containers.auth
-#'
-#' containers.auth is a method defined in Arvados class.
-#'
-#' @usage arv$containers.auth(uuid)
-#' @param uuid
-#' @return Container object.
-#' @name containers.auth
-NULL
-
-#' containers.lock
-#'
-#' containers.lock is a method defined in Arvados class.
-#'
-#' @usage arv$containers.lock(uuid)
-#' @param uuid
-#' @return Container object.
-#' @name containers.lock
-NULL
-
-#' containers.unlock
-#'
-#' containers.unlock is a method defined in Arvados class.
-#'
-#' @usage arv$containers.unlock(uuid)
-#' @param uuid
-#' @return Container object.
-#' @name containers.unlock
-NULL
-
-#' containers.secret_mounts
-#'
-#' containers.secret_mounts is a method defined in Arvados class.
-#'
-#' @usage arv$containers.secret_mounts(uuid)
-#' @param uuid
-#' @return Container object.
-#' @name containers.secret_mounts
-NULL
-
-#' containers.current
-#'
-#' containers.current is a method defined in Arvados class.
-#'
-#' @usage arv$containers.current(NULL)
-#' @return Container object.
-#' @name containers.current
-NULL
-
-#' containers.list
-#'
-#' containers.list is a method defined in Arvados class.
-#'
-#' @usage arv$containers.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return ContainerList object.
-#' @name containers.list
-NULL
-
-#' container_requests.get
-#'
-#' container_requests.get is a method defined in Arvados class.
-#'
-#' @usage arv$container_requests.get(uuid)
-#' @param uuid The UUID of the ContainerRequest in question.
-#' @return ContainerRequest object.
-#' @name container_requests.get
-NULL
-
-#' container_requests.create
-#'
-#' container_requests.create is a method defined in Arvados class.
-#'
-#' @usage arv$container_requests.create(containerrequest,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param containerRequest ContainerRequest object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return ContainerRequest object.
-#' @name container_requests.create
-NULL
-
-#' container_requests.update
-#'
-#' container_requests.update is a method defined in Arvados class.
-#'
-#' @usage arv$container_requests.update(containerrequest,
-#' uuid)
-#' @param containerRequest ContainerRequest object.
-#' @param uuid The UUID of the ContainerRequest in question.
-#' @return ContainerRequest object.
-#' @name container_requests.update
-NULL
-
-#' container_requests.delete
-#'
-#' container_requests.delete is a method defined in Arvados class.
-#'
-#' @usage arv$container_requests.delete(uuid)
-#' @param uuid The UUID of the ContainerRequest in question.
-#' @return ContainerRequest object.
-#' @name container_requests.delete
-NULL
-
-#' container_requests.list
-#'
-#' container_requests.list is a method defined in Arvados class.
-#'
-#' @usage arv$container_requests.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL,
-#' include_trash = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @param include_trash Include container requests whose owner project is trashed.
-#' @return ContainerRequestList object.
-#' @name container_requests.list
-NULL
-
-#' groups.get
-#'
-#' groups.get is a method defined in Arvados class.
-#'
-#' @usage arv$groups.get(uuid)
-#' @param uuid The UUID of the Group in question.
-#' @return Group object.
-#' @name groups.get
-NULL
-
-#' groups.create
-#'
-#' groups.create is a method defined in Arvados class.
-#'
-#' @usage arv$groups.create(group, ensure_unique_name = "false",
-#' cluster_id = NULL, async = "false")
-#' @param group Group object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @param async defer permissions update
-#' @return Group object.
-#' @name groups.create
-NULL
-
-#' groups.update
-#'
-#' groups.update is a method defined in Arvados class.
-#'
-#' @usage arv$groups.update(group, uuid,
-#' async = "false")
-#' @param group Group object.
-#' @param uuid The UUID of the Group in question.
-#' @param async defer permissions update
-#' @return Group object.
-#' @name groups.update
-NULL
-
-#' groups.delete
-#'
-#' groups.delete is a method defined in Arvados class.
-#'
-#' @usage arv$groups.delete(uuid)
-#' @param uuid The UUID of the Group in question.
-#' @return Group object.
-#' @name groups.delete
-NULL
-
-#' groups.contents
-#'
-#' groups.contents is a method defined in Arvados class.
-#'
-#' @usage arv$groups.contents(filters = NULL,
-#' where = NULL, order = NULL, distinct = NULL,
-#' limit = "100", offset = "0", count = "exact",
-#' cluster_id = NULL, bypass_federation = NULL,
-#' include_trash = NULL, uuid = NULL, recursive = NULL,
-#' include = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @param include_trash Include items whose is_trashed attribute is true.
-#' @param uuid
-#' @param recursive Include contents from child groups recursively.
-#' @param include Include objects referred to by listed field in "included" (only owner_uuid)
-#' @return Group object.
-#' @name groups.contents
-NULL
-
-#' groups.shared
-#'
-#' groups.shared is a method defined in Arvados class.
-#'
-#' @usage arv$groups.shared(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL,
-#' include_trash = NULL, include = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @param include_trash Include items whose is_trashed attribute is true.
-#' @param include
-#' @return Group object.
-#' @name groups.shared
-NULL
-
-#' groups.trash
-#'
-#' groups.trash is a method defined in Arvados class.
-#'
-#' @usage arv$groups.trash(uuid)
-#' @param uuid
-#' @return Group object.
-#' @name groups.trash
-NULL
-
-#' groups.untrash
-#'
-#' groups.untrash is a method defined in Arvados class.
-#'
-#' @usage arv$groups.untrash(uuid)
-#' @param uuid
-#' @return Group object.
-#' @name groups.untrash
-NULL
-
-#' groups.list
-#'
-#' groups.list is a method defined in Arvados class.
-#'
-#' @usage arv$groups.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL,
-#' include_trash = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @param include_trash Include items whose is_trashed attribute is true.
-#' @return GroupList object.
-#' @name groups.list
-NULL
-
-#' keep_services.get
-#'
-#' keep_services.get is a method defined in Arvados class.
-#'
-#' @usage arv$keep_services.get(uuid)
-#' @param uuid The UUID of the KeepService in question.
-#' @return KeepService object.
-#' @name keep_services.get
-NULL
-
-#' keep_services.create
-#'
-#' keep_services.create is a method defined in Arvados class.
-#'
-#' @usage arv$keep_services.create(keepservice,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param keepService KeepService object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return KeepService object.
-#' @name keep_services.create
-NULL
-
-#' keep_services.update
-#'
-#' keep_services.update is a method defined in Arvados class.
-#'
-#' @usage arv$keep_services.update(keepservice,
-#' uuid)
-#' @param keepService KeepService object.
-#' @param uuid The UUID of the KeepService in question.
-#' @return KeepService object.
-#' @name keep_services.update
-NULL
-
-#' keep_services.delete
-#'
-#' keep_services.delete is a method defined in Arvados class.
-#'
-#' @usage arv$keep_services.delete(uuid)
-#' @param uuid The UUID of the KeepService in question.
-#' @return KeepService object.
-#' @name keep_services.delete
-NULL
-
-#' keep_services.accessible
-#'
-#' keep_services.accessible is a method defined in Arvados class.
-#'
-#' @usage arv$keep_services.accessible(NULL)
-#' @return KeepService object.
-#' @name keep_services.accessible
-NULL
-
-#' keep_services.list
-#'
-#' keep_services.list is a method defined in Arvados class.
-#'
-#' @usage arv$keep_services.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return KeepServiceList object.
-#' @name keep_services.list
-NULL
-
-#' links.get
-#'
-#' links.get is a method defined in Arvados class.
-#'
-#' @usage arv$links.get(uuid)
-#' @param uuid The UUID of the Link in question.
-#' @return Link object.
-#' @name links.get
-NULL
-
-#' links.create
-#'
-#' links.create is a method defined in Arvados class.
-#'
-#' @usage arv$links.create(link, ensure_unique_name = "false",
-#' cluster_id = NULL)
-#' @param link Link object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return Link object.
-#' @name links.create
-NULL
-
-#' links.update
-#'
-#' links.update is a method defined in Arvados class.
-#'
-#' @usage arv$links.update(link, uuid)
-#' @param link Link object.
-#' @param uuid The UUID of the Link in question.
-#' @return Link object.
-#' @name links.update
-NULL
-
-#' links.delete
-#'
-#' links.delete is a method defined in Arvados class.
-#'
-#' @usage arv$links.delete(uuid)
-#' @param uuid The UUID of the Link in question.
-#' @return Link object.
-#' @name links.delete
-NULL
-
-#' links.list
-#'
-#' links.list is a method defined in Arvados class.
-#'
-#' @usage arv$links.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return LinkList object.
-#' @name links.list
-NULL
-
-#' links.get_permissions
-#'
-#' links.get_permissions is a method defined in Arvados class.
-#'
-#' @usage arv$links.get_permissions(uuid)
-#' @param uuid
-#' @return Link object.
-#' @name links.get_permissions
-NULL
-
-#' logs.get
-#'
-#' logs.get is a method defined in Arvados class.
-#'
-#' @usage arv$logs.get(uuid)
-#' @param uuid The UUID of the Log in question.
-#' @return Log object.
-#' @name logs.get
-NULL
-
-#' logs.create
-#'
-#' logs.create is a method defined in Arvados class.
-#'
-#' @usage arv$logs.create(log, ensure_unique_name = "false",
-#' cluster_id = NULL)
-#' @param log Log object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return Log object.
-#' @name logs.create
-NULL
-
-#' logs.update
-#'
-#' logs.update is a method defined in Arvados class.
-#'
-#' @usage arv$logs.update(log, uuid)
-#' @param log Log object.
-#' @param uuid The UUID of the Log in question.
-#' @return Log object.
-#' @name logs.update
-NULL
-
-#' logs.delete
-#'
-#' logs.delete is a method defined in Arvados class.
-#'
-#' @usage arv$logs.delete(uuid)
-#' @param uuid The UUID of the Log in question.
-#' @return Log object.
-#' @name logs.delete
-NULL
-
-#' logs.list
-#'
-#' logs.list is a method defined in Arvados class.
-#'
-#' @usage arv$logs.list(filters = NULL, where = NULL,
-#' order = NULL, select = NULL, distinct = NULL,
-#' limit = "100", offset = "0", count = "exact",
-#' cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return LogList object.
-#' @name logs.list
-NULL
-
-#' users.get
-#'
-#' users.get is a method defined in Arvados class.
-#'
-#' @usage arv$users.get(uuid)
-#' @param uuid The UUID of the User in question.
-#' @return User object.
-#' @name users.get
-NULL
-
-#' users.create
-#'
-#' users.create is a method defined in Arvados class.
-#'
-#' @usage arv$users.create(user, ensure_unique_name = "false",
-#' cluster_id = NULL)
-#' @param user User object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return User object.
-#' @name users.create
-NULL
-
-#' users.update
-#'
-#' users.update is a method defined in Arvados class.
-#'
-#' @usage arv$users.update(user, uuid, bypass_federation = NULL)
-#' @param user User object.
-#' @param uuid The UUID of the User in question.
-#' @param bypass_federation
-#' @return User object.
-#' @name users.update
-NULL
-
-#' users.delete
-#'
-#' users.delete is a method defined in Arvados class.
-#'
-#' @usage arv$users.delete(uuid)
-#' @param uuid The UUID of the User in question.
-#' @return User object.
-#' @name users.delete
-NULL
-
-#' users.current
-#'
-#' users.current is a method defined in Arvados class.
-#'
-#' @usage arv$users.current(NULL)
-#' @return User object.
-#' @name users.current
-NULL
-
-#' users.system
-#'
-#' users.system is a method defined in Arvados class.
-#'
-#' @usage arv$users.system(NULL)
-#' @return User object.
-#' @name users.system
-NULL
-
-#' users.activate
-#'
-#' users.activate is a method defined in Arvados class.
-#'
-#' @usage arv$users.activate(uuid)
-#' @param uuid
-#' @return User object.
-#' @name users.activate
-NULL
-
-#' users.setup
-#'
-#' users.setup is a method defined in Arvados class.
-#'
-#' @usage arv$users.setup(uuid = NULL, user = NULL,
-#' repo_name = NULL, vm_uuid = NULL, send_notification_email = "false")
-#' @param uuid
-#' @param user
-#' @param repo_name
-#' @param vm_uuid
-#' @param send_notification_email
-#' @return User object.
-#' @name users.setup
-NULL
-
-#' users.unsetup
-#'
-#' users.unsetup is a method defined in Arvados class.
-#'
-#' @usage arv$users.unsetup(uuid)
-#' @param uuid
-#' @return User object.
-#' @name users.unsetup
-NULL
-
-#' users.merge
-#'
-#' users.merge is a method defined in Arvados class.
-#'
-#' @usage arv$users.merge(new_owner_uuid,
-#' new_user_token = NULL, redirect_to_new_user = NULL,
-#' old_user_uuid = NULL, new_user_uuid = NULL)
-#' @param new_owner_uuid
-#' @param new_user_token
-#' @param redirect_to_new_user
-#' @param old_user_uuid
-#' @param new_user_uuid
-#' @return User object.
-#' @name users.merge
-NULL
-
-#' users.list
-#'
-#' users.list is a method defined in Arvados class.
-#'
-#' @usage arv$users.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return UserList object.
-#' @name users.list
-NULL
-
-#' repositories.get
-#'
-#' repositories.get is a method defined in Arvados class.
-#'
-#' @usage arv$repositories.get(uuid)
-#' @param uuid The UUID of the Repository in question.
-#' @return Repository object.
-#' @name repositories.get
-NULL
-
-#' repositories.create
-#'
-#' repositories.create is a method defined in Arvados class.
-#'
-#' @usage arv$repositories.create(repository,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param repository Repository object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return Repository object.
-#' @name repositories.create
-NULL
-
-#' repositories.update
-#'
-#' repositories.update is a method defined in Arvados class.
-#'
-#' @usage arv$repositories.update(repository,
-#' uuid)
-#' @param repository Repository object.
-#' @param uuid The UUID of the Repository in question.
-#' @return Repository object.
-#' @name repositories.update
-NULL
-
-#' repositories.delete
-#'
-#' repositories.delete is a method defined in Arvados class.
-#'
-#' @usage arv$repositories.delete(uuid)
-#' @param uuid The UUID of the Repository in question.
-#' @return Repository object.
-#' @name repositories.delete
-NULL
-
-#' repositories.get_all_permissions
-#'
-#' repositories.get_all_permissions is a method defined in Arvados class.
-#'
-#' @usage arv$repositories.get_all_permissions(NULL)
-#' @return Repository object.
-#' @name repositories.get_all_permissions
-NULL
-
-#' repositories.list
-#'
-#' repositories.list is a method defined in Arvados class.
-#'
-#' @usage arv$repositories.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return RepositoryList object.
-#' @name repositories.list
-NULL
-
-#' virtual_machines.get
-#'
-#' virtual_machines.get is a method defined in Arvados class.
-#'
-#' @usage arv$virtual_machines.get(uuid)
-#' @param uuid The UUID of the VirtualMachine in question.
-#' @return VirtualMachine object.
-#' @name virtual_machines.get
-NULL
-
-#' virtual_machines.create
-#'
-#' virtual_machines.create is a method defined in Arvados class.
-#'
-#' @usage arv$virtual_machines.create(virtualmachine,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param virtualMachine VirtualMachine object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return VirtualMachine object.
-#' @name virtual_machines.create
-NULL
-
-#' virtual_machines.update
-#'
-#' virtual_machines.update is a method defined in Arvados class.
-#'
-#' @usage arv$virtual_machines.update(virtualmachine,
-#' uuid)
-#' @param virtualMachine VirtualMachine object.
-#' @param uuid The UUID of the VirtualMachine in question.
-#' @return VirtualMachine object.
-#' @name virtual_machines.update
-NULL
-
-#' virtual_machines.delete
-#'
-#' virtual_machines.delete is a method defined in Arvados class.
-#'
-#' @usage arv$virtual_machines.delete(uuid)
-#' @param uuid The UUID of the VirtualMachine in question.
-#' @return VirtualMachine object.
-#' @name virtual_machines.delete
-NULL
-
-#' virtual_machines.logins
-#'
-#' virtual_machines.logins is a method defined in Arvados class.
-#'
-#' @usage arv$virtual_machines.logins(uuid)
-#' @param uuid
-#' @return VirtualMachine object.
-#' @name virtual_machines.logins
-NULL
-
-#' virtual_machines.get_all_logins
-#'
-#' virtual_machines.get_all_logins is a method defined in Arvados class.
-#'
-#' @usage arv$virtual_machines.get_all_logins(NULL)
-#' @return VirtualMachine object.
-#' @name virtual_machines.get_all_logins
-NULL
-
-#' virtual_machines.list
-#'
-#' virtual_machines.list is a method defined in Arvados class.
-#'
-#' @usage arv$virtual_machines.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return VirtualMachineList object.
-#' @name virtual_machines.list
-NULL
-
-#' workflows.get
-#'
-#' workflows.get is a method defined in Arvados class.
-#'
-#' @usage arv$workflows.get(uuid)
-#' @param uuid The UUID of the Workflow in question.
-#' @return Workflow object.
-#' @name workflows.get
-NULL
-
-#' workflows.create
-#'
-#' workflows.create is a method defined in Arvados class.
-#'
-#' @usage arv$workflows.create(workflow,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param workflow Workflow object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return Workflow object.
-#' @name workflows.create
-NULL
-
-#' workflows.update
-#'
-#' workflows.update is a method defined in Arvados class.
-#'
-#' @usage arv$workflows.update(workflow,
-#' uuid)
-#' @param workflow Workflow object.
-#' @param uuid The UUID of the Workflow in question.
-#' @return Workflow object.
-#' @name workflows.update
-NULL
-
-#' workflows.delete
-#'
-#' workflows.delete is a method defined in Arvados class.
-#'
-#' @usage arv$workflows.delete(uuid)
-#' @param uuid The UUID of the Workflow in question.
-#' @return Workflow object.
-#' @name workflows.delete
-NULL
-
-#' workflows.list
-#'
-#' workflows.list is a method defined in Arvados class.
-#'
-#' @usage arv$workflows.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return WorkflowList object.
-#' @name workflows.list
-NULL
-
-#' user_agreements.get
-#'
-#' user_agreements.get is a method defined in Arvados class.
-#'
-#' @usage arv$user_agreements.get(uuid)
-#' @param uuid The UUID of the UserAgreement in question.
-#' @return UserAgreement object.
-#' @name user_agreements.get
-NULL
-
-#' user_agreements.create
-#'
-#' user_agreements.create is a method defined in Arvados class.
-#'
-#' @usage arv$user_agreements.create(useragreement,
-#' ensure_unique_name = "false", cluster_id = NULL)
-#' @param userAgreement UserAgreement object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param cluster_id Create object on a remote federated cluster instead of the current one.
-#' @return UserAgreement object.
-#' @name user_agreements.create
-NULL
-
-#' user_agreements.update
-#'
-#' user_agreements.update is a method defined in Arvados class.
-#'
-#' @usage arv$user_agreements.update(useragreement,
-#' uuid)
-#' @param userAgreement UserAgreement object.
-#' @param uuid The UUID of the UserAgreement in question.
-#' @return UserAgreement object.
-#' @name user_agreements.update
-NULL
-
-#' user_agreements.delete
-#'
-#' user_agreements.delete is a method defined in Arvados class.
-#'
-#' @usage arv$user_agreements.delete(uuid)
-#' @param uuid The UUID of the UserAgreement in question.
-#' @return UserAgreement object.
-#' @name user_agreements.delete
-NULL
-
-#' user_agreements.signatures
-#'
-#' user_agreements.signatures is a method defined in Arvados class.
-#'
-#' @usage arv$user_agreements.signatures(NULL)
-#' @return UserAgreement object.
-#' @name user_agreements.signatures
-NULL
+#' @description
+#' Arvados class gives users ability to access Arvados REST API. It also allowes user to manipulate collections (and projects?)
-#' user_agreements.sign
-#'
-#' user_agreements.sign is a method defined in Arvados class.
-#'
-#' @usage arv$user_agreements.sign(NULL)
-#' @return UserAgreement object.
-#' @name user_agreements.sign
-NULL
-
-#' user_agreements.list
-#'
-#' user_agreements.list is a method defined in Arvados class.
-#'
-#' @usage arv$user_agreements.list(filters = NULL,
-#' where = NULL, order = NULL, select = NULL,
-#' distinct = NULL, limit = "100", offset = "0",
-#' count = "exact", cluster_id = NULL, bypass_federation = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param cluster_id List objects on a remote federated cluster instead of the current one.
-#' @param bypass_federation bypass federation behavior, list items from local instance database only
-#' @return UserAgreementList object.
-#' @name user_agreements.list
-NULL
-
-#' user_agreements.new
-#'
-#' user_agreements.new is a method defined in Arvados class.
-#'
-#' @usage arv$user_agreements.new(NULL)
-#' @return UserAgreement object.
-#' @name user_agreements.new
-NULL
-
-#' configs.get
-#'
-#' configs.get is a method defined in Arvados class.
-#'
-#' @usage arv$configs.get(NULL)
-#' @return object.
-#' @name configs.get
-NULL
-
-#' project.get
-#'
-#' projects.get is equivalent to groups.get method.
-#'
-#' @usage arv$projects.get(uuid)
-#' @param uuid The UUID of the Group in question.
-#' @return Group object.
-#' @name projects.get
-NULL
-
-#' project.create
-#'
-#' projects.create wrapps groups.create method by setting group_class attribute to "project".
-#'
-#' @usage arv$projects.create(group, ensure_unique_name = "false")
-#' @param group Group object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @return Group object.
-#' @name projects.create
-NULL
-
-#' project.update
-#'
-#' projects.update wrapps groups.update method by setting group_class attribute to "project".
-#'
-#' @usage arv$projects.update(group, uuid)
-#' @param group Group object.
-#' @param uuid The UUID of the Group in question.
-#' @return Group object.
-#' @name projects.update
-NULL
-
-#' project.delete
-#'
-#' projects.delete is equivalent to groups.delete method.
-#'
-#' @usage arv$project.delete(uuid)
-#' @param uuid The UUID of the Group in question.
-#' @return Group object.
-#' @name projects.delete
-NULL
-
-#' project.list
-#'
-#' projects.list wrapps groups.list method by setting group_class attribute to "project".
-#'
-#' @usage arv$projects.list(filters = NULL,
-#' where = NULL, order = NULL, distinct = NULL,
-#' limit = "100", offset = "0", count = "exact",
-#' include_trash = NULL, uuid = NULL, recursive = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @param include_trash Include items whose is_trashed attribute is true.
-#' @param uuid
-#' @param recursive Include contents from child groups recursively.
-#' @return Group object.
-#' @name projects.list
-NULL
-
-#' Arvados
-#'
-#' Arvados class gives users ability to access Arvados REST API.
-#'
-#' @section Usage:
-#' \preformatted{arv = Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)}
-#'
-#' @section Arguments:
-#' \describe{
-#' \item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.}
-#' \item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.}
-#' \item{numRetries}{Number which specifies how many times to retry failed service requests.}
-#' }
-#'
-#' @section Methods:
-#' \describe{
-#' \item{}{\code{\link{api_client_authorizations.create}}}
-#' \item{}{\code{\link{api_client_authorizations.create_system_auth}}}
-#' \item{}{\code{\link{api_client_authorizations.current}}}
-#' \item{}{\code{\link{api_client_authorizations.delete}}}
-#' \item{}{\code{\link{api_client_authorizations.get}}}
-#' \item{}{\code{\link{api_client_authorizations.list}}}
-#' \item{}{\code{\link{api_client_authorizations.update}}}
-#' \item{}{\code{\link{api_clients.create}}}
-#' \item{}{\code{\link{api_clients.delete}}}
-#' \item{}{\code{\link{api_clients.get}}}
-#' \item{}{\code{\link{api_clients.list}}}
-#' \item{}{\code{\link{api_clients.update}}}
-#' \item{}{\code{\link{authorized_keys.create}}}
-#' \item{}{\code{\link{authorized_keys.delete}}}
-#' \item{}{\code{\link{authorized_keys.get}}}
-#' \item{}{\code{\link{authorized_keys.list}}}
-#' \item{}{\code{\link{authorized_keys.update}}}
-#' \item{}{\code{\link{collections.create}}}
-#' \item{}{\code{\link{collections.delete}}}
-#' \item{}{\code{\link{collections.get}}}
-#' \item{}{\code{\link{collections.list}}}
-#' \item{}{\code{\link{collections.provenance}}}
-#' \item{}{\code{\link{collections.trash}}}
-#' \item{}{\code{\link{collections.untrash}}}
-#' \item{}{\code{\link{collections.update}}}
-#' \item{}{\code{\link{collections.used_by}}}
-#' \item{}{\code{\link{configs.get}}}
-#' \item{}{\code{\link{container_requests.create}}}
-#' \item{}{\code{\link{container_requests.delete}}}
-#' \item{}{\code{\link{container_requests.get}}}
-#' \item{}{\code{\link{container_requests.list}}}
-#' \item{}{\code{\link{container_requests.update}}}
-#' \item{}{\code{\link{containers.auth}}}
-#' \item{}{\code{\link{containers.create}}}
-#' \item{}{\code{\link{containers.current}}}
-#' \item{}{\code{\link{containers.delete}}}
-#' \item{}{\code{\link{containers.get}}}
-#' \item{}{\code{\link{containers.list}}}
-#' \item{}{\code{\link{containers.lock}}}
-#' \item{}{\code{\link{containers.secret_mounts}}}
-#' \item{}{\code{\link{containers.unlock}}}
-#' \item{}{\code{\link{containers.update}}}
-#' \item{}{\code{\link{groups.contents}}}
-#' \item{}{\code{\link{groups.create}}}
-#' \item{}{\code{\link{groups.delete}}}
-#' \item{}{\code{\link{groups.get}}}
-#' \item{}{\code{\link{groups.list}}}
-#' \item{}{\code{\link{groups.shared}}}
-#' \item{}{\code{\link{groups.trash}}}
-#' \item{}{\code{\link{groups.untrash}}}
-#' \item{}{\code{\link{groups.update}}}
-#' \item{}{\code{\link{keep_services.accessible}}}
-#' \item{}{\code{\link{keep_services.create}}}
-#' \item{}{\code{\link{keep_services.delete}}}
-#' \item{}{\code{\link{keep_services.get}}}
-#' \item{}{\code{\link{keep_services.list}}}
-#' \item{}{\code{\link{keep_services.update}}}
-#' \item{}{\code{\link{links.create}}}
-#' \item{}{\code{\link{links.delete}}}
-#' \item{}{\code{\link{links.get}}}
-#' \item{}{\code{\link{links.get_permissions}}}
-#' \item{}{\code{\link{links.list}}}
-#' \item{}{\code{\link{links.update}}}
-#' \item{}{\code{\link{logs.create}}}
-#' \item{}{\code{\link{logs.delete}}}
-#' \item{}{\code{\link{logs.get}}}
-#' \item{}{\code{\link{logs.list}}}
-#' \item{}{\code{\link{logs.update}}}
-#' \item{}{\code{\link{projects.create}}}
-#' \item{}{\code{\link{projects.delete}}}
-#' \item{}{\code{\link{projects.get}}}
-#' \item{}{\code{\link{projects.list}}}
-#' \item{}{\code{\link{projects.update}}}
-#' \item{}{\code{\link{repositories.create}}}
-#' \item{}{\code{\link{repositories.delete}}}
-#' \item{}{\code{\link{repositories.get}}}
-#' \item{}{\code{\link{repositories.get_all_permissions}}}
-#' \item{}{\code{\link{repositories.list}}}
-#' \item{}{\code{\link{repositories.update}}}
-#' \item{}{\code{\link{user_agreements.create}}}
-#' \item{}{\code{\link{user_agreements.delete}}}
-#' \item{}{\code{\link{user_agreements.get}}}
-#' \item{}{\code{\link{user_agreements.list}}}
-#' \item{}{\code{\link{user_agreements.new}}}
-#' \item{}{\code{\link{user_agreements.sign}}}
-#' \item{}{\code{\link{user_agreements.signatures}}}
-#' \item{}{\code{\link{user_agreements.update}}}
-#' \item{}{\code{\link{users.activate}}}
-#' \item{}{\code{\link{users.create}}}
-#' \item{}{\code{\link{users.current}}}
-#' \item{}{\code{\link{users.delete}}}
-#' \item{}{\code{\link{users.get}}}
-#' \item{}{\code{\link{users.list}}}
-#' \item{}{\code{\link{users.merge}}}
-#' \item{}{\code{\link{users.setup}}}
-#' \item{}{\code{\link{users.system}}}
-#' \item{}{\code{\link{users.unsetup}}}
-#' \item{}{\code{\link{users.update}}}
-#' \item{}{\code{\link{virtual_machines.create}}}
-#' \item{}{\code{\link{virtual_machines.delete}}}
-#' \item{}{\code{\link{virtual_machines.get}}}
-#' \item{}{\code{\link{virtual_machines.get_all_logins}}}
-#' \item{}{\code{\link{virtual_machines.list}}}
-#' \item{}{\code{\link{virtual_machines.logins}}}
-#' \item{}{\code{\link{virtual_machines.update}}}
-#' \item{}{\code{\link{workflows.create}}}
-#' \item{}{\code{\link{workflows.delete}}}
-#' \item{}{\code{\link{workflows.get}}}
-#' \item{}{\code{\link{workflows.list}}}
-#' \item{}{\code{\link{workflows.update}}}
-#' }
-#'
-#' @name Arvados
-#' @examples
-#' \dontrun{
-#' 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"))
-#' }
-NULL
-
-#' @export
+#' @export Arvados
Arvados <- R6::R6Class(
- "Arvados",
-
- public = list(
-
- initialize = function(authToken = NULL, hostName = NULL, numRetries = 0)
- {
- if(!is.null(hostName))
- Sys.setenv(ARVADOS_API_HOST = hostName)
-
- if(!is.null(authToken))
- Sys.setenv(ARVADOS_API_TOKEN = authToken)
-
- hostName <- Sys.getenv("ARVADOS_API_HOST")
- token <- Sys.getenv("ARVADOS_API_TOKEN")
-
- if(hostName == "" | token == "")
- stop(paste("Please provide host name and authentification token",
- "or set ARVADOS_API_HOST and ARVADOS_API_TOKEN",
- "environment variables."))
-
- private$token <- token
- private$host <- paste0("https://", hostName, "/arvados/v1/")
- private$numRetries <- numRetries
- private$REST <- RESTService$new(token, hostName,
- HttpRequest$new(), HttpParser$new(),
- numRetries)
-
- },
-
- projects.get = function(uuid)
- {
- self$groups.get(uuid)
- },
-
- projects.create = function(group, ensure_unique_name = "false")
- {
- group <- c("group_class" = "project", group)
- self$groups.create(group, ensure_unique_name)
- },
-
- projects.update = function(group, uuid)
- {
- group <- c("group_class" = "project", group)
- self$groups.update(group, uuid)
- },
-
- projects.list = function(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact",
- include_trash = NULL)
- {
- filters[[length(filters) + 1]] <- list("group_class", "=", "project")
- self$groups.list(filters, where, order, select, distinct,
- limit, offset, count, include_trash)
- },
-
- projects.delete = function(uuid)
- {
- self$groups.delete(uuid)
- },
-
- api_clients.get = function(uuid)
- {
- endPoint <- stringr::str_interp("api_clients/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_clients.create = function(apiclient,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("api_clients")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(apiclient) > 0)
- body <- jsonlite::toJSON(list(apiclient = apiclient),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_clients.update = function(apiclient, uuid)
- {
- endPoint <- stringr::str_interp("api_clients/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(apiclient) > 0)
- body <- jsonlite::toJSON(list(apiclient = apiclient),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_clients.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("api_clients/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_clients.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("api_clients")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_client_authorizations.get = function(uuid)
- {
- endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_client_authorizations.create = function(apiclientauthorization,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("api_client_authorizations")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(apiclientauthorization) > 0)
- body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_client_authorizations.update = function(apiclientauthorization, uuid)
- {
- endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(apiclientauthorization) > 0)
- body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_client_authorizations.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_client_authorizations.create_system_auth = function(api_client_id = NULL, scopes = NULL)
- {
- endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(api_client_id = api_client_id,
- scopes = scopes)
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_client_authorizations.current = function()
- {
- endPoint <- stringr::str_interp("api_client_authorizations/current")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- api_client_authorizations.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("api_client_authorizations")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- authorized_keys.get = function(uuid)
- {
- endPoint <- stringr::str_interp("authorized_keys/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- authorized_keys.create = function(authorizedkey,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("authorized_keys")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(authorizedkey) > 0)
- body <- jsonlite::toJSON(list(authorizedkey = authorizedkey),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- authorized_keys.update = function(authorizedkey, uuid)
- {
- endPoint <- stringr::str_interp("authorized_keys/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(authorizedkey) > 0)
- body <- jsonlite::toJSON(list(authorizedkey = authorizedkey),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- authorized_keys.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("authorized_keys/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- authorized_keys.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("authorized_keys")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.get = function(uuid)
- {
- endPoint <- stringr::str_interp("collections/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.create = function(collection,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("collections")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(collection) > 0)
- body <- jsonlite::toJSON(list(collection = collection),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.update = function(collection, uuid)
- {
- endPoint <- stringr::str_interp("collections/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(collection) > 0)
- body <- jsonlite::toJSON(list(collection = collection),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("collections/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.provenance = function(uuid)
- {
- endPoint <- stringr::str_interp("collections/${uuid}/provenance")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.used_by = function(uuid)
- {
- endPoint <- stringr::str_interp("collections/${uuid}/used_by")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.trash = function(uuid)
- {
- endPoint <- stringr::str_interp("collections/${uuid}/trash")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.untrash = function(uuid)
- {
- endPoint <- stringr::str_interp("collections/${uuid}/untrash")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- collections.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL,
- include_trash = NULL, include_old_versions = NULL)
- {
- endPoint <- stringr::str_interp("collections")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation,
- include_trash = include_trash, include_old_versions = include_old_versions)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.get = function(uuid)
- {
- endPoint <- stringr::str_interp("containers/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.create = function(container, ensure_unique_name = "false",
- cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("containers")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(container) > 0)
- body <- jsonlite::toJSON(list(container = container),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.update = function(container, uuid)
- {
- endPoint <- stringr::str_interp("containers/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(container) > 0)
- body <- jsonlite::toJSON(list(container = container),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("containers/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.auth = function(uuid)
- {
- endPoint <- stringr::str_interp("containers/${uuid}/auth")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.lock = function(uuid)
- {
- endPoint <- stringr::str_interp("containers/${uuid}/lock")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.unlock = function(uuid)
- {
- endPoint <- stringr::str_interp("containers/${uuid}/unlock")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.secret_mounts = function(uuid)
- {
- endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.current = function()
- {
- endPoint <- stringr::str_interp("containers/current")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- containers.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("containers")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- container_requests.get = function(uuid)
- {
- endPoint <- stringr::str_interp("container_requests/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- container_requests.create = function(containerrequest,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("container_requests")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(containerrequest) > 0)
- body <- jsonlite::toJSON(list(containerrequest = containerrequest),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- container_requests.update = function(containerrequest, uuid)
- {
- endPoint <- stringr::str_interp("container_requests/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(containerrequest) > 0)
- body <- jsonlite::toJSON(list(containerrequest = containerrequest),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- container_requests.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("container_requests/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- container_requests.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL,
- include_trash = NULL)
- {
- endPoint <- stringr::str_interp("container_requests")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation,
- include_trash = include_trash)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.get = function(uuid)
- {
- endPoint <- stringr::str_interp("groups/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.create = function(group, ensure_unique_name = "false",
- cluster_id = NULL, async = "false")
- {
- endPoint <- stringr::str_interp("groups")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id, async = async)
-
- if(length(group) > 0)
- body <- jsonlite::toJSON(list(group = group),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.update = function(group, uuid, async = "false")
- {
- endPoint <- stringr::str_interp("groups/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(async = async)
-
- if(length(group) > 0)
- body <- jsonlite::toJSON(list(group = group),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("groups/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.contents = function(filters = NULL,
- where = NULL, order = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact",
- cluster_id = NULL, bypass_federation = NULL,
- include_trash = NULL, uuid = NULL, recursive = NULL,
- include = NULL)
- {
- endPoint <- stringr::str_interp("groups/contents")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, distinct = distinct, limit = limit,
- offset = offset, count = count, cluster_id = cluster_id,
- bypass_federation = bypass_federation, include_trash = include_trash,
- uuid = uuid, recursive = recursive, include = include)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.shared = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL,
- include_trash = NULL, include = NULL)
- {
- endPoint <- stringr::str_interp("groups/shared")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation,
- include_trash = include_trash, include = include)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.trash = function(uuid)
- {
- endPoint <- stringr::str_interp("groups/${uuid}/trash")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.untrash = function(uuid)
- {
- endPoint <- stringr::str_interp("groups/${uuid}/untrash")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- groups.list = function(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact",
- cluster_id = NULL, bypass_federation = NULL,
- include_trash = NULL)
- {
- endPoint <- stringr::str_interp("groups")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation,
- include_trash = include_trash)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- keep_services.get = function(uuid)
- {
- endPoint <- stringr::str_interp("keep_services/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- keep_services.create = function(keepservice,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("keep_services")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(keepservice) > 0)
- body <- jsonlite::toJSON(list(keepservice = keepservice),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- keep_services.update = function(keepservice, uuid)
- {
- endPoint <- stringr::str_interp("keep_services/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(keepservice) > 0)
- body <- jsonlite::toJSON(list(keepservice = keepservice),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- keep_services.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("keep_services/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- keep_services.accessible = function()
- {
- endPoint <- stringr::str_interp("keep_services/accessible")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- keep_services.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("keep_services")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- links.get = function(uuid)
- {
- endPoint <- stringr::str_interp("links/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- links.create = function(link, ensure_unique_name = "false",
- cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("links")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(link) > 0)
- body <- jsonlite::toJSON(list(link = link),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- links.update = function(link, uuid)
- {
- endPoint <- stringr::str_interp("links/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(link) > 0)
- body <- jsonlite::toJSON(list(link = link),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- links.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("links/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- links.list = function(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact",
- cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("links")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- links.get_permissions = function(uuid)
- {
- endPoint <- stringr::str_interp("permissions/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- logs.get = function(uuid)
- {
- endPoint <- stringr::str_interp("logs/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- logs.create = function(log, ensure_unique_name = "false",
- cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("logs")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(log) > 0)
- body <- jsonlite::toJSON(list(log = log),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- logs.update = function(log, uuid)
- {
- endPoint <- stringr::str_interp("logs/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(log) > 0)
- body <- jsonlite::toJSON(list(log = log),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- logs.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("logs/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- logs.list = function(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact",
- cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("logs")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.get = function(uuid)
- {
- endPoint <- stringr::str_interp("users/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.create = function(user, ensure_unique_name = "false",
- cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("users")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(user) > 0)
- body <- jsonlite::toJSON(list(user = user),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.update = function(user, uuid, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("users/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(bypass_federation = bypass_federation)
-
- if(length(user) > 0)
- body <- jsonlite::toJSON(list(user = user),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("users/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.current = function()
- {
- endPoint <- stringr::str_interp("users/current")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.system = function()
- {
- endPoint <- stringr::str_interp("users/system")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.activate = function(uuid)
- {
- endPoint <- stringr::str_interp("users/${uuid}/activate")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.setup = function(uuid = NULL, user = NULL,
- repo_name = NULL, vm_uuid = NULL, send_notification_email = "false")
- {
- endPoint <- stringr::str_interp("users/setup")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(uuid = uuid, user = user,
- repo_name = repo_name, vm_uuid = vm_uuid,
- send_notification_email = send_notification_email)
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.unsetup = function(uuid)
- {
- endPoint <- stringr::str_interp("users/${uuid}/unsetup")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.merge = function(new_owner_uuid, new_user_token = NULL,
- redirect_to_new_user = NULL, old_user_uuid = NULL,
- new_user_uuid = NULL)
- {
- endPoint <- stringr::str_interp("users/merge")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(new_owner_uuid = new_owner_uuid,
- new_user_token = new_user_token, redirect_to_new_user = redirect_to_new_user,
- old_user_uuid = old_user_uuid, new_user_uuid = new_user_uuid)
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- users.list = function(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact",
- cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("users")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- repositories.get = function(uuid)
- {
- endPoint <- stringr::str_interp("repositories/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- repositories.create = function(repository,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("repositories")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(repository) > 0)
- body <- jsonlite::toJSON(list(repository = repository),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- repositories.update = function(repository, uuid)
- {
- endPoint <- stringr::str_interp("repositories/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(repository) > 0)
- body <- jsonlite::toJSON(list(repository = repository),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- repositories.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("repositories/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- repositories.get_all_permissions = function()
- {
- endPoint <- stringr::str_interp("repositories/get_all_permissions")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- repositories.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("repositories")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- virtual_machines.get = function(uuid)
- {
- endPoint <- stringr::str_interp("virtual_machines/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- virtual_machines.create = function(virtualmachine,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("virtual_machines")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(virtualmachine) > 0)
- body <- jsonlite::toJSON(list(virtualmachine = virtualmachine),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- virtual_machines.update = function(virtualmachine, uuid)
- {
- endPoint <- stringr::str_interp("virtual_machines/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(virtualmachine) > 0)
- body <- jsonlite::toJSON(list(virtualmachine = virtualmachine),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- virtual_machines.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("virtual_machines/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- virtual_machines.logins = function(uuid)
- {
- endPoint <- stringr::str_interp("virtual_machines/${uuid}/logins")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- virtual_machines.get_all_logins = function()
- {
- endPoint <- stringr::str_interp("virtual_machines/get_all_logins")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- virtual_machines.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("virtual_machines")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- workflows.get = function(uuid)
- {
- endPoint <- stringr::str_interp("workflows/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- workflows.create = function(workflow, ensure_unique_name = "false",
- cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("workflows")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(workflow) > 0)
- body <- jsonlite::toJSON(list(workflow = workflow),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- workflows.update = function(workflow, uuid)
- {
- endPoint <- stringr::str_interp("workflows/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(workflow) > 0)
- body <- jsonlite::toJSON(list(workflow = workflow),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- workflows.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("workflows/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- workflows.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("workflows")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.get = function(uuid)
- {
- endPoint <- stringr::str_interp("user_agreements/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.create = function(useragreement,
- ensure_unique_name = "false", cluster_id = NULL)
- {
- endPoint <- stringr::str_interp("user_agreements")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(ensure_unique_name = ensure_unique_name,
- cluster_id = cluster_id)
-
- if(length(useragreement) > 0)
- body <- jsonlite::toJSON(list(useragreement = useragreement),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.update = function(useragreement, uuid)
- {
- endPoint <- stringr::str_interp("user_agreements/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- if(length(useragreement) > 0)
- body <- jsonlite::toJSON(list(useragreement = useragreement),
- auto_unbox = TRUE)
- else
- body <- NULL
-
- response <- private$REST$http$exec("PUT", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.delete = function(uuid)
- {
- endPoint <- stringr::str_interp("user_agreements/${uuid}")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("DELETE", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.signatures = function()
- {
- endPoint <- stringr::str_interp("user_agreements/signatures")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.sign = function()
- {
- endPoint <- stringr::str_interp("user_agreements/sign")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("POST", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.list = function(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", cluster_id = NULL, bypass_federation = NULL)
- {
- endPoint <- stringr::str_interp("user_agreements")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- list(filters = filters, where = where,
- order = order, select = select, distinct = distinct,
- limit = limit, offset = offset, count = count,
- cluster_id = cluster_id, bypass_federation = bypass_federation)
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- user_agreements.new = function()
- {
- endPoint <- stringr::str_interp("user_agreements/new")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- configs.get = function()
- {
- endPoint <- stringr::str_interp("config")
- url <- paste0(private$host, endPoint)
- headers <- list(Authorization = paste("Bearer", private$token),
- "Content-Type" = "application/json")
- queryArgs <- NULL
-
- body <- NULL
-
- response <- private$REST$http$exec("GET", url, headers, body,
- queryArgs, private$numRetries)
- resource <- private$REST$httpParser$parseJSONResponse(response)
-
- if(!is.null(resource$errors))
- stop(resource$errors)
-
- resource
- },
-
- getHostName = function() private$host,
- getToken = function() private$token,
- setRESTService = function(newREST) private$REST <- newREST,
- getRESTService = function() private$REST
- ),
-
- private = list(
-
- token = NULL,
- host = NULL,
- REST = NULL,
- numRetries = NULL
- ),
-
- cloneable = FALSE
+ "Arvados",
+
+ public = list(
+
+ #' @description
+ #' Initialize new enviroment.
+ #' @param authToken ARVADOS_API_TOKEN from 'Get API Token' on Arvados.
+ #' @param hostName ARVADOS_API_HOST from 'Get API Token' on Arvados.
+ #' @param numRetries Specify number of times to retry failed service requests.
+ #' @return A new `Arvados` object.
+ #' @examples
+ #' arv <- Arvados$new(authToken = "ARVADOS_API_TOKEN", hostName = "ARVADOS_API_HOST", numRetries = 3)
+ initialize = function(authToken = NULL, hostName = NULL, numRetries = 0)
+ {
+ if(!is.null(hostName))
+ Sys.setenv(ARVADOS_API_HOST = hostName)
+
+ if(!is.null(authToken))
+ Sys.setenv(ARVADOS_API_TOKEN = authToken)
+
+ hostName <- Sys.getenv("ARVADOS_API_HOST")
+ token <- Sys.getenv("ARVADOS_API_TOKEN")
+
+ if(hostName == "" | token == "")
+ stop(paste("Please provide host name and authentification token",
+ "or set ARVADOS_API_HOST and ARVADOS_API_TOKEN",
+ "environment variables."))
+
+ private$token <- token
+ private$host <- paste0("https://", hostName, "/arvados/v1/")
+ private$numRetries <- numRetries
+ private$REST <- RESTService$new(token, hostName,
+ HttpRequest$new(), HttpParser$new(),
+ numRetries)
+
+ },
+
+ #' @description
+ #' project_exist enables checking if the project with such a UUID exist.
+ #' @param uuid The UUID of a project or a file.
+ #' @examples
+ #' arv$project_exist(uuid = projectUUID)
+ project_exist = function(uuid)
+ {
+ proj <- self$project_list(list(list("uuid", '=', uuid)))
+ value <- length(proj$items)
+
+ if (value == 1){
+ cat(format('TRUE'))
+ } else {
+ cat(format('FALSE'))
+ }
+ },
+
+ #' @description
+ #' project_get returns the demanded project.
+ #' @param uuid The UUID of the Group in question.
+ #' @examples
+ #' project <- arv$project_get(uuid = projectUUID)
+ project_get = function(uuid)
+ {
+ self$groups_get(uuid)
+ },
+
+ #' @description
+ #' project_create creates a new project of a given name and description.
+ #' @param name Name of the project.
+ #' @param description Description of the project.
+ #' @param ownerUUID The UUID of the maternal project to created one.
+ #' @param properties List of the properties of the project.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @examples
+ #' Properties <- list() # should contain a list of new properties to be added
+ #' new_project <- arv$project_create(name = "project name", description = "project description", owner_uuid = "project UUID", properties = NULL, ensureUniqueName = "false")
+ project_create = function(name, description, ownerUUID, properties = NULL, ensureUniqueName = "false")
+ {
+ group <- list(name = name, description = description, owner_uuid = ownerUUID, properties = properties)
+ group <- c("group_class" = "project", group)
+ self$groups_create(group, ensureUniqueName = ensureUniqueName)
+ },
+
+ #' @description
+ #' project_properties_set is a method defined in Arvados class that enables setting properties. Allows to set or overwrite the properties. In case there are set already it overwrites them.
+ #' @param listProperties List of new properties.
+ #' @param uuid The UUID of a project or a file.
+ #' @examples
+ #' Properties <- list() # should contain a list of new properties to be added
+ #' arv$project_properties_set(Properties, uuid)
+ project_properties_set = function(listProperties, uuid)
+ {
+ group <- c("group_class" = "project", list("properties" = listProperties))
+ self$groups_update(group, uuid)
+
+ },
+
+ #' @description
+ #' project_properties_append is a method defined in Arvados class that enables appending properties. Allows to add new properties.
+ #' @param listOfNewProperties List of new properties.
+ #' @param uuid The UUID of a project or a file.
+ #' @examples
+ #' newProperties <- list() # should contain a list of new properties to be added
+ #' arv$project_properties_append(properties = newProperties, uuid)
+ project_properties_append = function(properties, uuid)
+ {
+ proj <- self$project_list(list(list('uuid', '=', uuid)))
+ projProp <- proj$items[[1]]$properties
+
+ newListOfProperties <- c(projProp, properties)
+ uniqueProperties <- unique(unlist(newListOfProperties))
+ newListOfProperties <- suppressWarnings(newListOfProperties[which(newListOfProperties == uniqueProperties)])
+
+ group <- c("group_class" = "project", list("properties" = newListOfProperties))
+ self$groups_update(group, uuid);
+
+ },
+
+ #' @description
+ #' project_properties_get is a method defined in Arvados class that returns properties.
+ #' @param uuid The UUID of a project or a file.
+ #' @examples
+ #' arv$project_properties_get(projectUUID)
+ project_properties_get = function(uuid)
+ {
+ proj <- self$project_list(list(list('uuid', '=', uuid)))
+ proj$items[[1]]$properties
+ },
+
+ #' @description
+ #' project_properties_delete is a method defined in Arvados class that deletes list of properties.
+ #' @param oneProp Property to be deleted.
+ #' @param uuid The UUID of a project or a file.
+ #' @examples
+ #' Properties <- list() # should contain a list of new properties to be added
+ #' arv$project_properties_delete(Properties, projectUUID)
+ project_properties_delete = function(oneProp, uuid)
+ {
+ proj <- self$project_list(list(list('uuid', '=', uuid))) # find project
+ projProp <- proj$items[[1]]$properties
+ for (i in 1:length(projProp)){
+ solution <- identical(projProp[i],oneProp)
+ if (solution == TRUE) {
+ projProp <- projProp[names(projProp) != names(oneProp)]
+ self$project_properties_set(projProp, uuid)
+ }
+ }
+ },
+
+ #' @description
+ #' project_update enables updating project. New name, description and properties may be given.
+ #' @param ... Feature to be updated (name, description, properties).
+ #' @param uuid The UUID of a project in question.
+ #' @examples
+ #' newProperties <- list() # should contain a list of new properties to be added
+ #' arv$project_update(name = "new project name", properties = newProperties, uuid = projectUUID)
+ project_update = function(..., uuid) {
+ vec <- list(...)
+ for (i in 1:length(vec))
+ {
+ if (names(vec[i]) == 'properties') {
+ solution <- self$project_properties_append(vec$properties, uuid = uuid)
+ }
+ }
+ vecNew <- vec[names(vec) != "properties"]
+ vecNew <- c("group_class" = "project", vecNew)
+ z <- self$groups_update(vecNew, uuid)
+ },
+
+ #' @description
+ #' project_list enables listing project by its name, uuid, properties, permissions.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param includeTrash Include items whose is_trashed attribute is true.
+ #' @param uuid The UUID of a project in question.
+ #' @param recursive Include contents from child groups recursively.
+ #' @examples
+ #' listOfprojects <- arv$project_list(list(list("owner_uuid", "=", projectUUID))) # Sample query which show projects within the project of a given UUID
+ project_list = function(filters = NULL, where = NULL,
+ order = NULL, select = NULL, distinct = NULL,
+ limit = "100", offset = "0", count = "exact",
+ includeTrash = NULL)
+ {
+ filters[[length(filters) + 1]] <- list("group_class", "=", "project")
+ self$groups_list(filters, where, order, select, distinct,
+ limit, offset, count, includeTrash)
+ },
+
+ #' @description
+ #' project_delete trashes project of a given uuid. It can be restored from trash or deleted permanently.
+ #' @param uuid The UUID of the Group in question.
+ project_delete = function(uuid)
+ {
+ self$groups_delete(uuid)
+ },
+
+ #' @description
+ #' api_clients_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the apiClient in question.
+ api_clients_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("api_clients/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_clients_create is a method defined in Arvados class.
+ #' @param apiClient apiClient object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ api_clients_create = function(apiClient,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("api_clients")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(apiClient) > 0)
+ body <- jsonlite::toJSON(list(apiClient = apiClient),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_clients_update is a method defined in Arvados class.
+ #' @param apiClient apiClient object.
+ #' @param uuid The UUID of the apiClient in question.
+ api_clients_update = function(apiClient, uuid)
+ {
+ endPoint <- stringr::str_interp("api_clients/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(apiClient) > 0)
+ body <- jsonlite::toJSON(list(apiClient = apiClient),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_clients_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the apiClient in question.
+ api_clients_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("api_clients/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_clients_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ api_clients_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("api_clients")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_client_authorizations_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the apiClientAuthorization in question.
+ api_client_authorizations_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_client_authorizations_create is a method defined in Arvados class.
+ #' @param apiClientAuthorization apiClientAuthorization object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error on (ownerUUID, name) collision_
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ api_client_authorizations_create = function(apiClientAuthorization,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("api_client_authorizations")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(apiClientAuthorization) > 0)
+ body <- jsonlite::toJSON(list(apiClientAuthorization = apiClientAuthorization),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_client_authorizations_update is a method defined in Arvados class.
+ #' @param apiClientAuthorization apiClientAuthorization object.
+ #' @param uuid The UUID of the apiClientAuthorization in question.
+ api_client_authorizations_update = function(apiClientAuthorization, uuid)
+ {
+ endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(apiClientAuthorization) > 0)
+ body <- jsonlite::toJSON(list(apiClientAuthorization = apiClientAuthorization),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_client_authorizations_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the apiClientAuthorization in question.
+ api_client_authorizations_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_client_authorizations_create_system_auth is a method defined in Arvados class.
+ #' @param apiClientID
+ #' @param scopes
+ api_client_authorizations_create_system_auth = function(apiClientID = NULL, scopes = NULL)
+ {
+ endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(apiClientID = apiClientID,
+ scopes = scopes)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_client_authorizations_current is a method defined in Arvados class.
+ api_client_authorizations_current = function()
+ {
+ endPoint <- stringr::str_interp("api_client_authorizations/current")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' api_client_authorizations_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ api_client_authorizations_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("api_client_authorizations")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' authorized_keys_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the authorizedKey in question.
+ authorized_keys_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("authorized_keys/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' authorized_keys_create is a method defined in Arvados class.
+ #' @param authorizedKey authorizedKey object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ authorized_keys_create = function(authorizedKey,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("authorized_keys")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(authorizedKey) > 0)
+ body <- jsonlite::toJSON(list(authorizedKey = authorizedKey),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' authorized_keys_update is a method defined in Arvados class.
+ #' @param authorizedKey authorizedKey object.
+ #' @param uuid The UUID of the authorizedKey in question.
+ authorized_keys_update = function(authorizedKey, uuid)
+ {
+ endPoint <- stringr::str_interp("authorized_keys/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(authorizedKey) > 0)
+ body <- jsonlite::toJSON(list(authorizedKey = authorizedKey),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' authorized_keys_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the authorizedKey in question.
+ authorized_keys_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("authorized_keys/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' authorized_keys_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ authorized_keys_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("authorized_keys")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the Collection in question.
+ #' collection <- arv$collections_get(uuid = collectionUUID)
+ collections_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("collections/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_create is a method defined in Arvados class that enables collections creation.
+ #' @param name Name of the collection.
+ #' @param description Description of the collection.
+ #' @param ownerUUID UUID of the maternal project to created one.
+ #' @param properties Properties of the collection.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ #' @examples
+ #' Properties <- list() # should contain a list of new properties to be added
+ #' arv$collections_create(name = "collectionTitle", description = "collectionDescription", ownerUUID = "collectionOwner", properties = Properties)
+ collections_create = function(name, description, ownerUUID = NULL, properties = NULL, # name and description are obligatory
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("collections")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ collection <- list(name = name, description = description, owner_uuid = ownerUUID, properties = properties)
+ if(length(collection) > 0)
+ body <- jsonlite::toJSON(list(collection = collection),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors)){
+ if(identical(sub('Entity:.*',"", resource$errors), "//railsapi.internal/arvados/v1/collections: 422 Unprocessable ")){
+ resource <- cat(format("A collection with the given name already exists in this projects. If you want to update it use collections_update() instead"))
+ }else{
+ stop(resource$errors)
+ }
+ }
+
+ resource
+ },
+
+ #' @description
+ #' collections_update is a method defined in Arvados class.
+ #' @param name New name of the collection.
+ #' @param description New description of the collection.
+ #' @param ownerUUID UUID of the maternal project to created one.
+ #' @param properties New list of properties of the collection.
+ #' @param uuid The UUID of the Collection in question.
+ #' @examples
+ #' collection <- arv$collections_update(name = "newCollectionTitle", description = "newCollectionDescription", ownerUUID = "collectionOwner", properties = NULL, uuid = "collectionUUID")
+ collections_update = function(name, description, ownerUUID = NULL, properties = NULL, uuid)
+ {
+ endPoint <- stringr::str_interp("collections/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ collection <- list(name = name, description = description, ownerUUID = ownerUUID, properties = properties)
+ if(length(collection) > 0)
+ body <- jsonlite::toJSON(list(collection = collection),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the Collection in question.
+ #' @examples
+ #' arv$collection_delete(collectionUUID)
+ collections_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("collections/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_provenance is a method defined in Arvados class, it returns the collection by uuid.
+ #' @param uuid The UUID of the Collection in question.
+ #' @examples
+ #' collection <- arv$collections_provenance(collectionUUID)
+ collections_provenance = function(uuid)
+ {
+ endPoint <- stringr::str_interp("collections/${uuid}/provenance")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_used_by is a method defined in Arvados class, it returns collection by portable_data_hash.
+ #' @param uuid The UUID of the Collection in question.
+ collections_used_by = function(uuid)
+ {
+ endPoint <- stringr::str_interp("collections/${uuid}/used_by")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_trash is a method defined in Arvados class, it moves collection to trash.
+ #' @param uuid The UUID of the Collection in question.
+ #' @examples
+ #' arv$collections_trash(collectionUUID)
+ collections_trash = function(uuid)
+ {
+ endPoint <- stringr::str_interp("collections/${uuid}/trash")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_untrash is a method defined in Arvados class, it moves collection from trash to project.
+ #' @param uuid The UUID of the Collection in question.
+ #' @examples
+ #' arv$collections_untrash(collectionUUID)
+ collections_untrash = function(uuid)
+ {
+ endPoint <- stringr::str_interp("collections/${uuid}/untrash")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' collections_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ #' @param includeTrash Include collections whose is_trashed attribute is true.
+ #' @param includeOldVersions Include past collection versions.
+ #' @examples
+ #' collectionList <- arv$collections_list(list(list("name", "=", "Example")))
+ collections_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL,
+ includeTrash = NULL, includeOldVersions = NULL)
+ {
+ endPoint <- stringr::str_interp("collections")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation,
+ includeTrash = includeTrash, includeOldVersions = includeOldVersions)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the Container in question.
+ containers_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("containers/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_create is a method defined in Arvados class.
+ #' @param container Container object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ containers_create = function(container, ensureUniqueName = "false",
+ clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("containers")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(container) > 0)
+ body <- jsonlite::toJSON(list(container = container),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_update is a method defined in Arvados class.
+ #' @param container Container object.
+ #' @param uuid The UUID of the Container in question.
+ containers_update = function(container, uuid)
+ {
+ endPoint <- stringr::str_interp("containers/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(container) > 0)
+ body <- jsonlite::toJSON(list(container = container),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the Container in question.
+ containers_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("containers/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_auth is a method defined in Arvados class.
+ #' @param uuid The UUID of the Container in question.
+ containers_auth = function(uuid)
+ {
+ endPoint <- stringr::str_interp("containers/${uuid}/auth")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_lock is a method defined in Arvados class.
+ #' @param uuid The UUID of the Container in question.
+ containers_lock = function(uuid)
+ {
+ endPoint <- stringr::str_interp("containers/${uuid}/lock")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_unlock is a method defined in Arvados class.
+ #' @param uuid The UUID of the Container in question.
+ containers_unlock = function(uuid)
+ {
+ endPoint <- stringr::str_interp("containers/${uuid}/unlock")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_secret_mounts is a method defined in Arvados class.
+ #' @param uuid The UUID of the Container in question.
+ containers_secret_mounts = function(uuid)
+ {
+ endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_current is a method defined in Arvados class.
+ containers_current = function()
+ {
+ endPoint <- stringr::str_interp("containers/current")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' containers_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ containers_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("containers")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' container_requests_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the containerRequest in question.
+ container_requests_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("container_requests/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' container_requests_create is a method defined in Arvados class.
+ #' @param containerRequest containerRequest object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ container_requests_create = function(containerRequest,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("container_requests")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(containerRequest) > 0)
+ body <- jsonlite::toJSON(list(containerRequest = containerRequest),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' container_requests_update is a method defined in Arvados class.
+ #' @param containerRequest containerRequest object.
+ #' @param uuid The UUID of the containerRequest in question.
+ container_requests_update = function(containerRequest, uuid)
+ {
+ endPoint <- stringr::str_interp("container_requests/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(containerRequest) > 0)
+ body <- jsonlite::toJSON(list(containerRequest = containerRequest),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' container_requests_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the containerRequest in question.
+ container_requests_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("container_requests/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' container_requests_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation bypass federation behavior, list items from local instance database only
+ #' @param includeTrash Include container requests whose owner project is trashed.
+ container_requests_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL,
+ includeTrash = NULL)
+ {
+ endPoint <- stringr::str_interp("container_requests")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation,
+ includeTrash = includeTrash)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' groups_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the Group in question.
+ groups_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("groups/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' groups_create is a method defined in Arvados class that supports project creation.
+ #' @param group Group object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ #' @param async Defer permissions update.
+ groups_create = function(group, ensureUniqueName = "false",
+ clusterID = NULL, async = "false")
+ {
+ endPoint <- stringr::str_interp("groups")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID, async = async)
+
+ if(length(group) > 0)
+ body <- jsonlite::toJSON(list(group = group),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors)){
+ if (identical(sub('#.*', "", resource$errors), "//railsapi.internal/arvados/v1/groups: 422 Unprocessable Entity: ")) {
+ #if (identical(sub('P.*', "", resource$errors), "//railsapi.internal/arvados/v1/groups: 422 Unprocessable Entity: #\u003cActiveRecord::RecordNotUnique: ")) {
+ resource <- cat(format("Project of that name already exist. If you want to update it use project_update() instead"))
+ }else{
+ stop(resource$errors)
+ }
+ }
+
+ return(resource)
+ },
+
+ #' @description
+ #' groups_update is a method defined in Arvados class.
+ #' @param group Group object.
+ #' @param uuid The UUID of the Group in question.
+ #' @param async Defer permissions update.
+ groups_update = function(group, uuid, async = "false")
+ {
+ endPoint <- stringr::str_interp("groups/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- list(async = async)
+
+ if(length(group) > 0)
+ body <- jsonlite::toJSON(list(group = group),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' groups_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the Group in question.
+ groups_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("groups/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ dataTime <- gsub("T.*", "", resource$delete_at)
+ cat("The content will be deleted permanently at", dataTime)
+
+ resource
+ },
+
+ #' @description
+ #' groups_contents is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ #' @param includeTrash Include items whose is_trashed attribute is true.
+ #' @param uuid
+ #' @param recursive Include contents from child groups recursively.
+ #' @param include Include objects referred to by listed field in "included" (only ownerUUID).
+ groups_contents = function(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)
+ {
+ endPoint <- stringr::str_interp("groups/contents")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- list(filters = filters, where = where,
+ order = order, distinct = distinct, limit = limit,
+ offset = offset, count = count, clusterID = clusterID,
+ bypassFederation = bypassFederation, includeTrash = includeTrash,
+ uuid = uuid, recursive = recursive, include = include)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' groups_shared is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ #' @param includeTrash Include items whose is_trashed attribute is true.
+ #' @param include
+ groups_shared = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL,
+ includeTrash = NULL, include = NULL)
+ {
+ endPoint <- stringr::str_interp("groups/shared")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation,
+ includeTrash = includeTrash, include = include)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' groups_trash is a method defined in Arvados class.
+ #' @param uuid The UUID of the Group in question.
+ groups_trash = function(uuid)
+ {
+ endPoint <- stringr::str_interp("groups/${uuid}/trash")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' groups_untrash is a method defined in Arvados class.
+ #' @param uuid The UUID of the Group in question.
+ groups_untrash = function(uuid)
+ {
+ endPoint <- stringr::str_interp("groups/${uuid}/untrash")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' groups_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ #' @param includeTrash Include items whose is_trashed attribute is true.
+ groups_list = function(filters = NULL, where = NULL,
+ order = NULL, select = NULL, distinct = NULL,
+ limit = "100", offset = "0", count = "exact",
+ clusterID = NULL, bypassFederation = NULL,
+ includeTrash = NULL)
+ {
+ endPoint <- stringr::str_interp("groups")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation,
+ includeTrash = includeTrash)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' keep_services_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the keepService in question.
+ keep_services_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("keep_services/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' keep_services_create is a method defined in Arvados class.
+ #' @param keepService keepService object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ keep_services_create = function(keepService,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("keep_services")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(keepService) > 0)
+ body <- jsonlite::toJSON(list(keepService = keepService),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' keep_services_update is a method defined in Arvados class.
+ #' @param keepService keepService object.
+ #' @param uuid The UUID of the keepService in question.
+ keep_services_update = function(keepService, uuid)
+ {
+ endPoint <- stringr::str_interp("keep_services/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(keepService) > 0)
+ body <- jsonlite::toJSON(list(keepService = keepService),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' keep_services_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the keepService in question.
+ keep_services_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("keep_services/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' keep_services_accessible is a method defined in Arvados class.
+ keep_services_accessible = function()
+ {
+ endPoint <- stringr::str_interp("keep_services/accessible")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' keep_services_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ keep_services_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("keep_services")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' project_permission_give is a method defined in Arvados class that enables sharing files with another users.
+ #' @param type Possible options are can_read or can_write or can_manage.
+ #' @param uuid The UUID of a project or a file.
+ #' @param user The UUID of the person that gets the permission.
+ #' @examples
+ #' arv$project_permission_give(type = "can_read", uuid = objectUUID, user = userUUID)
+ project_permission_give = function(type, uuid, user)
+ {
+ endPoint <- stringr::str_interp("links")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ # it is possible to make it as pasting a list to function, not a 3 arg. What's better?
+ link <- list("link_class" = "permission", "name" = type, "head_uuid" = uuid, "tail_uuid" = user)
+
+ if(length(link) > 0)
+ body <- jsonlite::toJSON(list(link = link),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' project_permission_refuse is a method defined in Arvados class that unables sharing files with another users.
+ #' @param type Possible options are can_read or can_write or can_manage.
+ #' @param uuid The UUID of a project or a file.
+ #' @param user The UUID of a person that permissions are taken from.
+ #' @examples
+ #' arv$project_permission_refuse(type = "can_read", uuid = objectUUID, user = userUUID)
+ project_permission_refuse = function(type, uuid, user)
+ {
+ examples <- self$links_list(list(list("head_uuid","=", uuid)))
+
+ theUser <- examples[which(sapply(examples$items, "[[", "tail_uuid") == user)]
+ theType <- theUser$items[which(sapply(theUser$items, "[[", "name") == type)]
+ solution <- theType[which(sapply(theType, "[[", "link_class") == 'permission')]
+
+ if (length(solution) == 0) {
+ cat(format('No permission granted'))
+ } else {
+ self$links_delete(solution[[1]]$uuid)
+ }
+
+ },
+
+ #' @description
+ #' project_permission_update is a method defined in Arvados class that enables updating permissions.
+ #' @param typeNew New option like can_read or can_write or can_manage.
+ #' @param typeOld Old option.
+ #' @param uuid The UUID of a project or a file.
+ #' @param user The UUID of the person that the permission is being updated.
+ #' @examples
+ #' arv$project_permission_update(typeOld = "can_read", typeNew = "can_write", uuid = objectUUID, user = userUUID)
+ project_permission_update = function(typeOld, typeNew, uuid, user)
+ {
+ link <- list("name" = typeNew)
+
+ examples <- self$links_list(list(list("head_uuid","=", uuid)))
+
+ theUser <- examples[which(sapply(examples$items, "[[", "tail_uuid") == user)]
+ theType <- theUser$items[which(sapply(theUser$items, "[[", "name") == typeOld)]
+ solution <- theType[which(sapply(theType, "[[", "link_class") == 'permission')]
+
+ if (length(solution) == 0) {
+ cat(format('No permission granted'))
+ } else {
+ self$links_update(link, solution[[1]]$uuid)
+ }
+ },
+
+ #' @description
+ #' project_permission_check is a method defined in Arvados class that enables checking file permissions.
+ #' @param uuid The UUID of a project or a file.
+ #' @param user The UUID of the person that the permission is being updated.
+ #' @param type Possible options are can_read or can_write or can_manage.
+ #' @examples
+ #' arv$project_permission_check(type = "can_read", uuid = objectUUID, user = userUUID)
+ project_permission_check = function(uuid, user, type = NULL)
+ {
+ examples <- self$links_list(list(list("head_uuid","=", uuid)))
+
+ theUser <- examples[which(sapply(examples$items, "[[", "tail_uuid") == user)]
+
+ if (length(type) == 0 ){
+ theUser
+ } else {
+ theType <- theUser$items[which(sapply(theUser$items, "[[", "name") == type)]
+ permisions <- theType[which(sapply(theType, "[[", "link_class") == 'permission')]
+ print(permisions[[1]]$name)
+ }
+ },
+
+ #' @description
+ #' links_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the Link in question.
+ links_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("links/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' links_create is a method defined in Arvados class.
+ #' @param link Link object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ links_create = function(link, ensureUniqueName = "false",
+ clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("links")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(link) > 0)
+ body <- jsonlite::toJSON(list(link = link),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' links_update is a method defined in Arvados class.
+ #' @param link Link object.
+ #' @param uuid The UUID of the Link in question.
+ links_update = function(link, uuid, async = "false")
+ {
+ endPoint <- stringr::str_interp("links/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(async = async)
+
+ if(length(link) > 0)
+ body <- jsonlite::toJSON(list(link = link),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' links_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the Link in question.
+ links_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("links/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' links_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ links_list = function(filters = NULL, where = NULL,
+ order = NULL, select = NULL, distinct = NULL,
+ limit = "100", offset = "0", count = "exact",
+ clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("links")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' links_get_permissions is a method defined in Arvados class.
+ #' @param uuid The UUID of the Log in question.
+ links_get_permissions = function(uuid)
+ {
+ endPoint <- stringr::str_interp("permissions/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' logs_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the Log in question.
+ logs_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("logs/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' logs_create is a method defined in Arvados class.
+ #' @param log Log object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ logs_create = function(log, ensureUniqueName = "false",
+ clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("logs")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(log) > 0)
+ body <- jsonlite::toJSON(list(log = log),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' logs_update is a method defined in Arvados class.
+ #' @param log Log object.
+ #' @param uuid The UUID of the Log in question.
+ logs_update = function(log, uuid)
+ {
+ endPoint <- stringr::str_interp("logs/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(log) > 0)
+ body <- jsonlite::toJSON(list(log = log),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' logs_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the Log in question.
+ logs_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("logs/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' logs_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ logs_list = function(filters = NULL, where = NULL,
+ order = NULL, select = NULL, distinct = NULL,
+ limit = "100", offset = "0", count = "exact",
+ clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("logs")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the User in question.
+ users_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("users/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_create is a method defined in Arvados class.
+ #' @param user User object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ users_create = function(user, ensureUniqueName = "false",
+ clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("users")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(user) > 0)
+ body <- jsonlite::toJSON(list(user = user),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_update is a method defined in Arvados class.
+ #' @param user User object.
+ #' @param uuid The UUID of the User in question.
+ #' @param bypassFederation
+ users_update = function(user, uuid, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("users/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(bypassFederation = bypassFederation)
+
+ if(length(user) > 0)
+ body <- jsonlite::toJSON(list(user = user),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the User in question.
+ users_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("users/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_current is a method defined in Arvados class.
+ users_current = function()
+ {
+ endPoint <- stringr::str_interp("users/current")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_system is a method defined in Arvados class.
+ users_system = function()
+ {
+ endPoint <- stringr::str_interp("users/system")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_activate is a method defined in Arvados class.
+ #' @param uuid The UUID of the User in question.
+ users_activate = function(uuid)
+ {
+ endPoint <- stringr::str_interp("users/${uuid}/activate")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_setup is a method defined in Arvados class.
+ #' @param uuid
+ #' @param user
+ #' @param repo_name
+ #' @param vm_uuid
+ #' @param send_notification_email
+ users_setup = function(uuid = NULL, user = NULL,
+ repo_name = NULL, vm_uuid = NULL, send_notification_email = "false")
+ {
+ endPoint <- stringr::str_interp("users/setup")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(uuid = uuid, user = user,
+ repo_name = repo_name, vm_uuid = vm_uuid,
+ send_notification_email = send_notification_email)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_unsetup is a method defined in Arvados class.
+ #' @param uuid The UUID of the User in question.
+ users_unsetup = function(uuid)
+ {
+ endPoint <- stringr::str_interp("users/${uuid}/unsetup")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_merge is a method defined in Arvados class.
+ #' @param newOwnerUUID
+ #' @param newUserToken
+ #' @param redirectToNewUser
+ #' @param oldUserUUID
+ #' @param newUserUUID
+ users_merge = function(newOwnerUUID, newUserToken = NULL,
+ redirectToNewUser = NULL, oldUserUUID = NULL,
+ newUserUUID = NULL)
+ {
+ endPoint <- stringr::str_interp("users/merge")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(newOwnerUUID = newOwnerUUID,
+ newUserToken = newUserToken, redirectToNewUser = redirectToNewUser,
+ oldUserUUID = oldUserUUID, newUserUUID = newUserUUID)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' users_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ users_list = function(filters = NULL, where = NULL,
+ order = NULL, select = NULL, distinct = NULL,
+ limit = "100", offset = "0", count = "exact",
+ clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("users")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' repositories_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the Repository in question.
+ repositories_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("repositories/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' repositories_create is a method defined in Arvados class.
+ #' @param repository Repository object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ repositories_create = function(repository,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("repositories")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(repository) > 0)
+ body <- jsonlite::toJSON(list(repository = repository),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' repositories_update is a method defined in Arvados class.
+ #' @param repository Repository object.
+ #' @param uuid The UUID of the Repository in question.
+ repositories_update = function(repository, uuid)
+ {
+ endPoint <- stringr::str_interp("repositories/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(repository) > 0)
+ body <- jsonlite::toJSON(list(repository = repository),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' repositories_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the Repository in question.
+ repositories_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("repositories/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' repositories_get_all_permissions is a method defined in Arvados class.
+ repositories_get_all_permissions = function()
+ {
+ endPoint <- stringr::str_interp("repositories/get_all_permissions")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' repositories_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ repositories_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("repositories")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' virtual_machines_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the virtualMachine in question.
+ virtual_machines_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("virtual_machines/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' virtual_machines_create is a method defined in Arvados class.
+ #' @param virtualMachine virtualMachine object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ virtual_machines_create = function(virtualMachine,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("virtual_machines")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(virtualMachine) > 0)
+ body <- jsonlite::toJSON(list(virtualMachine = virtualMachine),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' virtual_machines_update is a method defined in Arvados class.
+ #' @param virtualMachine virtualMachine object.
+ #' @param uuid The UUID of the virtualMachine in question.
+ virtual_machines_update = function(virtualMachine, uuid)
+ {
+ endPoint <- stringr::str_interp("virtual_machines/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(virtualMachine) > 0)
+ body <- jsonlite::toJSON(list(virtualMachine = virtualMachine),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' virtual_machines_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the virtualMachine in question.
+ virtual_machines_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("virtual_machines/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' virtual_machines_logins is a method defined in Arvados class.
+ #' @param uuid The UUID of the virtualMachine in question.
+ virtual_machines_logins = function(uuid)
+ {
+ endPoint <- stringr::str_interp("virtual_machines/${uuid}/logins")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' virtual_machines_get_all_logins is a method defined in Arvados class.
+ virtual_machines_get_all_logins = function()
+ {
+ endPoint <- stringr::str_interp("virtual_machines/get_all_logins")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' virtual_machines_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation bypass federation behavior, list items from local instance database only
+ virtual_machines_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("virtual_machines")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' workflows_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the Workflow in question.
+ workflows_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("workflows/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' workflows_create is a method defined in Arvados class.
+ #' @param workflow Workflow object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ workflows_create = function(workflow, ensureUniqueName = "false",
+ clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("workflows")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(workflow) > 0)
+ body <- jsonlite::toJSON(list(workflow = workflow),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' workflows_update is a method defined in Arvados class.
+ #' @param workflow Workflow object.
+ #' @param uuid The UUID of the Workflow in question.
+ workflows_update = function(workflow, uuid)
+ {
+ endPoint <- stringr::str_interp("workflows/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(workflow) > 0)
+ body <- jsonlite::toJSON(list(workflow = workflow),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' workflows_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the Workflow in question.
+ workflows_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("workflows/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' workflows_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ workflows_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("workflows")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' user_agreements_get is a method defined in Arvados class.
+ #' @param uuid The UUID of the userAgreement in question.
+ user_agreements_get = function(uuid)
+ {
+ endPoint <- stringr::str_interp("user_agreements/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' user_agreements_create is a method defined in Arvados class.
+ #' @param userAgreement userAgreement object.
+ #' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
+ #' @param clusterID Create object on a remote federated cluster instead of the current one.
+ user_agreements_create = function(userAgreement,
+ ensureUniqueName = "false", clusterID = NULL)
+ {
+ endPoint <- stringr::str_interp("user_agreements")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(ensureUniqueName = ensureUniqueName,
+ clusterID = clusterID)
+
+ if(length(userAgreement) > 0)
+ body <- jsonlite::toJSON(list(userAgreement = userAgreement),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' user_agreements_update is a method defined in Arvados class.
+ #' @param userAgreement userAgreement object.
+ #' @param uuid The UUID of the userAgreement in question.
+ user_agreements_update = function(userAgreement, uuid)
+ {
+ endPoint <- stringr::str_interp("user_agreements/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ if(length(userAgreement) > 0)
+ body <- jsonlite::toJSON(list(userAgreement = userAgreement),
+ auto_unbox = TRUE)
+ else
+ body <- NULL
+
+ response <- private$REST$http$exec("PUT", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' user_agreements_delete is a method defined in Arvados class.
+ #' @param uuid The UUID of the userAgreement in question.
+ user_agreements_delete = function(uuid)
+ {
+ endPoint <- stringr::str_interp("user_agreements/${uuid}")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("DELETE", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' user_agreements_signatures is a method defined in Arvados class.
+ user_agreements_signatures = function()
+ {
+ endPoint <- stringr::str_interp("user_agreements/signatures")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' user_agreements_sign is a method defined in Arvados class.
+ user_agreements_sign = function()
+ {
+ endPoint <- stringr::str_interp("user_agreements/sign")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("POST", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' user_agreements_list is a method defined in Arvados class.
+ #' @param filters
+ #' @param where
+ #' @param order
+ #' @param select
+ #' @param distinct
+ #' @param limit
+ #' @param offset
+ #' @param count
+ #' @param clusterID List objects on a remote federated cluster instead of the current one.
+ #' @param bypassFederation Bypass federation behavior, list items from local instance database only.
+ user_agreements_list = function(filters = NULL,
+ where = NULL, order = NULL, select = NULL,
+ distinct = NULL, limit = "100", offset = "0",
+ count = "exact", clusterID = NULL, bypassFederation = NULL)
+ {
+ endPoint <- stringr::str_interp("user_agreements")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- list(filters = filters, where = where,
+ order = order, select = select, distinct = distinct,
+ limit = limit, offset = offset, count = count,
+ clusterID = clusterID, bypassFederation = bypassFederation)
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' user_agreements_new is a method defined in Arvados class.
+ user_agreements_new = function()
+ {
+ endPoint <- stringr::str_interp("user_agreements/new")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ #' @description
+ #' configs_get is a method defined in Arvados class.
+ configs_get = function()
+ {
+ endPoint <- stringr::str_interp("config")
+ url <- paste0(private$host, endPoint)
+ headers <- list(Authorization = paste("Bearer", private$token),
+ "Content-Type" = "application/json")
+ queryArgs <- NULL=
+
+ body <- NULL
+
+ response <- private$REST$http$exec("GET", url, headers, body,
+ queryArgs, private$numRetries)
+ resource <- private$REST$httpParser$parseJSONResponse(response)
+
+ if(!is.null(resource$errors))
+ stop(resource$errors)
+
+ resource
+ },
+
+ getHostName = function() private$host,
+ getToken = function() private$token,
+ setRESTService = function(newREST) private$REST <- newREST,
+ getRESTService = function() private$REST
+ ),
+
+ private = list(
+
+ token = NULL,
+ host = NULL,
+ REST = NULL,
+ numRetries = NULL
+ ),
+
+ cloneable = FALSE
)
+
+
diff --git a/sdk/R/R/ArvadosFile.R b/sdk/R/R/ArvadosFile.R
index fb1d3b335..938d12a7f 100644
--- a/sdk/R/R/ArvadosFile.R
+++ b/sdk/R/R/ArvadosFile.R
@@ -2,55 +2,10 @@
#
# SPDX-License-Identifier: Apache-2.0
-#' ArvadosFile
+#' R6 Class Representing a ArvadosFile
#'
+#' @description
#' ArvadosFile class represents a file inside Arvados collection.
-#'
-#' @section Usage:
-#' \preformatted{file = ArvadosFile$new(name)}
-#'
-#' @section Arguments:
-#' \describe{
-#' \item{name}{Name of the file.}
-#' }
-#'
-#' @section Methods:
-#' \describe{
-#' \item{getName()}{Returns name of the file.}
-#' \item{getRelativePath()}{Returns file path relative to the root.}
-#' \item{read(contentType = "raw", offset = 0, length = 0)}{Read file content.}
-#' \item{write(content, contentType = "text/html")}{Write to file (override current content of the file).}
-#' \item{connection(rw)}{Get connection opened in "read" or "write" mode.}
-#' \item{flush()}{Write connections content to a file (override current content of the file).}
-#' \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
-#' \item{getSizeInBytes()}{Returns file size in bytes.}
-#' \item{move(destination)}{Moves file to a new location inside collection.}
-#' \item{copy(destination)}{Copies file to a new location inside collection.}
-#' }
-#'
-#' @name ArvadosFile
-#' @examples
-#' \dontrun{
-#' myFile <- ArvadosFile$new("myFile")
-#'
-#' myFile$write("This is new file content")
-#' fileContent <- myFile$read()
-#' fileContent <- myFile$read("text")
-#' fileContent <- myFile$read("raw", offset = 8, length = 4)
-#'
-#' #Write a table:
-#' arvConnection <- myFile$connection("w")
-#' write.table(mytable, arvConnection)
-#' arvadosFile$flush()
-#'
-#' #Read a table:
-#' arvConnection <- myFile$connection("r")
-#' mytable <- read.table(arvConnection)
-#'
-#' myFile$move("newFolder/myFile")
-#' myFile$copy("newFolder/myFile")
-#' }
-NULL
#' @export
ArvadosFile <- R6::R6Class(
@@ -59,6 +14,12 @@ ArvadosFile <- R6::R6Class(
public = list(
+ #' @description
+ #' Initialize new enviroment.
+ #' @param name Name of the new enviroment.
+ #' @return A new `ArvadosFile` object.
+ #' @examples
+ #' myFile <- ArvadosFile$new("myFile")
initialize = function(name)
{
if(name == "")
@@ -67,13 +28,26 @@ ArvadosFile <- R6::R6Class(
private$name <- name
},
+ #' @description
+ #' Returns name of the file.
+ #' @examples
+ #' arvadosFile$getName()
getName = function() private$name,
+ #' @description
+ #' Returns collections file content as character vector.
+ #' @param fullPath Checking if TRUE.
+ #' @examples
+ #' arvadosFile$getFileListing()
getFileListing = function(fullpath = TRUE)
{
self$getName()
},
+ #' @description
+ #' Returns collections content size in bytes.
+ #' @examples
+ #' arvadosFile$getSizeInBytes()
getSizeInBytes = function()
{
if(is.null(private$collection))
@@ -96,13 +70,19 @@ ArvadosFile <- R6::R6Class(
return(NULL)
},
+ #' @description
+ #' Returns collection UUID.
getCollection = function() private$collection,
+ #' @description
+ #' Sets new collection.
setCollection = function(collection, setRecursively = TRUE)
{
private$collection <- collection
},
+ #' @description
+ #' Returns file path relative to the root.
getRelativePath = function()
{
relativePath <- c(private$name)
@@ -118,10 +98,23 @@ ArvadosFile <- R6::R6Class(
paste0(relativePath, collapse = "/")
},
+ #' @description
+ #' Returns project UUID.
getParent = function() private$parent,
+ #' @description
+ #' Sets project collection.
setParent = function(newParent) private$parent <- newParent,
+ #' @description
+ #' Read file content.
+ #' @param contentType Type of content. Possible is "text", "raw".
+ #' @param offset Describes the location of a piece of data compared to another location
+ #' @param length Length of content
+ #' @examples
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' arvadosFile <- collection$get(fileName)
+ #' fileContent <- arvadosFile$read("text")
read = function(contentType = "raw", offset = 0, length = 0)
{
if(is.null(private$collection))
@@ -138,6 +131,13 @@ ArvadosFile <- R6::R6Class(
fileContent
},
+ #' @description
+ #' Get connection opened in "read" or "write" mode.
+ #' @param rw Type of connection.
+ #' @examples
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' arvadosFile <- collection$get(fileName)
+ #' arvConnection <- arvadosFile$connection("w")
connection = function(rw)
{
if (rw == "r" || rw == "rb")
@@ -155,6 +155,13 @@ ArvadosFile <- R6::R6Class(
}
},
+ #' @description
+ #' Write connections content to a file or override current content of the file.
+ #' @examples
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' arvadosFile <- collection$get(fileName)
+ #' myFile$write("This is new file content")
+ #' arvadosFile$flush()
flush = function()
{
v <- textConnectionValue(private$buffer)
@@ -162,6 +169,14 @@ ArvadosFile <- R6::R6Class(
self$write(paste(v, collapse='\n'))
},
+ #' @description
+ #' Write to file or override current content of the file.
+ #' @param content File to write.
+ #' @param contentType Type of content. Possible is "text", "raw".
+ #' @examples
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' arvadosFile <- collection$get(fileName)
+ #' myFile$write("This is new file content")
write = function(content, contentType = "text/html")
{
if(is.null(private$collection))
@@ -175,6 +190,11 @@ ArvadosFile <- R6::R6Class(
writeResult
},
+ #' @description
+ #' Moves file to a new location inside collection.
+ #' @param destination Path to new folder.
+ #' @examples
+ #' arvadosFile$move(newPath)
move = function(destination)
{
if(is.null(private$collection))
@@ -207,6 +227,11 @@ ArvadosFile <- R6::R6Class(
self
},
+ #' @description
+ #' Copies file to a new location inside collection.
+ #' @param destination Path to new folder.
+ #' @examples
+ #' arvadosFile$copy("NewName.format")
copy = function(destination)
{
if(is.null(private$collection))
@@ -238,6 +263,9 @@ ArvadosFile <- R6::R6Class(
newFile
},
+ #' @description
+ #' Duplicate file and gives it a new name.
+ #' @param newName New name for duplicated file.
duplicate = function(newName = NULL)
{
name <- if(!is.null(newName)) newName else private$name
@@ -261,7 +289,10 @@ ArvadosFile <- R6::R6Class(
# We also need to set content's collection to NULL because
# add method throws exception if we try to add content that already
# belongs to a collection.
+
parentsCollection <- newParent$getCollection()
+ #parent$.__enclos_env__$private$children <- c(parent$.__enclos_env__$private$children, self)
+ #private$parent <- parent
content$setCollection(NULL, setRecursively = FALSE)
newParent$setCollection(NULL, setRecursively = FALSE)
newParent$add(content)
@@ -273,6 +304,9 @@ ArvadosFile <- R6::R6Class(
{
# We temporary set parents collection to NULL. This will ensure that
# remove method doesn't remove this file from REST.
+
+ #private$parent$.__enclos_env__$private$removeChild(private$name)
+ #private$parent <- NULL
parent <- private$parent
parentsCollection <- parent$getCollection()
parent$setCollection(NULL, setRecursively = FALSE)
diff --git a/sdk/R/R/ArvadosR.R b/sdk/R/R/ArvadosR.R
new file mode 100644
index 000000000..892053dba
--- /dev/null
+++ b/sdk/R/R/ArvadosR.R
@@ -0,0 +1,25 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+#' @title ArvadosR
+#'
+#' @description
+#' \if{html}{\figure{dax.png}{options: style='float: right' alt='logo' width='120'}}
+#'
+#' Arvados is an open source platform for managing, processing, and sharing genomic and other large scientific and biomedical data. With Arvados, bioinformaticians run and scale compute-intensive workflows, developers create biomedical applications, and IT administrators manage large compute and storage resources.
+#'
+#' @author \itemize{
+#' \item Lucas Di Pentima
+#' \item Ward Vandewege
+#' \item Fuad Muhic
+#' \item Peter Amstutz
+#' \item Aneta Stanczyk
+#' \item Piotr Nowosielski}
+#'
+#' @seealso \itemize{
+#' \item \code{\link{https://github.com/arvados/arvados/blob/main/README.md}}
+#' \item \code{\link{https://github.com/arvados/arvados/tree/main/sdk/R}}}
+#'
+#' @name ArvadosR
+NULL
diff --git a/sdk/R/R/Collection.R b/sdk/R/R/Collection.R
index 9ed758c0a..e362de604 100644
--- a/sdk/R/R/Collection.R
+++ b/sdk/R/R/Collection.R
@@ -2,62 +2,43 @@
#
# SPDX-License-Identifier: Apache-2.0
-#' Collection
+#' R6 Class Representing Arvados Collection
#'
-#' Collection class provides interface for working with Arvados collections.
+#' @description
+#' Collection class provides interface for working with Arvados collections,
+#' for exaplme actions like creating, updating, moving or removing are possible.
#'
-#' @section Usage:
-#' \preformatted{collection = Collection$new(arv, uuid)}
+#' @seealso
+#' \code{\link{https://github.com/arvados/arvados/tree/main/sdk/R}}
#'
-#' @section Arguments:
-#' \describe{
-#' \item{arv}{Arvados object.}
-#' \item{uuid}{UUID of a collection.}
-#' }
-#'
-#' @section Methods:
-#' \describe{
-#' \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.}
-#' \item{create(files)}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
-#' \item{remove(fileNames)}{Remove one or more files from the collection.}
-#' \item{move(content, destination)}{Moves ArvadosFile or Subcollection to another location in the collection.}
-#' \item{copy(content, destination)}{Copies ArvadosFile or Subcollection to another location in the collection.}
-#' \item{getFileListing()}{Returns collections file content as character vector.}
-#' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
-#' }
-#'
-#' @name Collection
-#' @examples
-#' \dontrun{
-#' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
-#' collection <- Collection$new(arv, "uuid")
-#'
-#' createdFiles <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
-#'
-#' collection$remove("location/to/my/file.cpp")
-#'
-#' collection$move("folder/file.cpp", "file.cpp")
-#'
-#' arvadosFile <- collection$get("location/to/my/file.cpp")
-#' arvadosSubcollection <- collection$get("location/to/my/directory/")
-#' }
-NULL
-
#' @export
+
Collection <- R6::R6Class(
"Collection",
public = list(
- uuid = NULL,
-
- initialize = function(api, uuid)
+ #' @field uuid Autentic for Collection UUID.
+ uuid = NULL,
+
+ #' @description
+ #' Initialize new enviroment.
+ #' @param api Arvados enviroment.
+ #' @param uuid The UUID Autentic for Collection UUID.
+ #' @return A new `Collection` object.
+ #' @examples
+ #' collection <- Collection$new(arv, CollectionUUID)
+ initialize = function(api, uuid)
{
private$REST <- api$getRESTService()
self$uuid <- uuid
},
+ #' @description
+ #' Adds ArvadosFile or Subcollection specified by content to the collection. Used only with ArvadosFile or Subcollection.
+ #' @param content Content to be added.
+ #' @param relativePath Path to add content.
add = function(content, relativePath = "")
{
if(is.null(private$tree))
@@ -98,6 +79,180 @@ Collection <- R6::R6Class(
}
},
+ #' @description
+ #' Read file content.
+ #' @param file Name of the file.
+ #' @param col Collection from which the file is read.
+ #' @param sep Separator used in reading tsv, csv file format.
+ #' @param istable Used in reading txt file to check if the file is table or not.
+ #' @param fileclass Used in reading fasta file to set file class.
+ #' @param Ncol Used in reading binary file to set numbers of columns in data.frame.
+ #' @param Nrow Used in reading binary file to set numbers of rows in data.frame size.
+ #' @examples
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' readFile <- collection$readArvFile(arvadosFile, istable = 'yes') # table
+ #' readFile <- collection$readArvFile(arvadosFile, istable = 'no') # text
+ #' readFile <- collection$readArvFile(arvadosFile) # xlsx, csv, tsv, rds, rdata
+ #' readFile <- collection$readArvFile(arvadosFile, fileclass = 'fasta') # fasta
+ #' readFile <- collection$readArvFile(arvadosFile, Ncol= 4, Nrow = 32) # binary, only numbers
+ #' readFile <- collection$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text
+ readArvFile = function(file, con, sep = ',', istable = NULL, fileclass = "SeqFastadna", Ncol = NULL, Nrow = NULL, wantedFunction = NULL)
+ {
+ arvFile <- self$get(file)
+ FileName <- arvFile$getName()
+ FileName <- tolower(FileName)
+ FileFormat <- gsub(".*\\.", "", FileName)
+
+ # set enviroment
+ ARVADOS_API_TOKEN <- Sys.getenv("ARVADOS_API_TOKEN")
+ ARVADOS_API_HOST <- Sys.getenv("ARVADOS_API_HOST")
+ my_collection <- self$uuid
+ key <- gsub("/", "_", ARVADOS_API_TOKEN)
+
+ Sys.setenv(
+ "AWS_ACCESS_KEY_ID" = key,
+ "AWS_SECRET_ACCESS_KEY" = key,
+ "AWS_DEFAULT_REGION" = "collections",
+ "AWS_S3_ENDPOINT" = gsub("api[.]", "", ARVADOS_API_HOST))
+
+ if (FileFormat == "txt") {
+ if (is.null(istable)){
+ stop(paste('You need to paste whether it is a text or table file'))
+ } else if (istable == 'no') {
+ fileContent <- arvFile$read("text") # used to read
+ fileContent <- gsub("[\r\n]", " ", fileContent)
+ } else if (istable == 'yes') {
+ arvConnection <- arvFile$connection("r") # used to make possible use different function later
+ fileContent <- read.table(arvConnection)
+ }
+ }
+ else if (FileFormat == "xlsx") {
+ fileContent <- aws.s3::s3read_using(FUN = openxlsx::read.xlsx, object = file, bucket = my_collection)
+ }
+ else if (FileFormat == "csv" || FileFormat == "tsv") {
+ arvConnection <- arvFile$connection("r")
+ if (FileFormat == "tsv"){
+ mytable <- read.table(arvConnection, sep = '\t')
+ } else if (FileFormat == "csv" & sep == '\t') {
+ mytable <- read.table(arvConnection, sep = '\t')
+ } else if (FileFormat == "csv") {
+ mytable <- read.table(arvConnection, sep = ',')
+ } else {
+ stop(paste('File format not supported, use arvadosFile$connection() and customise it'))
+ }
+ }
+ else if (FileFormat == "fasta") {
+ fastafile <- aws.s3::s3read_using(FUN = seqinr::read.fasta, as.string = TRUE, object = file, bucket = my_collection)
+ }
+ else if (FileFormat == "dat" || FileFormat == "bin") {
+ fileContent <- gzcon(arvFile$connection("rb"))
+
+ # function to precess data to binary format
+ read_bin.file <- function(fileContent) {
+ # read binfile
+ column.names <- readBin(fileContent, character(), n = Ncol)
+ bindata <- readBin(fileContent, numeric(), Nrow*Ncol+Ncol)
+ # check
+ res <- which(bindata < 0.0000001)
+ if (is.list(res)) {
+ bindata <- bindata[-res]
+ } else {
+ bindata <- bindata
+ }
+ # make a dataframe
+ data <- data.frame(matrix(data = NA, nrow = Nrow, ncol = Ncol))
+ for (i in 1:Ncol) {
+ data[,i] <- bindata[(1+Nrow*(i-1)):(Nrow*i)]
+ }
+ colnames(data) = column.names
+
+ len <- which(is.na(data[,Ncol])) # error if sth went wrong
+ if (length(len) == 0) {
+ data
+ } else {
+ stop(paste("there is a factor or text in the table, customize the function by typing more arguments"))
+ }
+ }
+ if (is.null(Nrow) | is.null(Ncol)){
+ stop(paste('You need to specify numbers of columns and rows'))
+ }
+ if (is.null(istable)) {
+ fileContent <- read_bin.file(fileContent) # call a function
+ } else if (istable == "factor") { # if there is a table with col name
+ fileContent <- read_bin.file(fileContent)
+ }
+ }
+ else if (FileFormat == "rds" || FileFormat == "rdata") {
+ arvConnection <- arvFile$connection("rb")
+ mytable <- readRDS(gzcon(arvConnection))
+ }
+ else {
+ stop(parse(('File format not supported, use arvadosFile$connection() and customise it')))
+ }
+ },
+
+ #' @description
+ #' Write file content
+ #' @param name Name of the file.
+ #' @param file File to be saved.
+ #' @param istable Used in writing txt file to check if the file is table or not.
+ #' @examples
+ #' collection <- Collection$new(arv, collectionUUID)
+ #' writeFile <- collection$writeFile("myoutput.csv", file, istable = NULL) # csv
+ #' writeFile <- collection$writeFile("myoutput.fasta", file, istable = NULL) # fasta
+ #' writeFile <- collection$writeFile("myoutputtable.txt", file, istable = "yes") # txt table
+ #' writeFile <- collection$writeFile("myoutputtext.txt", file, istable = "no") # txt text
+ #' writeFile <- collection$writeFile("myoutputbinary.dat", file) # binary
+ #' writeFile <- collection$writeFile("myoutputxlsx.xlsx", file) # xlsx
+ writeFile = function(name, file, istable = NULL, seqName = NULL)
+ {
+ # prepare file and connection
+ arvFile <- collection$create(name)[[1]]
+ arvFile <- collection$get(name)
+ arvConnection <- arvFile$connection("w")
+ # get file format
+ FileName <- arvFile$getName()
+ FileName <- tolower(FileName)
+ FileFormat <- gsub(".*\\.", "", FileName)
+
+ # set enviroment
+ ARVADOS_API_TOKEN <- Sys.getenv("ARVADOS_API_TOKEN")
+ ARVADOS_API_HOST <- Sys.getenv("ARVADOS_API_HOST")
+ my_collection <- self$uuid
+ key <- gsub("/", "_", ARVADOS_API_TOKEN)
+
+ Sys.setenv(
+ "AWS_ACCESS_KEY_ID" = key,
+ "AWS_SECRET_ACCESS_KEY" = key,
+ "AWS_DEFAULT_REGION" = "collections",
+ "AWS_S3_ENDPOINT" = gsub("api[.]", "", ARVADOS_API_HOST))
+
+ if (FileFormat == "txt") {
+ if (istable == "yes") {
+ aws.s3::s3write_using(file, FUN = write.table, object = name, bucket = my_collection)
+ } else if (istable == "no") {
+ aws.s3::s3write_using(file, FUN = writeChar, object = name, bucket = my_collection)
+ } else {
+ stop(paste("Specify parametr istable"))
+ }
+ } else if (FileFormat == "csv") {
+ aws.s3::s3write_using(file, FUN = write.csv, object = name, bucket = my_collection)
+ } else if (FileFormat == "fasta") {
+ aws.s3::s3write_using(file, FUN = seqinr::write.fasta, name = seqName, object = name, bucket = my_collection)
+ } else if (FileFormat == "xlsx") {
+ aws.s3::s3write_using(file, FUN = openxlsx::write.xlsx, object = name, bucket = my_collection)
+ } else if (FileFormat == "dat" || FileFormat == "bin") {
+ aws.s3::s3write_using(file, FUN = writeBin, object = name, bucket = my_collection)
+ } else {
+ stop(parse(('File format not supported, use arvadosFile$connection() and customise it')))
+ }
+ },
+
+ #' @description
+ #' Creates one or more ArvadosFiles and adds them to the collection at specified path.
+ #' @param files Content to be created.
+ #' @examples
+ #' collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))
create = function(files)
{
if(is.null(private$tree))
@@ -116,7 +271,7 @@ Collection <- R6::R6Class(
private$REST$create(file, self$uuid)
newTreeBranch$setCollection(self)
- newTreeBranch
+ newTreeBranch
})
}
else
@@ -127,6 +282,11 @@ Collection <- R6::R6Class(
}
},
+ #' @description
+ #' Remove one or more files from the collection.
+ #' @param paths Content to be removed.
+ #' @examples
+ #' collection$remove(fileName.format)
remove = function(paths)
{
if(is.null(private$tree))
@@ -160,6 +320,12 @@ Collection <- R6::R6Class(
}
},
+ #' @description
+ #' Moves ArvadosFile or Subcollection to another location in the collection.
+ #' @param content Content to be moved.
+ #' @param destination Path to move content.
+ #' @examples
+ #' collection$move("fileName.format", path)
move = function(content, destination)
{
if(is.null(private$tree))
@@ -175,6 +341,12 @@ Collection <- R6::R6Class(
elementToMove$move(destination)
},
+ #' @description
+ #' Copies ArvadosFile or Subcollection to another location in the collection.
+ #' @param content Content to be moved.
+ #' @param destination Path to move content.
+ #' @examples
+ #' copied <- collection$copy("oldName.format", "newName.format")
copy = function(content, destination)
{
if(is.null(private$tree))
@@ -190,6 +362,10 @@ Collection <- R6::R6Class(
elementToCopy$copy(destination)
},
+ #' @description
+ #' Refreshes the environment.
+ #' @examples
+ #' collection$refresh()
refresh = function()
{
if(!is.null(private$tree))
@@ -199,6 +375,10 @@ Collection <- R6::R6Class(
}
},
+ #' @description
+ #' Returns collections file content as character vector.
+ #' @examples
+ #' list <- collection$getFileListing()
getFileListing = function()
{
if(is.null(private$tree))
@@ -208,10 +388,15 @@ Collection <- R6::R6Class(
content[order(tolower(content))]
},
+ #' @description
+ #' If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.
+ #' @param relativePath Path from content is taken.
+ #' @examples
+ #' arvadosFile <- collection$get(fileName)
get = function(relativePath)
{
if(is.null(private$tree))
- private$generateCollectionTreeStructure()
+ private$generateCollectionTreeStructure(relativePath)
private$tree$getElement(relativePath)
},
@@ -219,14 +404,14 @@ Collection <- R6::R6Class(
getRESTService = function() private$REST,
setRESTService = function(newRESTService) private$REST <- newRESTService
),
-
private = list(
REST = NULL,
+ #' @tree beautiful tree of sth
tree = NULL,
fileContent = NULL,
- generateCollectionTreeStructure = function()
+ generateCollectionTreeStructure = function(relativePath = NULL)
{
if(is.null(self$uuid))
stop("Collection uuid is not defined.")
@@ -234,7 +419,7 @@ Collection <- R6::R6Class(
if(is.null(private$REST))
stop("REST service is not defined.")
- private$fileContent <- private$REST$getCollectionContent(self$uuid)
+ private$fileContent <- private$REST$getCollectionContent(self$uuid, relativePath)
private$tree <- CollectionTree$new(private$fileContent, self)
}
),
@@ -254,3 +439,10 @@ print.Collection = function(x, ...)
cat(paste0("Type: ", "\"", "Arvados Collection", "\""), sep = "\n")
cat(paste0("uuid: ", "\"", x$uuid, "\""), sep = "\n")
}
+
+
+
+
+
+
+
diff --git a/sdk/R/R/HttpRequest.R b/sdk/R/R/HttpRequest.R
index 18b36f968..4540902d2 100644
--- a/sdk/R/R/HttpRequest.R
+++ b/sdk/R/R/HttpRequest.R
@@ -30,7 +30,6 @@ HttpRequest <- R6::R6Class(
if(toString(Sys.getenv("ARVADOS_API_HOST_INSECURE") == "TRUE"))
config$options = list(ssl_verifypeer = 0L)
- # times = 1 regular call + numberOfRetries
response <- httr::RETRY(verb, url = url, body = body,
config = config, times = retryTimes + 1)
},
diff --git a/sdk/R/R/RESTService.R b/sdk/R/R/RESTService.R
index 9c65e7286..5cbcb65f7 100644
--- a/sdk/R/R/RESTService.R
+++ b/sdk/R/R/RESTService.R
@@ -110,10 +110,11 @@ RESTService <- R6::R6Class(
serverResponse
},
- getCollectionContent = function(uuid)
+ getCollectionContent = function(uuid, relativePath = NULL)
+
{
collectionURL <- URLencode(paste0(self$getWebDavHostName(),
- "c=", uuid))
+ "c=", uuid, "/", relativePath))
headers <- list("Authorization" = paste("Bearer", self$token))
@@ -227,8 +228,12 @@ RESTService <- R6::R6Class(
serverResponse <- self$http$exec("PUT", fileURL, headers, body,
retryTimes = self$numRetries)
- if(serverResponse$status_code < 200 || serverResponse$status_code >= 300)
- stop(paste("Server code:", serverResponse$status_code))
+ if (serverResponse$status_code < 200){ # to wyrzuca błędy
+ stop(paste("Server code:", serverResponse$status_code))}
+ else if (serverResponse$status_code >= 300 & serverResponse$status_code < 422) {
+ stop(paste("Server code:", serverResponse$status_code))}
+ else if (serverResponse$status_code == 422 ) {
+ stop(paste("Project of that name already exists. If you want to change it use project_update() instead"))}
paste("File created:", relativePath)
}
diff --git a/sdk/R/R/Subcollection.R b/sdk/R/R/Subcollection.R
index 981bd687a..752a39665 100644
--- a/sdk/R/R/Subcollection.R
+++ b/sdk/R/R/Subcollection.R
@@ -2,46 +2,11 @@
#
# SPDX-License-Identifier: Apache-2.0
-#' Subcollection
+#' R6 Class Representing a Subcollection
#'
+#' @description
#' Subcollection class represents a folder inside Arvados collection.
#' It is essentially a composite of arvadosFiles and other subcollections.
-#'
-#' @section Usage:
-#' \preformatted{subcollection = Subcollection$new(name)}
-#'
-#' @section Arguments:
-#' \describe{
-#' \item{name}{Name of the subcollection.}
-#' }
-#'
-#' @section Methods:
-#' \describe{
-#' \item{getName()}{Returns name of the subcollection.}
-#' \item{getRelativePath()}{Returns subcollection path relative to the root.}
-#' \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the subcollection.}
-#' \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
-#' \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
-#' \item{getFileListing()}{Returns subcollections file content as character vector.}
-#' \item{getSizeInBytes()}{Returns subcollections content size in bytes.}
-#' \item{move(destination)}{Moves subcollection to a new location inside collection.}
-#' \item{copy(destination)}{Copies subcollection to a new location inside collection.}
-#' }
-#'
-#' @name Subcollection
-#' @examples
-#' \dontrun{
-#' myFolder <- Subcollection$new("myFolder")
-#' myFile <- ArvadosFile$new("myFile")
-#'
-#' myFolder$add(myFile)
-#' myFolder$get("myFile")
-#' myFolder$remove("myFile")
-#'
-#' myFolder$move("newLocation/myFolder")
-#' myFolder$copy("newLocation/myFolder")
-#' }
-NULL
#' @export
Subcollection <- R6::R6Class(
@@ -50,13 +15,21 @@ Subcollection <- R6::R6Class(
public = list(
+ #' @description
+ #' Initialize new enviroment.
+ #' @param name Name of the new enviroment.
+ #' @return A new `Subcollection` object.
initialize = function(name)
{
private$name <- name
},
+ #' @description
+ #' Returns name of the file.
getName = function() private$name,
+ #' @description
+ #' Returns Subcollection's path relative to the root.
getRelativePath = function()
{
relativePath <- c(private$name)
@@ -72,6 +45,9 @@ Subcollection <- R6::R6Class(
paste0(relativePath, collapse = "/")
},
+ #' @description
+ #' Adds ArvadosFile or Subcollection specified by content to the Subcollection.
+ #' @param content Content to be added.
add = function(content)
{
if("ArvadosFile" %in% class(content) ||
@@ -115,6 +91,9 @@ Subcollection <- R6::R6Class(
}
},
+ #' @description
+ #' Removes ArvadosFile or Subcollection specified by name from the Subcollection.
+ #' @param name Name of the file to be removed.
remove = function(name)
{
if(is.character(name))
@@ -146,12 +125,17 @@ Subcollection <- R6::R6Class(
}
},
+ #' @description
+ #' Returns Subcollections file content as character vector.
+ #' @param fullPath Checking if the path to file exists.
getFileListing = function(fullPath = TRUE)
{
content <- private$getContentAsCharVector(fullPath)
content[order(tolower(content))]
},
+ #' @description
+ #' Returns subcollections content size in bytes.
getSizeInBytes = function()
{
if(is.null(private$collection))
@@ -164,6 +148,9 @@ Subcollection <- R6::R6Class(
return(sum(fileSizes))
},
+ #' @description
+ #' Moves Subcollection to a new location inside collection.
+ #' @param destination Path to move the file.
move = function(destination)
{
if(is.null(private$collection))
@@ -196,6 +183,9 @@ Subcollection <- R6::R6Class(
self
},
+ #' @description
+ #' Copies Subcollection to a new location inside collection.
+ #' @param destination Path to copy the file.
copy = function(destination)
{
if(is.null(private$collection))
@@ -227,6 +217,9 @@ Subcollection <- R6::R6Class(
newContent
},
+ #' @description
+ #' Duplicate Subcollection and gives it a new name.
+ #' @param newName New name for duplicated file.
duplicate = function(newName = NULL)
{
name <- if(!is.null(newName)) newName else private$name
@@ -237,6 +230,9 @@ Subcollection <- R6::R6Class(
root
},
+ #' @description
+ #' If name is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.
+ #' @param name Name of the file.
get = function(name)
{
for(child in private$children)
@@ -248,14 +244,18 @@ Subcollection <- R6::R6Class(
return(NULL)
},
+ #' @description
+ #' Returns files in Subcollection.
getFirst = function()
{
if(length(private$children) == 0)
- return(NULL)
+ return(NULL)
private$children[[1]]
},
+ #' @description
+ #' Sets Collection by its UUID.
setCollection = function(collection, setRecursively = TRUE)
{
private$collection = collection
@@ -267,10 +267,16 @@ Subcollection <- R6::R6Class(
}
},
+ #' @description
+ #' Returns Collection of Subcollection.
getCollection = function() private$collection,
+ #' @description
+ #' Returns Collection UUID.
getParent = function() private$parent,
+ #' @description
+ #' Sets new Collection.
setParent = function(newParent) private$parent <- newParent
),
diff --git a/sdk/R/README.Rmd b/sdk/R/README.Rmd
deleted file mode 100644
index 8cc89d902..000000000
--- a/sdk/R/README.Rmd
+++ /dev/null
@@ -1,339 +0,0 @@
-[comment]: # (Copyright (c) The Arvados Authors. All rights reserved.)
-[comment]: # ()
-[comment]: # (SPDX-License-Identifier: CC-BY-SA-3.0)
-
-## R SDK for Arvados
-
-This SDK focuses on providing support for accessing Arvados projects, collections, and the files within collections.
-The API is not final and feedback is solicited from users on ways in which it could be improved.
-
-### Installation
-
-```{r include=FALSE}
-knitr::opts_chunk$set(eval=FALSE)
-```
-
-```{r}
-install.packages("ArvadosR", repos=c("https://r.arvados.org", getOption("repos")["CRAN"]), dependencies=TRUE)
-```
-
-Note: on Linux, you may have to install supporting packages.
-
-On Centos 7, this is:
-
-```{bash}
-yum install libxml2-devel openssl-devel curl-devel
-```
-
-On Debian, this is:
-
-```{bash}
-apt-get install build-essential libxml2-dev libssl-dev libcurl4-gnutls-dev
-```
-
-Minimum R version required to run ArvadosR is 3.3.0.
-
-
-### Usage
-
-#### Initializing API
-
-* Load Library and Initialize API:
-
-```{r}
-library('ArvadosR')
-# use environment variables ARVADOS_API_TOKEN and ARVADOS_API_HOST
-arv <- Arvados$new()
-
-# provide them explicitly
-arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
-```
-
-Optionally, add numRetries parameter to specify number of times to retry failed service requests.
-Default is 0.
-
-```{r}
-arv <- Arvados$new("your Arvados token", "example.arvadosapi.com", numRetries = 3)
-```
-
-This parameter can be set at any time using setNumRetries
-
-```{r}
-arv$setNumRetries(5)
-```
-
-
-#### Working with collections
-
-* Get a collection:
-
-```{r}
-collection <- arv$collections.get("uuid")
-```
-
-Be aware that the result from `collections.get` is _not_ a
-`Collection` class. The object returned from this method lets you
-access collection fields like "name" and "description". The
-`Collection` class lets you access the files in the collection for
-reading and writing, and is described in the next section.
-
-* List collections:
-
-```{r}
-# offset of 0 and default limit of 100
-collectionList <- arv$collections.list(list(list("name", "like", "Test%")))
-
-collectionList <- arv$collections.list(list(list("name", "like", "Test%")), limit = 10, offset = 2)
-
-# count of total number of items (may be more than returned due to paging)
-collectionList$items_available
-
-# items which match the filter criteria
-collectionList$items
-```
-
-* List all collections even if the number of items is greater than maximum API limit:
-
-```{r}
-collectionList <- listAll(arv$collections.list, list(list("name", "like", "Test%")))
-```
-
-* Delete a collection:
-
-```{r}
-deletedCollection <- arv$collections.delete("uuid")
-```
-
-* Update a collection's metadata:
-
-```{r}
-updatedCollection <- arv$collections.update(list(name = "New name", description = "New description"), "uuid")
-```
-
-* Create a new collection:
-
-```{r}
-newCollection <- arv$collections.create(list(name = "Example", description = "This is a test collection"))
-```
-
-
-#### Manipulating collection content
-
-* Initialize a collection object:
-
-```{r}
-collection <- Collection$new(arv, "uuid")
-```
-
-* Get list of files:
-
-```{r}
-files <- collection$getFileListing()
-```
-
-* Get ArvadosFile or Subcollection from internal tree-like structure:
-
-```{r}
-arvadosFile <- collection$get("location/to/my/file.cpp")
-```
-
-or
-
-```{r}
-arvadosSubcollection <- collection$get("location/to/my/directory/")
-```
-
-* Read a table:
-
-```{r}
-arvadosFile <- collection$get("myinput.txt")
-arvConnection <- arvadosFile$connection("r")
-mytable <- read.table(arvConnection)
-```
-
-* Write a table:
-
-```{r}
-arvadosFile <- collection$create("myoutput.txt")[[1]]
-arvConnection <- arvadosFile$connection("w")
-write.table(mytable, arvConnection)
-arvadosFile$flush()
-```
-
-* Write to existing file (overwrites current content of the file):
-
-```{r}
-arvadosFile <- collection$get("location/to/my/file.cpp")
-arvadosFile$write("This is new file content")
-```
-
-* Read whole file or just a portion of it:
-
-```{r}
-fileContent <- arvadosFile$read()
-fileContent <- arvadosFile$read("text")
-fileContent <- arvadosFile$read("raw", offset = 1024, length = 512)
-```
-
-* Get ArvadosFile or Subcollection size:
-
-```{r}
-size <- arvadosFile$getSizeInBytes()
-```
-
-or
-
-```{r}
-size <- arvadosSubcollection$getSizeInBytes()
-```
-
-* Create new file in a collection (returns a vector of one or more ArvadosFile objects):
-
-```{r}
-collection$create(files)
-```
-
-Example:
-
-```{r}
-mainFile <- collection$create("cpp/src/main.cpp")[[1]]
-fileList <- collection$create(c("cpp/src/main.cpp", "cpp/src/util.h"))
-```
-
-* Delete file from a collection:
-
-```{r}
-collection$remove("location/to/my/file.cpp")
-```
-
-You can remove both Subcollection and ArvadosFile.
-If subcollection contains more files or folders they will be removed recursively.
-
-You can also remove multiple files at once:
-
-```{r}
-collection$remove(c("path/to/my/file.cpp", "path/to/other/file.cpp"))
-```
-
-* Delete file or folder from a Subcollection:
-
-```{r}
-subcollection <- collection$get("mySubcollection/")
-subcollection$remove("fileInsideSubcollection.exe")
-subcollection$remove("folderInsideSubcollection/")
-```
-
-* Move or rename a file or folder within a collection (moving between collections is currently not supported):
-
-Directly from collection
-
-```{r}
-collection$move("folder/file.cpp", "file.cpp")
-```
-
-Or from file
-
-```{r}
-file <- collection$get("location/to/my/file.cpp")
-file$move("newDestination/file.cpp")
-```
-
-Or from subcollection
-
-```{r}
-subcollection <- collection$get("location/to/folder")
-subcollection$move("newDestination/folder")
-```
-
-Make sure to include new file name in destination.
-In second example file$move("newDestination/") will not work.
-
-* Copy file or folder within a collection (copying between collections is currently not supported):
-
-Directly from collection
-
-```{r}
-collection$copy("folder/file.cpp", "file.cpp")
-```
-
-Or from file
-
-```{r}
-file <- collection$get("location/to/my/file.cpp")
-file$copy("destination/file.cpp")
-```
-
-Or from subcollection
-
-```{r}
-subcollection <- collection$get("location/to/folder")
-subcollection$copy("destination/folder")
-```
-
-#### Working with Aravdos projects
-
-* Get a project:
-
-```{r}
-project <- arv$projects.get("uuid")
-```
-
-* List projects:
-
-```{r}
-list subprojects of a project
-projects <- arv$projects.list(list(list("owner_uuid", "=", "aaaaa-j7d0g-ccccccccccccccc")))
-
-list projects which have names beginning with Example
-examples <- arv$projects.list(list(list("name","like","Example%")))
-```
-
-* List all projects even if the number of items is greater than maximum API limit:
-
-```{r}
-projects <- listAll(arv$projects.list, list(list("name","like","Example%")))
-```
-
-* Delete a project:
-
-```{r}
-deletedProject <- arv$projects.delete("uuid")
-```
-
-* Update project:
-
-```{r}
-updatedProject <- arv$projects.update(list(name = "new_name", description = "new description"), "uuid")
-```
-
-* Create project:
-
-```{r}
-newProject <- arv$projects.update(list(name = "project_name", description = "project description"))
-```
-
-#### Help
-
-* View help page of Arvados classes by puting ? before class name:
-
-```{r}
-?Arvados
-?Collection
-?Subcollection
-?ArvadosFile
-```
-
-* View help page of any method defined in Arvados class by puting ? before method name:
-
-```{r}
-?collections.update
-?jobs.get
-```
-
-### Building the ArvadosR package
-
-```{bash}
-cd arvados/sdk && R CMD build R
-```
-
-This will create a tarball of the ArvadosR package in the current directory.
diff --git a/sdk/R/README.md b/sdk/R/README.md
new file mode 100644
index 000000000..5f7a11748
--- /dev/null
+++ b/sdk/R/README.md
@@ -0,0 +1,293 @@
+[comment]: # (Copyright © The Arvados Authors. All rights reserved.)
+[comment]: # ()
+[comment]: # (SPDX-License-Identifier: CC-BY-SA-3.0)
+
+# R SDK for Arvados <img align="right" src="man/figures/dax.png" height="240px">
+
+This SDK focuses on providing support for accessing Arvados projects, collections, and the files within collections. The API is not final and feedback is solicited from users on ways in which it could be improved.
+
+## Why Arvados?
+* Memory efficient
+* Availability
+* Many available workflows
+* Transparent
+* Fast-developing
+
+## Key Topics
+* Installation
+* Usage
+ * Initializing API
+ * Working with collections
+ * Manipulating collection content
+ * Working with Arvados projects
+ * Help
+* Building the ArvadosR package
+
+## Installation
+
+Minimum R version required to run ArvadosR is 3.3.0.
+
+```r
+install.packages("ArvadosR", repos=c("https://r.arvados.org", getOption("repos")["CRAN"]), dependencies=TRUE)
+library('ArvadosR')
+```
+
+> **Note**
+> On Linux, you may have to install supporting packages.
+>
+> On Centos 7, this is:
+> ```r
+> yum install libxml2-devel openssl-devel curl-devel
+> ```
+> On Debian, this is:
+> ```r
+> apt-get install build-essential libxml2-dev libssl-dev libcurl4-gnutls-dev
+> ```
+
+
+## Usage
+### Initializing API
+```r
+# use environment variables ARVADOS_API_TOKEN and ARVADOS_API_HOST
+arv <- Arvados$new()
+
+# provide them explicitly
+arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
+```
+Optionally, add `numRetries` parameter to specify number of times to retry failed service requests. Default is 0.
+```r
+arv <- Arvados$new("your Arvados token", "example.arvadosapi.com", numRetries = 3)
+```
+This parameter can be set at any time using `setNumRetries`
+```r
+arv$setNumRetries(5)
+```
+### Working with collections
+##### Get a collection:
+```r
+collection <- arv$collections_get("uuid")
+```
+Be aware that the result from `collections_get` is not a Collection class. The object returned from this method lets you access collection fields like “name” and “description”. The Collection class lets you access the files in the collection for reading and writing, and is described in the next section.
+##### List collections:
+```r
+# offset of 0 and default limit of 100
+collectionList <- arv$collections_list(list(list("name", "like", "Test%")))
+
+collectionList <- arv$collections_list(list(list("name", "like", "Test%")), limit = 10, offset = 2)
+
+# count of total number of items (may be more than returned due to paging)
+collectionList$items_available
+
+# items which match the filter criteria
+collectionList$items
+```
+##### List all collections even if the number of items is greater than maximum API limit:
+```r
+collectionList <- listAll(arv$collections_list, list(list("name", "like", "Test%")))
+```
+##### Delete a collection:
+```r
+deletedCollection <- arv$collections_delete("uuid")
+```
+##### Update a collection’s metadata:
+```r
+collection <- arv$collections_update(name = "newCollectionTitle", description = "newCollectionDescription", ownerUUID = "collectionOwner", properties = NULL, uuid = "collectionUUID")
+```
+##### Create a new collection:
+```r
+newCollection <- arv$collections_create(name = "collectionTitle", description = "collectionDescription", ownerUUID = "collectionOwner", properties = Properties)
+```
+### Manipulating collection content
+##### Initialize a collection object:
+```r
+collection <- Collection$new(arv, "uuid")
+```
+##### Get list of files:
+```r
+files <- collection$getFileListing()
+```
+##### Get ArvadosFile or Subcollection from internal tree-like structure:
+```r
+arvadosFile <- collection$get("location/to/my/file.cpp")
+# or
+arvadosSubcollection <- collection$get("location/to/my/directory/")
+```
+##### Read a table:
+```r
+arvadosFile <- collection$get("myinput.txt")
+arvConnection <- arvadosFile$connection("r")
+mytable <- read.table(arvConnection)
+```
+##### Write a table:
+```r
+arvadosFile <- collection$create("myoutput.txt")[[1]]
+arvConnection <- arvadosFile$connection("w")
+write.table(mytable, arvConnection)
+arvadosFile$flush()
+```
+##### Write to existing file (overwrites current content of the file):
+```r
+arvadosFile <- collection$get("location/to/my/file.cpp")
+arvadosFile$write("This is new file content")
+```
+##### Read whole file or just a portion of it:
+```r
+fileContent <- arvadosFile$read()
+fileContent <- arvadosFile$read("text")
+fileContent <- arvadosFile$read("raw", offset = 1024, length = 512)
+```
+##### Get ArvadosFile or Subcollection size:
+```r
+size <- arvadosFile$getSizeInBytes()
+# or
+size <- arvadosSubcollection$getSizeInBytes()
+```
+##### Create new file in a collection (returns a vector of one or more ArvadosFile objects):
+```r
+collection$create(files)
+```
+> **Example**
+> ```r
+> mainFile <- collection$create("cpp/src/main.cpp")[[1]]
+> fileList <- collection$create(c("cpp/src/main.cpp", "cpp/src/util.h"))
+> ```
+##### Delete file from a collection:
+```r
+collection$remove("location/to/my/file.cpp")
+```
+You can remove both Subcollection and ArvadosFile. If subcollection contains more files or folders they will be removed recursively.
+
+> **Note**
+> You can also remove multiple files at once:
+> ```r
+> collection$remove(c("path/to/my/file.cpp", "path/to/other/file.cpp"))
+> ```
+
+##### Delete file or folder from a Subcollection:
+```r
+subcollection <- collection$get("mySubcollection/")
+subcollection$remove("fileInsideSubcollection.exe")
+subcollection$remove("folderInsideSubcollection/")
+```
+##### Move or rename a file or folder within a collection (moving between collections is currently not supported):
+###### Directly from collection
+```r
+collection$move("folder/file.cpp", "file.cpp")
+```
+###### Or from file
+```r
+file <- collection$get("location/to/my/file.cpp")
+file$move("newDestination/file.cpp")
+```
+###### Or from subcollection
+```r
+subcollection <- collection$get("location/to/folder")
+subcollection$move("newDestination/folder")
+```
+> **Note**
+> Make sure to include new file name in destination. In second example `file$move(“newDestination/”)` will not work.
+##### Copy file or folder within a collection (copying between collections is currently not supported):
+###### Directly from collection
+```r
+collection$copy("folder/file.cpp", "file.cpp")
+```
+###### Or from file
+```r
+file <- collection$get("location/to/my/file.cpp")
+file$copy("destination/file.cpp")
+```
+###### Or from subcollection
+```r
+subcollection <- collection$get("location/to/folder")
+subcollection$copy("destination/folder")
+```
+### Working with Aravdos projects
+##### Get a project:
+```r
+project <- arv$project_get("uuid")
+```
+##### List projects:
+```r
+list subprojects of a project
+projects <- arv$project_list(list(list("owner_uuid", "=", "aaaaa-j7d0g-ccccccccccccccc")))
+
+list projects which have names beginning with Example
+examples <- arv$project_list(list(list("name","like","Example%")))
+```
+##### List all projects even if the number of items is greater than maximum API limit:
+```r
+projects <- listAll(arv$project_list, list(list("name","like","Example%")))
+```
+###### Delete a project:
+```r
+deletedProject <- arv$project_delete("uuid")
+```
+###### Update project:
+```r
+updatedProject <- arv$project_update(name = "new project name", properties = newProperties, uuid = "projectUUID")
+```
+###### Create project:
+```r
+newProject <- arv$project_create(name = "project name", description = "project description", owner_uuid = "project UUID", properties = NULL, ensureUniqueName = "false")
+```
+### Help
+##### View help page of Arvados classes by puting `?` before class name:
+```r
+?Arvados
+?Collection
+?Subcollection
+?ArvadosFile
+```
+##### View help page of any method defined in Arvados class by puting `?` before method name:
+```r
+?collections_update
+?jobs_get
+```
+
+ <!-- Taka konwencja USAGE -->
+
+ ## Building the ArvadosR package
+ ```r
+cd arvados/sdk && R CMD build R
+```
+This will create a tarball of the ArvadosR package in the current directory.
+
+
+ <!-- Czy dodawać Documentation / Community / Development and Contributing / Licensing? Ale tylko do części Rowej? Wszystko? Wcale? -->
+## Documentation
+
+Complete documentation, including the [User Guide](https://doc.arvados.org/user/index.html), [Installation documentation](https://doc.arvados.org/install/index.html), [Administrator documentation](https://doc.arvados.org/admin/index.html) and
+[API documentation](https://doc.arvados.org/api/index.html) is available at http://doc.arvados.org/
+
+If you wish to build the Arvados documentation from a local git clone, see
+[doc/README.textile](doc/README.textile) for instructions.
+
+## Community
+
+[](https://gitter.im/arvados/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+
+The [Arvados community channel](https://gitter.im/arvados/community)
+channel at [gitter.im](https://gitter.im) is available for live
+discussion and support.
+
+The [Arvados developement channel](https://gitter.im/arvados/development)
+channel at [gitter.im](https://gitter.im) is used to coordinate development.
+
+The [Arvados user mailing list](http://lists.arvados.org/mailman/listinfo/arvados)
+is used to announce new versions and other news.
+
+All participants are expected to abide by the [Arvados Code of Conduct](CODE_OF_CONDUCT.md).
+
+## Reporting bugs
+
+[Report a bug](https://dev.arvados.org/projects/arvados/issues/new) on [dev.arvados.org](https://dev.arvados.org).
+
+## Development and Contributing
+
+See [CONTRIBUTING](CONTRIBUTING.md) for information about Arvados development and how to contribute to the Arvados project.
+
+The [development road map](https://dev.arvados.org/issues/gantt?utf8=%E2%9C%93&set_filter=1&gantt=1&f%5B%5D=project_id&op%5Bproject_id%5D=%3D&v%5Bproject_id%5D%5B%5D=49&f%5B%5D=&zoom=1) outlines some of the project priorities over the next twelve months.
+
+## Licensing
+
+Arvados is Free Software. See [COPYING](COPYING) for information about the open source licenses used in Arvados.
diff --git a/sdk/R/man/Arvados.Rd b/sdk/R/man/Arvados.Rd
index b55dd00dc..d028d0a07 100644
--- a/sdk/R/man/Arvados.Rd
+++ b/sdk/R/man/Arvados.Rd
@@ -1,206 +1,2911 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{Arvados}
-\alias{Arvados}
-\title{Arvados}
-\description{
-Arvados class gives users ability to access Arvados REST API.
-}
-\section{Usage}{
-
-\preformatted{arv = Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)}
-}
-
-\section{Arguments}{
-
-\describe{
- \item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.}
- \item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.}
- \item{numRetries}{Number which specifies how many times to retry failed service requests.}
-}
-}
-
-\section{Methods}{
-
-\describe{
- \item{}{\code{\link{api_client_authorizations.create}}}
- \item{}{\code{\link{api_client_authorizations.create_system_auth}}}
- \item{}{\code{\link{api_client_authorizations.current}}}
- \item{}{\code{\link{api_client_authorizations.delete}}}
- \item{}{\code{\link{api_client_authorizations.get}}}
- \item{}{\code{\link{api_client_authorizations.list}}}
- \item{}{\code{\link{api_client_authorizations.update}}}
- \item{}{\code{\link{api_clients.create}}}
- \item{}{\code{\link{api_clients.delete}}}
- \item{}{\code{\link{api_clients.get}}}
- \item{}{\code{\link{api_clients.list}}}
- \item{}{\code{\link{api_clients.update}}}
- \item{}{\code{\link{authorized_keys.create}}}
- \item{}{\code{\link{authorized_keys.delete}}}
- \item{}{\code{\link{authorized_keys.get}}}
- \item{}{\code{\link{authorized_keys.list}}}
- \item{}{\code{\link{authorized_keys.update}}}
- \item{}{\code{\link{collections.create}}}
- \item{}{\code{\link{collections.delete}}}
- \item{}{\code{\link{collections.get}}}
- \item{}{\code{\link{collections.list}}}
- \item{}{\code{\link{collections.provenance}}}
- \item{}{\code{\link{collections.trash}}}
- \item{}{\code{\link{collections.untrash}}}
- \item{}{\code{\link{collections.update}}}
- \item{}{\code{\link{collections.used_by}}}
- \item{}{\code{\link{container_requests.create}}}
- \item{}{\code{\link{container_requests.delete}}}
- \item{}{\code{\link{container_requests.get}}}
- \item{}{\code{\link{container_requests.list}}}
- \item{}{\code{\link{container_requests.update}}}
- \item{}{\code{\link{containers.auth}}}
- \item{}{\code{\link{containers.create}}}
- \item{}{\code{\link{containers.current}}}
- \item{}{\code{\link{containers.delete}}}
- \item{}{\code{\link{containers.get}}}
- \item{}{\code{\link{containers.list}}}
- \item{}{\code{\link{containers.lock}}}
- \item{}{\code{\link{containers.secret_mounts}}}
- \item{}{\code{\link{containers.unlock}}}
- \item{}{\code{\link{containers.update}}}
- \item{}{\code{\link{groups.contents}}}
- \item{}{\code{\link{groups.create}}}
- \item{}{\code{\link{groups.delete}}}
- \item{}{\code{\link{groups.get}}}
- \item{}{\code{\link{groups.list}}}
- \item{}{\code{\link{groups.trash}}}
- \item{}{\code{\link{groups.untrash}}}
- \item{}{\code{\link{groups.update}}}
- \item{}{\code{\link{humans.create}}}
- \item{}{\code{\link{humans.delete}}}
- \item{}{\code{\link{humans.get}}}
- \item{}{\code{\link{humans.list}}}
- \item{}{\code{\link{humans.update}}}
- \item{}{\code{\link{jobs.cancel}}}
- \item{}{\code{\link{jobs.create}}}
- \item{}{\code{\link{jobs.delete}}}
- \item{}{\code{\link{jobs.get}}}
- \item{}{\code{\link{jobs.list}}}
- \item{}{\code{\link{jobs.lock}}}
- \item{}{\code{\link{jobs.queue}}}
- \item{}{\code{\link{jobs.queue_size}}}
- \item{}{\code{\link{jobs.update}}}
- \item{}{\code{\link{job_tasks.create}}}
- \item{}{\code{\link{job_tasks.delete}}}
- \item{}{\code{\link{job_tasks.get}}}
- \item{}{\code{\link{job_tasks.list}}}
- \item{}{\code{\link{job_tasks.update}}}
- \item{}{\code{\link{keep_disks.create}}}
- \item{}{\code{\link{keep_disks.delete}}}
- \item{}{\code{\link{keep_disks.get}}}
- \item{}{\code{\link{keep_disks.list}}}
- \item{}{\code{\link{keep_disks.ping}}}
- \item{}{\code{\link{keep_disks.update}}}
- \item{}{\code{\link{keep_services.accessible}}}
- \item{}{\code{\link{keep_services.create}}}
- \item{}{\code{\link{keep_services.delete}}}
- \item{}{\code{\link{keep_services.get}}}
- \item{}{\code{\link{keep_services.list}}}
- \item{}{\code{\link{keep_services.update}}}
- \item{}{\code{\link{links.create}}}
- \item{}{\code{\link{links.delete}}}
- \item{}{\code{\link{links.get}}}
- \item{}{\code{\link{links.get_permissions}}}
- \item{}{\code{\link{links.list}}}
- \item{}{\code{\link{links.update}}}
- \item{}{\code{\link{logs.create}}}
- \item{}{\code{\link{logs.delete}}}
- \item{}{\code{\link{logs.get}}}
- \item{}{\code{\link{logs.list}}}
- \item{}{\code{\link{logs.update}}}
- \item{}{\code{\link{nodes.create}}}
- \item{}{\code{\link{nodes.delete}}}
- \item{}{\code{\link{nodes.get}}}
- \item{}{\code{\link{nodes.list}}}
- \item{}{\code{\link{nodes.ping}}}
- \item{}{\code{\link{nodes.update}}}
- \item{}{\code{\link{pipeline_instances.cancel}}}
- \item{}{\code{\link{pipeline_instances.create}}}
- \item{}{\code{\link{pipeline_instances.delete}}}
- \item{}{\code{\link{pipeline_instances.get}}}
- \item{}{\code{\link{pipeline_instances.list}}}
- \item{}{\code{\link{pipeline_instances.update}}}
- \item{}{\code{\link{pipeline_templates.create}}}
- \item{}{\code{\link{pipeline_templates.delete}}}
- \item{}{\code{\link{pipeline_templates.get}}}
- \item{}{\code{\link{pipeline_templates.list}}}
- \item{}{\code{\link{pipeline_templates.update}}}
- \item{}{\code{\link{projects.create}}}
- \item{}{\code{\link{projects.delete}}}
- \item{}{\code{\link{projects.get}}}
- \item{}{\code{\link{projects.list}}}
- \item{}{\code{\link{projects.update}}}
- \item{}{\code{\link{repositories.create}}}
- \item{}{\code{\link{repositories.delete}}}
- \item{}{\code{\link{repositories.get}}}
- \item{}{\code{\link{repositories.get_all_permissions}}}
- \item{}{\code{\link{repositories.list}}}
- \item{}{\code{\link{repositories.update}}}
- \item{}{\code{\link{specimens.create}}}
- \item{}{\code{\link{specimens.delete}}}
- \item{}{\code{\link{specimens.get}}}
- \item{}{\code{\link{specimens.list}}}
- \item{}{\code{\link{specimens.update}}}
- \item{}{\code{\link{traits.create}}}
- \item{}{\code{\link{traits.delete}}}
- \item{}{\code{\link{traits.get}}}
- \item{}{\code{\link{traits.list}}}
- \item{}{\code{\link{traits.update}}}
- \item{}{\code{\link{user_agreements.create}}}
- \item{}{\code{\link{user_agreements.delete}}}
- \item{}{\code{\link{user_agreements.get}}}
- \item{}{\code{\link{user_agreements.list}}}
- \item{}{\code{\link{user_agreements.new}}}
- \item{}{\code{\link{user_agreements.sign}}}
- \item{}{\code{\link{user_agreements.signatures}}}
- \item{}{\code{\link{user_agreements.update}}}
- \item{}{\code{\link{users.activate}}}
- \item{}{\code{\link{users.create}}}
- \item{}{\code{\link{users.current}}}
- \item{}{\code{\link{users.delete}}}
- \item{}{\code{\link{users.get}}}
- \item{}{\code{\link{users.list}}}
- \item{}{\code{\link{users.merge}}}
- \item{}{\code{\link{users.setup}}}
- \item{}{\code{\link{users.system}}}
- \item{}{\code{\link{users.unsetup}}}
- \item{}{\code{\link{users.update}}}
- \item{}{\code{\link{virtual_machines.create}}}
- \item{}{\code{\link{virtual_machines.delete}}}
- \item{}{\code{\link{virtual_machines.get}}}
- \item{}{\code{\link{virtual_machines.get_all_logins}}}
- \item{}{\code{\link{virtual_machines.list}}}
- \item{}{\code{\link{virtual_machines.logins}}}
- \item{}{\code{\link{virtual_machines.update}}}
- \item{}{\code{\link{workflows.create}}}
- \item{}{\code{\link{workflows.delete}}}
- \item{}{\code{\link{workflows.get}}}
- \item{}{\code{\link{workflows.list}}}
- \item{}{\code{\link{workflows.update}}}
-}
-}
-
-\examples{
-\dontrun{
-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"))
-}
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Arvados.R
+\name{Arvados}
+\alias{Arvados}
+\title{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?)
+}
+\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)
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{Arvados$new()}}
+\item \href{#method-project_exist}{\code{Arvados$project_exist()}}
+\item \href{#method-project_get}{\code{Arvados$project_get()}}
+\item \href{#method-project_create}{\code{Arvados$project_create()}}
+\item \href{#method-project_properties_set}{\code{Arvados$project_properties_set()}}
+\item \href{#method-project_properties_append}{\code{Arvados$project_properties_append()}}
+\item \href{#method-project_properties_get}{\code{Arvados$project_properties_get()}}
+\item \href{#method-project_properties_delete}{\code{Arvados$project_properties_delete()}}
+\item \href{#method-project_update}{\code{Arvados$project_update()}}
+\item \href{#method-project_list}{\code{Arvados$project_list()}}
+\item \href{#method-project_delete}{\code{Arvados$project_delete()}}
+\item \href{#method-api_clients_get}{\code{Arvados$api_clients_get()}}
+\item \href{#method-api_clients_create}{\code{Arvados$api_clients_create()}}
+\item \href{#method-api_clients_update}{\code{Arvados$api_clients_update()}}
+\item \href{#method-api_clients_delete}{\code{Arvados$api_clients_delete()}}
+\item \href{#method-api_clients_list}{\code{Arvados$api_clients_list()}}
+\item \href{#method-api_client_authorizations_get}{\code{Arvados$api_client_authorizations_get()}}
+\item \href{#method-api_client_authorizations_create}{\code{Arvados$api_client_authorizations_create()}}
+\item \href{#method-api_client_authorizations_update}{\code{Arvados$api_client_authorizations_update()}}
+\item \href{#method-api_client_authorizations_delete}{\code{Arvados$api_client_authorizations_delete()}}
+\item \href{#method-api_client_authorizations_create_system_auth}{\code{Arvados$api_client_authorizations_create_system_auth()}}
+\item \href{#method-api_client_authorizations_current}{\code{Arvados$api_client_authorizations_current()}}
+\item \href{#method-api_client_authorizations_list}{\code{Arvados$api_client_authorizations_list()}}
+\item \href{#method-authorized_keys_get}{\code{Arvados$authorized_keys_get()}}
+\item \href{#method-authorized_keys_create}{\code{Arvados$authorized_keys_create()}}
+\item \href{#method-authorized_keys_update}{\code{Arvados$authorized_keys_update()}}
+\item \href{#method-authorized_keys_delete}{\code{Arvados$authorized_keys_delete()}}
+\item \href{#method-authorized_keys_list}{\code{Arvados$authorized_keys_list()}}
+\item \href{#method-collections_get}{\code{Arvados$collections_get()}}
+\item \href{#method-collections_create}{\code{Arvados$collections_create()}}
+\item \href{#method-collections_update}{\code{Arvados$collections_update()}}
+\item \href{#method-collections_delete}{\code{Arvados$collections_delete()}}
+\item \href{#method-collections_provenance}{\code{Arvados$collections_provenance()}}
+\item \href{#method-collections_used_by}{\code{Arvados$collections_used_by()}}
+\item \href{#method-collections_trash}{\code{Arvados$collections_trash()}}
+\item \href{#method-collections_untrash}{\code{Arvados$collections_untrash()}}
+\item \href{#method-collections_list}{\code{Arvados$collections_list()}}
+\item \href{#method-containers_get}{\code{Arvados$containers_get()}}
+\item \href{#method-containers_create}{\code{Arvados$containers_create()}}
+\item \href{#method-containers_update}{\code{Arvados$containers_update()}}
+\item \href{#method-containers_delete}{\code{Arvados$containers_delete()}}
+\item \href{#method-containers_auth}{\code{Arvados$containers_auth()}}
+\item \href{#method-containers_lock}{\code{Arvados$containers_lock()}}
+\item \href{#method-containers_unlock}{\code{Arvados$containers_unlock()}}
+\item \href{#method-containers_secret_mounts}{\code{Arvados$containers_secret_mounts()}}
+\item \href{#method-containers_current}{\code{Arvados$containers_current()}}
+\item \href{#method-containers_list}{\code{Arvados$containers_list()}}
+\item \href{#method-container_requests_get}{\code{Arvados$container_requests_get()}}
+\item \href{#method-container_requests_create}{\code{Arvados$container_requests_create()}}
+\item \href{#method-container_requests_update}{\code{Arvados$container_requests_update()}}
+\item \href{#method-container_requests_delete}{\code{Arvados$container_requests_delete()}}
+\item \href{#method-container_requests_list}{\code{Arvados$container_requests_list()}}
+\item \href{#method-groups_get}{\code{Arvados$groups_get()}}
+\item \href{#method-groups_create}{\code{Arvados$groups_create()}}
+\item \href{#method-groups_update}{\code{Arvados$groups_update()}}
+\item \href{#method-groups_delete}{\code{Arvados$groups_delete()}}
+\item \href{#method-groups_contents}{\code{Arvados$groups_contents()}}
+\item \href{#method-groups_shared}{\code{Arvados$groups_shared()}}
+\item \href{#method-groups_trash}{\code{Arvados$groups_trash()}}
+\item \href{#method-groups_untrash}{\code{Arvados$groups_untrash()}}
+\item \href{#method-groups_list}{\code{Arvados$groups_list()}}
+\item \href{#method-keep_services_get}{\code{Arvados$keep_services_get()}}
+\item \href{#method-keep_services_create}{\code{Arvados$keep_services_create()}}
+\item \href{#method-keep_services_update}{\code{Arvados$keep_services_update()}}
+\item \href{#method-keep_services_delete}{\code{Arvados$keep_services_delete()}}
+\item \href{#method-keep_services_accessible}{\code{Arvados$keep_services_accessible()}}
+\item \href{#method-keep_services_list}{\code{Arvados$keep_services_list()}}
+\item \href{#method-project_permission_give}{\code{Arvados$project_permission_give()}}
+\item \href{#method-project_permission_refuse}{\code{Arvados$project_permission_refuse()}}
+\item \href{#method-project_permission_update}{\code{Arvados$project_permission_update()}}
+\item \href{#method-project_permission_check}{\code{Arvados$project_permission_check()}}
+\item \href{#method-links_get}{\code{Arvados$links_get()}}
+\item \href{#method-links_create}{\code{Arvados$links_create()}}
+\item \href{#method-links_update}{\code{Arvados$links_update()}}
+\item \href{#method-links_delete}{\code{Arvados$links_delete()}}
+\item \href{#method-links_list}{\code{Arvados$links_list()}}
+\item \href{#method-links_get_permissions}{\code{Arvados$links_get_permissions()}}
+\item \href{#method-logs_get}{\code{Arvados$logs_get()}}
+\item \href{#method-logs_create}{\code{Arvados$logs_create()}}
+\item \href{#method-logs_update}{\code{Arvados$logs_update()}}
+\item \href{#method-logs_delete}{\code{Arvados$logs_delete()}}
+\item \href{#method-logs_list}{\code{Arvados$logs_list()}}
+\item \href{#method-users_get}{\code{Arvados$users_get()}}
+\item \href{#method-users_create}{\code{Arvados$users_create()}}
+\item \href{#method-users_update}{\code{Arvados$users_update()}}
+\item \href{#method-users_delete}{\code{Arvados$users_delete()}}
+\item \href{#method-users_current}{\code{Arvados$users_current()}}
+\item \href{#method-users_system}{\code{Arvados$users_system()}}
+\item \href{#method-users_activate}{\code{Arvados$users_activate()}}
+\item \href{#method-users_setup}{\code{Arvados$users_setup()}}
+\item \href{#method-users_unsetup}{\code{Arvados$users_unsetup()}}
+\item \href{#method-users_merge}{\code{Arvados$users_merge()}}
+\item \href{#method-users_list}{\code{Arvados$users_list()}}
+\item \href{#method-repositories_get}{\code{Arvados$repositories_get()}}
+\item \href{#method-repositories_create}{\code{Arvados$repositories_create()}}
+\item \href{#method-repositories_update}{\code{Arvados$repositories_update()}}
+\item \href{#method-repositories_delete}{\code{Arvados$repositories_delete()}}
+\item \href{#method-repositories_get_all_permissions}{\code{Arvados$repositories_get_all_permissions()}}
+\item \href{#method-repositories_list}{\code{Arvados$repositories_list()}}
+\item \href{#method-virtual_machines_get}{\code{Arvados$virtual_machines_get()}}
+\item \href{#method-virtual_machines_create}{\code{Arvados$virtual_machines_create()}}
+\item \href{#method-virtual_machines_update}{\code{Arvados$virtual_machines_update()}}
+\item \href{#method-virtual_machines_delete}{\code{Arvados$virtual_machines_delete()}}
+\item \href{#method-virtual_machines_logins}{\code{Arvados$virtual_machines_logins()}}
+\item \href{#method-virtual_machines_get_all_logins}{\code{Arvados$virtual_machines_get_all_logins()}}
+\item \href{#method-virtual_machines_list}{\code{Arvados$virtual_machines_list()}}
+\item \href{#method-workflows_get}{\code{Arvados$workflows_get()}}
+\item \href{#method-workflows_create}{\code{Arvados$workflows_create()}}
+\item \href{#method-workflows_update}{\code{Arvados$workflows_update()}}
+\item \href{#method-workflows_delete}{\code{Arvados$workflows_delete()}}
+\item \href{#method-workflows_list}{\code{Arvados$workflows_list()}}
+\item \href{#method-user_agreements_get}{\code{Arvados$user_agreements_get()}}
+\item \href{#method-user_agreements_create}{\code{Arvados$user_agreements_create()}}
+\item \href{#method-user_agreements_update}{\code{Arvados$user_agreements_update()}}
+\item \href{#method-user_agreements_delete}{\code{Arvados$user_agreements_delete()}}
+\item \href{#method-user_agreements_signatures}{\code{Arvados$user_agreements_signatures()}}
+\item \href{#method-user_agreements_sign}{\code{Arvados$user_agreements_sign()}}
+\item \href{#method-user_agreements_list}{\code{Arvados$user_agreements_list()}}
+\item \href{#method-user_agreements_new}{\code{Arvados$user_agreements_new()}}
+\item \href{#method-configs_get}{\code{Arvados$configs_get()}}
+\item \href{#method-getHostName}{\code{Arvados$getHostName()}}
+\item \href{#method-getToken}{\code{Arvados$getToken()}}
+\item \href{#method-setRESTService}{\code{Arvados$setRESTService()}}
+\item \href{#method-getRESTService}{\code{Arvados$getRESTService()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-new"></a>}}
+\if{latex}{\out{\hypertarget{method-new}{}}}
+\subsection{Method \code{new()}}{
+Initialize new enviroment.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{authToken}}{ARVADOS_API_TOKEN from 'Get API Token' on Arvados.}
+
+\item{\code{hostName}}{ARVADOS_API_HOST from 'Get API Token' on Arvados.}
+
+\item{\code{numRetries}}{Specify number of times to retry failed service requests.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Returns}{
+A new `Arvados` object.
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arv <- Arvados$new(authToken = "ARVADOS_API_TOKEN", hostName = "ARVADOS_API_HOST", numRetries = 3)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-project_exist"></a>}}
+\if{latex}{\out{\hypertarget{method-project_exist}{}}}
+\subsection{Method \code{project_exist()}}{
+project_exist enables checking if the project with such a UUID exist.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$project_exist(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of a project or a file.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arv$project_exist(uuid = projectUUID)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-project_get"></a>}}
+\if{latex}{\out{\hypertarget{method-project_get}{}}}
+\subsection{Method \code{project_get()}}{
+project_get returns the demanded project.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$project_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Group in question.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{project <- arv$project_get(uuid = projectUUID)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-project_create"></a>}}
+\if{latex}{\out{\hypertarget{method-project_create}{}}}
+\subsection{Method \code{project_create()}}{
+project_create creates a new project of a given name and description.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$project_create(
+ name,
+ description,
+ ownerUUID,
+ properties = NULL,
+ ensureUniqueName = "false"
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{name}}{Name of the project.}
+
+\item{\code{description}}{Description of the project.}
+
+\item{\code{ownerUUID}}{The UUID of the maternal project to created one.}
+
+\item{\code{properties}}{List of the properties of the project.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{Properties <- list() # should contain a list of new properties to be added
+new_project <- arv$project_create(name = "project name", description = "project description", owner_uuid = "project UUID", properties = NULL, ensureUniqueName = "false")
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-project_properties_set"></a>}}
+\if{latex}{\out{\hypertarget{method-project_properties_set}{}}}
+\subsection{Method \code{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.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$project_properties_set(listProperties, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{listProperties}}{List of new properties.}
+
+\item{\code{uuid}}{The UUID of a project or a file.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{Properties <- list() # should contain a list of new properties to be added
+arv$project_properties_set(Properties, uuid)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-project_properties_append"></a>}}
+\if{latex}{\out{\hypertarget{method-project_properties_append}{}}}
+\subsection{Method \code{project_properties_append()}}{
+project_properties_append is a method defined in Arvados class that enables appending properties. Allows to add new properties.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$project_properties_append(properties, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of a project or a file.}
+
+\item{\code{listOfNewProperties}}{List of new properties.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{newProperties <- list() # should contain a list of new properties to be added
+arv$project_properties_append(properties = newProperties, uuid)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-project_properties_get"></a>}}
+\if{latex}{\out{\hypertarget{method-project_properties_get}{}}}
+\subsection{Method \code{project_properties_get()}}{
+project_properties_get is a method defined in Arvados class that returns properties.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$project_properties_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of a project or a file.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arv$project_properties_get(projectUUID)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-project_properties_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-project_properties_delete}{}}}
+\subsection{Method \code{project_properties_delete()}}{
+project_properties_delete is a method defined in Arvados class that deletes list of properties.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$project_properties_delete(oneProp, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{oneProp}}{Property to be deleted.}
+
+\item{\code{uuid}}{The UUID of a project or a file.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{Properties <- list() # should contain a list of new properties to be added
+arv$project_properties_delete(Properties, projectUUID)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-project_update"></a>}}
+\if{latex}{\out{\hypertarget{method-project_update}{}}}
+\subsection{Method \code{project_update()}}{
+project_update enables updating project. New name, description and properties may be given.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$project_update(..., uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{...}}{Feature to be updated (name, description, properties).}
+
+\item{\code{uuid}}{The UUID of a project in question.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{newProperties <- list() # should contain a list of new properties to be added
+arv$project_update(name = "new project name", properties = newProperties, uuid = projectUUID)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-project_list"></a>}}
+\if{latex}{\out{\hypertarget{method-project_list}{}}}
+\subsection{Method \code{project_list()}}{
+project_list enables listing project by its name, uuid, properties, permissions.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$project_list(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ select = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ includeTrash = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{includeTrash}}{Include items whose is_trashed attribute is true.}
+
+\item{\code{uuid}}{The UUID of a project in question.}
+
+\item{\code{recursive}}{Include contents from child groups recursively.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{listOfprojects <- arv$project_list(list(list("owner_uuid", "=", projectUUID))) # Sample query which show projects within the project of a given UUID
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-project_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-project_delete}{}}}
+\subsection{Method \code{project_delete()}}{
+project_delete trashes project of a given uuid. It can be restored from trash or deleted permanently.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$project_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Group in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-api_clients_get"></a>}}
+\if{latex}{\out{\hypertarget{method-api_clients_get}{}}}
+\subsection{Method \code{api_clients_get()}}{
+api_clients_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$api_clients_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the apiClient in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-api_clients_create"></a>}}
+\if{latex}{\out{\hypertarget{method-api_clients_create}{}}}
+\subsection{Method \code{api_clients_create()}}{
+api_clients_create is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$api_clients_create(
+ apiClient,
+ ensureUniqueName = "false",
+ clusterID = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{apiClient}}{apiClient object.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-api_clients_update"></a>}}
+\if{latex}{\out{\hypertarget{method-api_clients_update}{}}}
+\subsection{Method \code{api_clients_update()}}{
+api_clients_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$api_clients_update(apiClient, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{apiClient}}{apiClient object.}
+
+\item{\code{uuid}}{The UUID of the apiClient in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-api_clients_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-api_clients_delete}{}}}
+\subsection{Method \code{api_clients_delete()}}{
+api_clients_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$api_clients_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the apiClient in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-api_clients_list"></a>}}
+\if{latex}{\out{\hypertarget{method-api_clients_list}{}}}
+\subsection{Method \code{api_clients_list()}}{
+api_clients_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$api_clients_list(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ select = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ clusterID = NULL,
+ bypassFederation = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-api_client_authorizations_get"></a>}}
+\if{latex}{\out{\hypertarget{method-api_client_authorizations_get}{}}}
+\subsection{Method \code{api_client_authorizations_get()}}{
+api_client_authorizations_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$api_client_authorizations_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the apiClientAuthorization in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-api_client_authorizations_create"></a>}}
+\if{latex}{\out{\hypertarget{method-api_client_authorizations_create}{}}}
+\subsection{Method \code{api_client_authorizations_create()}}{
+api_client_authorizations_create is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$api_client_authorizations_create(
+ apiClientAuthorization,
+ ensureUniqueName = "false",
+ clusterID = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{apiClientAuthorization}}{apiClientAuthorization object.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error on (ownerUUID, name) collision_}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-api_client_authorizations_update"></a>}}
+\if{latex}{\out{\hypertarget{method-api_client_authorizations_update}{}}}
+\subsection{Method \code{api_client_authorizations_update()}}{
+api_client_authorizations_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$api_client_authorizations_update(apiClientAuthorization, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{apiClientAuthorization}}{apiClientAuthorization object.}
+
+\item{\code{uuid}}{The UUID of the apiClientAuthorization in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-api_client_authorizations_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-api_client_authorizations_delete}{}}}
+\subsection{Method \code{api_client_authorizations_delete()}}{
+api_client_authorizations_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$api_client_authorizations_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the apiClientAuthorization in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-api_client_authorizations_create_system_auth"></a>}}
+\if{latex}{\out{\hypertarget{method-api_client_authorizations_create_system_auth}{}}}
+\subsection{Method \code{api_client_authorizations_create_system_auth()}}{
+api_client_authorizations_create_system_auth is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$api_client_authorizations_create_system_auth(
+ apiClientID = NULL,
+ scopes = NULL
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-api_client_authorizations_current"></a>}}
+\if{latex}{\out{\hypertarget{method-api_client_authorizations_current}{}}}
+\subsection{Method \code{api_client_authorizations_current()}}{
+api_client_authorizations_current is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$api_client_authorizations_current()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-api_client_authorizations_list"></a>}}
+\if{latex}{\out{\hypertarget{method-api_client_authorizations_list}{}}}
+\subsection{Method \code{api_client_authorizations_list()}}{
+api_client_authorizations_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$api_client_authorizations_list(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ select = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ clusterID = NULL,
+ bypassFederation = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-authorized_keys_get"></a>}}
+\if{latex}{\out{\hypertarget{method-authorized_keys_get}{}}}
+\subsection{Method \code{authorized_keys_get()}}{
+authorized_keys_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$authorized_keys_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the authorizedKey in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-authorized_keys_create"></a>}}
+\if{latex}{\out{\hypertarget{method-authorized_keys_create}{}}}
+\subsection{Method \code{authorized_keys_create()}}{
+authorized_keys_create is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$authorized_keys_create(
+ authorizedKey,
+ ensureUniqueName = "false",
+ clusterID = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{authorizedKey}}{authorizedKey object.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-authorized_keys_update"></a>}}
+\if{latex}{\out{\hypertarget{method-authorized_keys_update}{}}}
+\subsection{Method \code{authorized_keys_update()}}{
+authorized_keys_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$authorized_keys_update(authorizedKey, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{authorizedKey}}{authorizedKey object.}
+
+\item{\code{uuid}}{The UUID of the authorizedKey in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-authorized_keys_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-authorized_keys_delete}{}}}
+\subsection{Method \code{authorized_keys_delete()}}{
+authorized_keys_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$authorized_keys_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the authorizedKey in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-authorized_keys_list"></a>}}
+\if{latex}{\out{\hypertarget{method-authorized_keys_list}{}}}
+\subsection{Method \code{authorized_keys_list()}}{
+authorized_keys_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$authorized_keys_list(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ select = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ clusterID = NULL,
+ bypassFederation = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-collections_get"></a>}}
+\if{latex}{\out{\hypertarget{method-collections_get}{}}}
+\subsection{Method \code{collections_get()}}{
+collections_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$collections_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Collection in question.
+collection <- arv$collections_get(uuid = collectionUUID)}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-collections_create"></a>}}
+\if{latex}{\out{\hypertarget{method-collections_create}{}}}
+\subsection{Method \code{collections_create()}}{
+collections_create is a method defined in Arvados class that enables collections creation.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$collections_create(
+ name,
+ description,
+ ownerUUID = NULL,
+ properties = NULL,
+ ensureUniqueName = "false",
+ clusterID = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{name}}{Name of the collection.}
+
+\item{\code{description}}{Description of the collection.}
+
+\item{\code{ownerUUID}}{UUID of the maternal project to created one.}
+
+\item{\code{properties}}{Properties of the collection.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{Properties <- list() # should contain a list of new properties to be added
+arv$collections_create(name = "collectionTitle", description = "collectionDescription", ownerUUID = "collectionOwner", properties = Properties)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-collections_update"></a>}}
+\if{latex}{\out{\hypertarget{method-collections_update}{}}}
+\subsection{Method \code{collections_update()}}{
+collections_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$collections_update(
+ name,
+ description,
+ ownerUUID = NULL,
+ properties = NULL,
+ uuid
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{name}}{New name of the collection.}
+
+\item{\code{description}}{New description of the collection.}
+
+\item{\code{ownerUUID}}{UUID of the maternal project to created one.}
+
+\item{\code{properties}}{New list of properties of the collection.}
+
+\item{\code{uuid}}{The UUID of the Collection in question.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{collection <- arv$collections_create(name = "newCollectionTitle", description = "newCollectionDescription", ownerUUID = "collectionOwner", properties = NULL)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-collections_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-collections_delete}{}}}
+\subsection{Method \code{collections_delete()}}{
+collections_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$collections_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Collection in question.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arv$collection_delete(collectionUUID)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-collections_provenance"></a>}}
+\if{latex}{\out{\hypertarget{method-collections_provenance}{}}}
+\subsection{Method \code{collections_provenance()}}{
+collections_provenance is a method defined in Arvados class, it returns the collection by uuid.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$collections_provenance(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Collection in question.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{collection <- arv$collections_provenance(collectionUUID)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-collections_used_by"></a>}}
+\if{latex}{\out{\hypertarget{method-collections_used_by}{}}}
+\subsection{Method \code{collections_used_by()}}{
+collections_used_by is a method defined in Arvados class, it returns collection by portable_data_hash.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$collections_used_by(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Collection in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-collections_trash"></a>}}
+\if{latex}{\out{\hypertarget{method-collections_trash}{}}}
+\subsection{Method \code{collections_trash()}}{
+collections_trash is a method defined in Arvados class, it moves collection to trash.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$collections_trash(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Collection in question.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arv$collections_trash(collectionUUID)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-collections_untrash"></a>}}
+\if{latex}{\out{\hypertarget{method-collections_untrash}{}}}
+\subsection{Method \code{collections_untrash()}}{
+collections_untrash is a method defined in Arvados class, it moves collection from trash to project.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$collections_untrash(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Collection in question.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arv$collections_untrash(collectionUUID)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-collections_list"></a>}}
+\if{latex}{\out{\hypertarget{method-collections_list}{}}}
+\subsection{Method \code{collections_list()}}{
+collections_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$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
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+
+\item{\code{includeTrash}}{Include collections whose is_trashed attribute is true.}
+
+\item{\code{includeOldVersions}}{Include past collection versions.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{collectionList <- arv$collections.list(list(list("name", "=", "Example")))
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-containers_get"></a>}}
+\if{latex}{\out{\hypertarget{method-containers_get}{}}}
+\subsection{Method \code{containers_get()}}{
+containers_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$containers_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Container in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-containers_create"></a>}}
+\if{latex}{\out{\hypertarget{method-containers_create}{}}}
+\subsection{Method \code{containers_create()}}{
+containers_create is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$containers_create(
+ container,
+ ensureUniqueName = "false",
+ clusterID = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{container}}{Container object.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-containers_update"></a>}}
+\if{latex}{\out{\hypertarget{method-containers_update}{}}}
+\subsection{Method \code{containers_update()}}{
+containers_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$containers_update(container, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{container}}{Container object.}
+
+\item{\code{uuid}}{The UUID of the Container in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-containers_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-containers_delete}{}}}
+\subsection{Method \code{containers_delete()}}{
+containers_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$containers_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Container in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-containers_auth"></a>}}
+\if{latex}{\out{\hypertarget{method-containers_auth}{}}}
+\subsection{Method \code{containers_auth()}}{
+containers_auth is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$containers_auth(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Container in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-containers_lock"></a>}}
+\if{latex}{\out{\hypertarget{method-containers_lock}{}}}
+\subsection{Method \code{containers_lock()}}{
+containers_lock is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$containers_lock(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Container in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-containers_unlock"></a>}}
+\if{latex}{\out{\hypertarget{method-containers_unlock}{}}}
+\subsection{Method \code{containers_unlock()}}{
+containers_unlock is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$containers_unlock(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Container in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-containers_secret_mounts"></a>}}
+\if{latex}{\out{\hypertarget{method-containers_secret_mounts}{}}}
+\subsection{Method \code{containers_secret_mounts()}}{
+containers_secret_mounts is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$containers_secret_mounts(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Container in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-containers_current"></a>}}
+\if{latex}{\out{\hypertarget{method-containers_current}{}}}
+\subsection{Method \code{containers_current()}}{
+containers_current is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$containers_current()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-containers_list"></a>}}
+\if{latex}{\out{\hypertarget{method-containers_list}{}}}
+\subsection{Method \code{containers_list()}}{
+containers_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$containers_list(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ select = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ clusterID = NULL,
+ bypassFederation = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-container_requests_get"></a>}}
+\if{latex}{\out{\hypertarget{method-container_requests_get}{}}}
+\subsection{Method \code{container_requests_get()}}{
+container_requests_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$container_requests_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the containerRequest in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-container_requests_create"></a>}}
+\if{latex}{\out{\hypertarget{method-container_requests_create}{}}}
+\subsection{Method \code{container_requests_create()}}{
+container_requests_create is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$container_requests_create(
+ containerRequest,
+ ensureUniqueName = "false",
+ clusterID = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{containerRequest}}{containerRequest object.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-container_requests_update"></a>}}
+\if{latex}{\out{\hypertarget{method-container_requests_update}{}}}
+\subsection{Method \code{container_requests_update()}}{
+container_requests_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$container_requests_update(containerRequest, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{containerRequest}}{containerRequest object.}
+
+\item{\code{uuid}}{The UUID of the containerRequest in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-container_requests_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-container_requests_delete}{}}}
+\subsection{Method \code{container_requests_delete()}}{
+container_requests_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$container_requests_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the containerRequest in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-container_requests_list"></a>}}
+\if{latex}{\out{\hypertarget{method-container_requests_list}{}}}
+\subsection{Method \code{container_requests_list()}}{
+container_requests_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$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
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{bypass federation behavior, list items from local instance database only}
+
+\item{\code{includeTrash}}{Include container requests whose owner project is trashed.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-groups_get"></a>}}
+\if{latex}{\out{\hypertarget{method-groups_get}{}}}
+\subsection{Method \code{groups_get()}}{
+groups_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$groups_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Group in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-groups_create"></a>}}
+\if{latex}{\out{\hypertarget{method-groups_create}{}}}
+\subsection{Method \code{groups_create()}}{
+groups_create is a method defined in Arvados class that supports project creation.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$groups_create(
+ group,
+ ensureUniqueName = "false",
+ clusterID = NULL,
+ async = "false"
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{group}}{Group object.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+
+\item{\code{async}}{Defer permissions update.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-groups_update"></a>}}
+\if{latex}{\out{\hypertarget{method-groups_update}{}}}
+\subsection{Method \code{groups_update()}}{
+groups_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$groups_update(group, uuid, async = "false")}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{group}}{Group object.}
+
+\item{\code{uuid}}{The UUID of the Group in question.}
+
+\item{\code{async}}{Defer permissions update.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-groups_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-groups_delete}{}}}
+\subsection{Method \code{groups_delete()}}{
+groups_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$groups_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Group in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-groups_contents"></a>}}
+\if{latex}{\out{\hypertarget{method-groups_contents}{}}}
+\subsection{Method \code{groups_contents()}}{
+groups_contents is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$groups_contents(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ clusterID = NULL,
+ bypassFederation = NULL,
+ includeTrash = NULL,
+ uuid = NULL,
+ recursive = NULL,
+ include = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+
+\item{\code{includeTrash}}{Include items whose is_trashed attribute is true.}
+
+\item{\code{recursive}}{Include contents from child groups recursively.}
+
+\item{\code{include}}{Include objects referred to by listed field in "included" (only ownerUUID).}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-groups_shared"></a>}}
+\if{latex}{\out{\hypertarget{method-groups_shared}{}}}
+\subsection{Method \code{groups_shared()}}{
+groups_shared is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$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
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+
+\item{\code{includeTrash}}{Include items whose is_trashed attribute is true.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-groups_trash"></a>}}
+\if{latex}{\out{\hypertarget{method-groups_trash}{}}}
+\subsection{Method \code{groups_trash()}}{
+groups_trash is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$groups_trash(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Group in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-groups_untrash"></a>}}
+\if{latex}{\out{\hypertarget{method-groups_untrash}{}}}
+\subsection{Method \code{groups_untrash()}}{
+groups_untrash is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$groups_untrash(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Group in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-groups_list"></a>}}
+\if{latex}{\out{\hypertarget{method-groups_list}{}}}
+\subsection{Method \code{groups_list()}}{
+groups_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$groups_list(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ select = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ clusterID = NULL,
+ bypassFederation = NULL,
+ includeTrash = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+
+\item{\code{includeTrash}}{Include items whose is_trashed attribute is true.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-keep_services_get"></a>}}
+\if{latex}{\out{\hypertarget{method-keep_services_get}{}}}
+\subsection{Method \code{keep_services_get()}}{
+keep_services_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$keep_services_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the keepService in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-keep_services_create"></a>}}
+\if{latex}{\out{\hypertarget{method-keep_services_create}{}}}
+\subsection{Method \code{keep_services_create()}}{
+keep_services_create is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$keep_services_create(
+ keepService,
+ ensureUniqueName = "false",
+ clusterID = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{keepService}}{keepService object.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-keep_services_update"></a>}}
+\if{latex}{\out{\hypertarget{method-keep_services_update}{}}}
+\subsection{Method \code{keep_services_update()}}{
+keep_services_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$keep_services_update(keepService, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{keepService}}{keepService object.}
+
+\item{\code{uuid}}{The UUID of the keepService in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-keep_services_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-keep_services_delete}{}}}
+\subsection{Method \code{keep_services_delete()}}{
+keep_services_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$keep_services_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the keepService in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-keep_services_accessible"></a>}}
+\if{latex}{\out{\hypertarget{method-keep_services_accessible}{}}}
+\subsection{Method \code{keep_services_accessible()}}{
+keep_services_accessible is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$keep_services_accessible()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-keep_services_list"></a>}}
+\if{latex}{\out{\hypertarget{method-keep_services_list}{}}}
+\subsection{Method \code{keep_services_list()}}{
+keep_services_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$keep_services_list(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ select = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ clusterID = NULL,
+ bypassFederation = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-project_permission_give"></a>}}
+\if{latex}{\out{\hypertarget{method-project_permission_give}{}}}
+\subsection{Method \code{project_permission_give()}}{
+project_permission_give is a method defined in Arvados class that enables sharing files with another users.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$project_permission_give(type, uuid, user)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{type}}{Possible options are can_read or can_write or can_manage.}
+
+\item{\code{uuid}}{The UUID of a project or a file.}
+
+\item{\code{user}}{The UUID of the person that gets the permission.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arv$project_permission_give(type = "can_read", uuid = objectUUID, user = userUUID)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-project_permission_refuse"></a>}}
+\if{latex}{\out{\hypertarget{method-project_permission_refuse}{}}}
+\subsection{Method \code{project_permission_refuse()}}{
+project_permission_refuse is a method defined in Arvados class that unables sharing files with another users.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$project_permission_refuse(type, uuid, user)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{type}}{Possible options are can_read or can_write or can_manage.}
+
+\item{\code{uuid}}{The UUID of a project or a file.}
+
+\item{\code{user}}{The UUID of a person that permissions are taken from.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arv$project_permission_refuse(type = "can_read", uuid = objectUUID, user = userUUID)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-project_permission_update"></a>}}
+\if{latex}{\out{\hypertarget{method-project_permission_update}{}}}
+\subsection{Method \code{project_permission_update()}}{
+project_permission_update is a method defined in Arvados class that enables updating permissions.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$project_permission_update(typeOld, typeNew, uuid, user)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{typeOld}}{Old option.}
+
+\item{\code{typeNew}}{New option like can_read or can_write or can_manage.}
+
+\item{\code{uuid}}{The UUID of a project or a file.}
+
+\item{\code{user}}{The UUID of the person that the permission is being updated.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arv$project_permission_update(typeOld = "can_read", typeNew = "can_write", uuid = objectUUID, user = userUUID)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-project_permission_check"></a>}}
+\if{latex}{\out{\hypertarget{method-project_permission_check}{}}}
+\subsection{Method \code{project_permission_check()}}{
+project_permission_check is a method defined in Arvados class that enables checking file permissions.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$project_permission_check(uuid, user, type = NULL)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of a project or a file.}
+
+\item{\code{user}}{The UUID of the person that the permission is being updated.}
+
+\item{\code{type}}{Possible options are can_read or can_write or can_manage.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arv$project_permission_check(type = "can_read", uuid = objectUUID, user = userUUID)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-links_get"></a>}}
+\if{latex}{\out{\hypertarget{method-links_get}{}}}
+\subsection{Method \code{links_get()}}{
+links_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$links_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Link in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-links_create"></a>}}
+\if{latex}{\out{\hypertarget{method-links_create}{}}}
+\subsection{Method \code{links_create()}}{
+links_create is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$links_create(link, ensureUniqueName = "false", clusterID = NULL)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{link}}{Link object.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-links_update"></a>}}
+\if{latex}{\out{\hypertarget{method-links_update}{}}}
+\subsection{Method \code{links_update()}}{
+links_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$links_update(link, uuid, async = "false")}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{link}}{Link object.}
+
+\item{\code{uuid}}{The UUID of the Link in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-links_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-links_delete}{}}}
+\subsection{Method \code{links_delete()}}{
+links_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$links_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Link in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-links_list"></a>}}
+\if{latex}{\out{\hypertarget{method-links_list}{}}}
+\subsection{Method \code{links_list()}}{
+links_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$links_list(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ select = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ clusterID = NULL,
+ bypassFederation = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-links_get_permissions"></a>}}
+\if{latex}{\out{\hypertarget{method-links_get_permissions}{}}}
+\subsection{Method \code{links_get_permissions()}}{
+links_get_permissions is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$links_get_permissions(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Log in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-logs_get"></a>}}
+\if{latex}{\out{\hypertarget{method-logs_get}{}}}
+\subsection{Method \code{logs_get()}}{
+logs_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$logs_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Log in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-logs_create"></a>}}
+\if{latex}{\out{\hypertarget{method-logs_create}{}}}
+\subsection{Method \code{logs_create()}}{
+logs_create is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$logs_create(log, ensureUniqueName = "false", clusterID = NULL)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{log}}{Log object.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-logs_update"></a>}}
+\if{latex}{\out{\hypertarget{method-logs_update}{}}}
+\subsection{Method \code{logs_update()}}{
+logs_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$logs_update(log, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{log}}{Log object.}
+
+\item{\code{uuid}}{The UUID of the Log in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-logs_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-logs_delete}{}}}
+\subsection{Method \code{logs_delete()}}{
+logs_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$logs_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Log in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-logs_list"></a>}}
+\if{latex}{\out{\hypertarget{method-logs_list}{}}}
+\subsection{Method \code{logs_list()}}{
+logs_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$logs_list(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ select = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ clusterID = NULL,
+ bypassFederation = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-users_get"></a>}}
+\if{latex}{\out{\hypertarget{method-users_get}{}}}
+\subsection{Method \code{users_get()}}{
+users_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$users_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the User in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-users_create"></a>}}
+\if{latex}{\out{\hypertarget{method-users_create}{}}}
+\subsection{Method \code{users_create()}}{
+users_create is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$users_create(user, ensureUniqueName = "false", clusterID = NULL)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{user}}{User object.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-users_update"></a>}}
+\if{latex}{\out{\hypertarget{method-users_update}{}}}
+\subsection{Method \code{users_update()}}{
+users_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$users_update(user, uuid, bypassFederation = NULL)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{user}}{User object.}
+
+\item{\code{uuid}}{The UUID of the User in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-users_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-users_delete}{}}}
+\subsection{Method \code{users_delete()}}{
+users_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$users_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the User in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-users_current"></a>}}
+\if{latex}{\out{\hypertarget{method-users_current}{}}}
+\subsection{Method \code{users_current()}}{
+users_current is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$users_current()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-users_system"></a>}}
+\if{latex}{\out{\hypertarget{method-users_system}{}}}
+\subsection{Method \code{users_system()}}{
+users_system is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$users_system()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-users_activate"></a>}}
+\if{latex}{\out{\hypertarget{method-users_activate}{}}}
+\subsection{Method \code{users_activate()}}{
+users_activate is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$users_activate(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the User in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-users_setup"></a>}}
+\if{latex}{\out{\hypertarget{method-users_setup}{}}}
+\subsection{Method \code{users_setup()}}{
+users_setup is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$users_setup(
+ uuid = NULL,
+ user = NULL,
+ repo_name = NULL,
+ vm_uuid = NULL,
+ send_notification_email = "false"
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-users_unsetup"></a>}}
+\if{latex}{\out{\hypertarget{method-users_unsetup}{}}}
+\subsection{Method \code{users_unsetup()}}{
+users_unsetup is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$users_unsetup(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the User in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-users_merge"></a>}}
+\if{latex}{\out{\hypertarget{method-users_merge}{}}}
+\subsection{Method \code{users_merge()}}{
+users_merge is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$users_merge(
+ newOwnerUUID,
+ newUserToken = NULL,
+ redirectToNewUser = NULL,
+ oldUserUUID = NULL,
+ newUserUUID = NULL
+)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-users_list"></a>}}
+\if{latex}{\out{\hypertarget{method-users_list}{}}}
+\subsection{Method \code{users_list()}}{
+users_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$users_list(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ select = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ clusterID = NULL,
+ bypassFederation = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-repositories_get"></a>}}
+\if{latex}{\out{\hypertarget{method-repositories_get}{}}}
+\subsection{Method \code{repositories_get()}}{
+repositories_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$repositories_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Repository in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-repositories_create"></a>}}
+\if{latex}{\out{\hypertarget{method-repositories_create}{}}}
+\subsection{Method \code{repositories_create()}}{
+repositories_create is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$repositories_create(
+ repository,
+ ensureUniqueName = "false",
+ clusterID = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{repository}}{Repository object.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-repositories_update"></a>}}
+\if{latex}{\out{\hypertarget{method-repositories_update}{}}}
+\subsection{Method \code{repositories_update()}}{
+repositories_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$repositories_update(repository, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{repository}}{Repository object.}
+
+\item{\code{uuid}}{The UUID of the Repository in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-repositories_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-repositories_delete}{}}}
+\subsection{Method \code{repositories_delete()}}{
+repositories_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$repositories_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Repository in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-repositories_get_all_permissions"></a>}}
+\if{latex}{\out{\hypertarget{method-repositories_get_all_permissions}{}}}
+\subsection{Method \code{repositories_get_all_permissions()}}{
+repositories_get_all_permissions is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$repositories_get_all_permissions()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-repositories_list"></a>}}
+\if{latex}{\out{\hypertarget{method-repositories_list}{}}}
+\subsection{Method \code{repositories_list()}}{
+repositories_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$repositories_list(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ select = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ clusterID = NULL,
+ bypassFederation = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-virtual_machines_get"></a>}}
+\if{latex}{\out{\hypertarget{method-virtual_machines_get}{}}}
+\subsection{Method \code{virtual_machines_get()}}{
+virtual_machines_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$virtual_machines_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the virtualMachine in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-virtual_machines_create"></a>}}
+\if{latex}{\out{\hypertarget{method-virtual_machines_create}{}}}
+\subsection{Method \code{virtual_machines_create()}}{
+virtual_machines_create is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$virtual_machines_create(
+ virtualMachine,
+ ensureUniqueName = "false",
+ clusterID = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{virtualMachine}}{virtualMachine object.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-virtual_machines_update"></a>}}
+\if{latex}{\out{\hypertarget{method-virtual_machines_update}{}}}
+\subsection{Method \code{virtual_machines_update()}}{
+virtual_machines_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$virtual_machines_update(virtualMachine, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{virtualMachine}}{virtualMachine object.}
+
+\item{\code{uuid}}{The UUID of the virtualMachine in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-virtual_machines_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-virtual_machines_delete}{}}}
+\subsection{Method \code{virtual_machines_delete()}}{
+virtual_machines_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$virtual_machines_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the virtualMachine in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-virtual_machines_logins"></a>}}
+\if{latex}{\out{\hypertarget{method-virtual_machines_logins}{}}}
+\subsection{Method \code{virtual_machines_logins()}}{
+virtual_machines_logins is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$virtual_machines_logins(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the virtualMachine in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-virtual_machines_get_all_logins"></a>}}
+\if{latex}{\out{\hypertarget{method-virtual_machines_get_all_logins}{}}}
+\subsection{Method \code{virtual_machines_get_all_logins()}}{
+virtual_machines_get_all_logins is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$virtual_machines_get_all_logins()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-virtual_machines_list"></a>}}
+\if{latex}{\out{\hypertarget{method-virtual_machines_list}{}}}
+\subsection{Method \code{virtual_machines_list()}}{
+virtual_machines_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$virtual_machines_list(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ select = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ clusterID = NULL,
+ bypassFederation = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{bypass federation behavior, list items from local instance database only}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-workflows_get"></a>}}
+\if{latex}{\out{\hypertarget{method-workflows_get}{}}}
+\subsection{Method \code{workflows_get()}}{
+workflows_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$workflows_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Workflow in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-workflows_create"></a>}}
+\if{latex}{\out{\hypertarget{method-workflows_create}{}}}
+\subsection{Method \code{workflows_create()}}{
+workflows_create is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$workflows_create(
+ workflow,
+ ensureUniqueName = "false",
+ clusterID = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{workflow}}{Workflow object.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-workflows_update"></a>}}
+\if{latex}{\out{\hypertarget{method-workflows_update}{}}}
+\subsection{Method \code{workflows_update()}}{
+workflows_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$workflows_update(workflow, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{workflow}}{Workflow object.}
+
+\item{\code{uuid}}{The UUID of the Workflow in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-workflows_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-workflows_delete}{}}}
+\subsection{Method \code{workflows_delete()}}{
+workflows_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$workflows_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the Workflow in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-workflows_list"></a>}}
+\if{latex}{\out{\hypertarget{method-workflows_list}{}}}
+\subsection{Method \code{workflows_list()}}{
+workflows_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$workflows_list(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ select = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ clusterID = NULL,
+ bypassFederation = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-user_agreements_get"></a>}}
+\if{latex}{\out{\hypertarget{method-user_agreements_get}{}}}
+\subsection{Method \code{user_agreements_get()}}{
+user_agreements_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$user_agreements_get(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the userAgreement in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-user_agreements_create"></a>}}
+\if{latex}{\out{\hypertarget{method-user_agreements_create}{}}}
+\subsection{Method \code{user_agreements_create()}}{
+user_agreements_create is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$user_agreements_create(
+ userAgreement,
+ ensureUniqueName = "false",
+ clusterID = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{userAgreement}}{userAgreement object.}
+
+\item{\code{ensureUniqueName}}{Adjust name to ensure uniqueness instead of returning an error.}
+
+\item{\code{clusterID}}{Create object on a remote federated cluster instead of the current one.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-user_agreements_update"></a>}}
+\if{latex}{\out{\hypertarget{method-user_agreements_update}{}}}
+\subsection{Method \code{user_agreements_update()}}{
+user_agreements_update is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$user_agreements_update(userAgreement, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{userAgreement}}{userAgreement object.}
+
+\item{\code{uuid}}{The UUID of the userAgreement in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-user_agreements_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-user_agreements_delete}{}}}
+\subsection{Method \code{user_agreements_delete()}}{
+user_agreements_delete is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$user_agreements_delete(uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{uuid}}{The UUID of the userAgreement in question.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-user_agreements_signatures"></a>}}
+\if{latex}{\out{\hypertarget{method-user_agreements_signatures}{}}}
+\subsection{Method \code{user_agreements_signatures()}}{
+user_agreements_signatures is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$user_agreements_signatures()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-user_agreements_sign"></a>}}
+\if{latex}{\out{\hypertarget{method-user_agreements_sign}{}}}
+\subsection{Method \code{user_agreements_sign()}}{
+user_agreements_sign is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$user_agreements_sign()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-user_agreements_list"></a>}}
+\if{latex}{\out{\hypertarget{method-user_agreements_list}{}}}
+\subsection{Method \code{user_agreements_list()}}{
+user_agreements_list is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$user_agreements_list(
+ filters = NULL,
+ where = NULL,
+ order = NULL,
+ select = NULL,
+ distinct = NULL,
+ limit = "100",
+ offset = "0",
+ count = "exact",
+ clusterID = NULL,
+ bypassFederation = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{clusterID}}{List objects on a remote federated cluster instead of the current one.}
+
+\item{\code{bypassFederation}}{Bypass federation behavior, list items from local instance database only.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-user_agreements_new"></a>}}
+\if{latex}{\out{\hypertarget{method-user_agreements_new}{}}}
+\subsection{Method \code{user_agreements_new()}}{
+user_agreements_new is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$user_agreements_new()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-configs_get"></a>}}
+\if{latex}{\out{\hypertarget{method-configs_get}{}}}
+\subsection{Method \code{configs_get()}}{
+configs_get is a method defined in Arvados class.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$configs_get()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getHostName"></a>}}
+\if{latex}{\out{\hypertarget{method-getHostName}{}}}
+\subsection{Method \code{getHostName()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$getHostName()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getToken"></a>}}
+\if{latex}{\out{\hypertarget{method-getToken}{}}}
+\subsection{Method \code{getToken()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$getToken()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-setRESTService"></a>}}
+\if{latex}{\out{\hypertarget{method-setRESTService}{}}}
+\subsection{Method \code{setRESTService()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$setRESTService(newREST)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getRESTService"></a>}}
+\if{latex}{\out{\hypertarget{method-getRESTService}{}}}
+\subsection{Method \code{getRESTService()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Arvados$getRESTService()}\if{html}{\out{</div>}}
+}
+
+}
+}
diff --git a/sdk/R/man/ArvadosFile.Rd b/sdk/R/man/ArvadosFile.Rd
index 514e9e846..8275b7b60 100644
--- a/sdk/R/man/ArvadosFile.Rd
+++ b/sdk/R/man/ArvadosFile.Rd
@@ -1,58 +1,435 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ArvadosFile.R
-\name{ArvadosFile}
-\alias{ArvadosFile}
-\title{ArvadosFile}
-\description{
-ArvadosFile class represents a file inside Arvados collection.
-}
-\section{Usage}{
-
-\preformatted{file = ArvadosFile$new(name)}
-}
-
-\section{Arguments}{
-
-\describe{
- \item{name}{Name of the file.}
-}
-}
-
-\section{Methods}{
-
-\describe{
- \item{getName()}{Returns name of the file.}
- \item{getRelativePath()}{Returns file path relative to the root.}
- \item{read(contentType = "raw", offset = 0, length = 0)}{Read file content.}
- \item{write(content, contentType = "text/html")}{Write to file (override current content of the file).}
- \item{connection(rw)}{Get connection opened in "read" or "write" mode.}
- \item{flush()}{Write connections content to a file (override current content of the file).}
- \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
- \item{getSizeInBytes()}{Returns file size in bytes.}
- \item{move(destination)}{Moves file to a new location inside collection.}
- \item{copy(destination)}{Copies file to a new location inside collection.}
-}
-}
-
-\examples{
-\dontrun{
-myFile <- ArvadosFile$new("myFile")
-
-myFile$write("This is new file content")
-fileContent <- myFile$read()
-fileContent <- myFile$read("text")
-fileContent <- myFile$read("raw", offset = 8, length = 4)
-
-#Write a table:
-arvConnection <- myFile$connection("w")
-write.table(mytable, arvConnection)
-arvadosFile$flush()
-
-#Read a table:
-arvConnection <- myFile$connection("r")
-mytable <- read.table(arvConnection)
-
-myFile$move("newFolder/myFile")
-myFile$copy("newFolder/myFile")
-}
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ArvadosFile.R
+\name{ArvadosFile}
+\alias{ArvadosFile}
+\title{R6 Class Representing a ArvadosFile}
+\description{
+ArvadosFile class represents a file inside Arvados collection.
+}
+\examples{
+
+## ------------------------------------------------
+## Method `ArvadosFile$new`
+## ------------------------------------------------
+
+myFile <- ArvadosFile$new("myFile")
+
+## ------------------------------------------------
+## Method `ArvadosFile$getName`
+## ------------------------------------------------
+
+arvadosFile$getName()
+
+## ------------------------------------------------
+## Method `ArvadosFile$getFileListing`
+## ------------------------------------------------
+
+arvadosFile$getFileListing()
+
+## ------------------------------------------------
+## Method `ArvadosFile$getSizeInBytes`
+## ------------------------------------------------
+
+arvadosFile$getSizeInBytes()
+
+## ------------------------------------------------
+## Method `ArvadosFile$read`
+## ------------------------------------------------
+
+collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+fileContent <- arvadosFile$read("text")
+
+## ------------------------------------------------
+## Method `ArvadosFile$connection`
+## ------------------------------------------------
+
+collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+arvConnection <- arvadosFile$connection("w")
+
+## ------------------------------------------------
+## Method `ArvadosFile$flush`
+## ------------------------------------------------
+
+collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+myFile$write("This is new file content")
+arvadosFile$flush()
+
+## ------------------------------------------------
+## Method `ArvadosFile$write`
+## ------------------------------------------------
+
+collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+myFile$write("This is new file content")
+
+## ------------------------------------------------
+## Method `ArvadosFile$move`
+## ------------------------------------------------
+
+arvadosFile$move(newPath)
+
+## ------------------------------------------------
+## Method `ArvadosFile$copy`
+## ------------------------------------------------
+
+arvadosFile$copy("NewName.format")
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{ArvadosFile$new()}}
+\item \href{#method-getName}{\code{ArvadosFile$getName()}}
+\item \href{#method-getFileListing}{\code{ArvadosFile$getFileListing()}}
+\item \href{#method-getSizeInBytes}{\code{ArvadosFile$getSizeInBytes()}}
+\item \href{#method-get}{\code{ArvadosFile$get()}}
+\item \href{#method-getFirst}{\code{ArvadosFile$getFirst()}}
+\item \href{#method-getCollection}{\code{ArvadosFile$getCollection()}}
+\item \href{#method-setCollection}{\code{ArvadosFile$setCollection()}}
+\item \href{#method-getRelativePath}{\code{ArvadosFile$getRelativePath()}}
+\item \href{#method-getParent}{\code{ArvadosFile$getParent()}}
+\item \href{#method-setParent}{\code{ArvadosFile$setParent()}}
+\item \href{#method-read}{\code{ArvadosFile$read()}}
+\item \href{#method-connection}{\code{ArvadosFile$connection()}}
+\item \href{#method-flush}{\code{ArvadosFile$flush()}}
+\item \href{#method-write}{\code{ArvadosFile$write()}}
+\item \href{#method-move}{\code{ArvadosFile$move()}}
+\item \href{#method-copy}{\code{ArvadosFile$copy()}}
+\item \href{#method-duplicate}{\code{ArvadosFile$duplicate()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-new"></a>}}
+\if{latex}{\out{\hypertarget{method-new}{}}}
+\subsection{Method \code{new()}}{
+Initialize new enviroment.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$new(name)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{name}}{Name of the new enviroment.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Returns}{
+A new `ArvadosFile` object.
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{myFile <- ArvadosFile$new("myFile")
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getName"></a>}}
+\if{latex}{\out{\hypertarget{method-getName}{}}}
+\subsection{Method \code{getName()}}{
+Returns name of the file.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$getName()}\if{html}{\out{</div>}}
+}
+
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arvadosFile$getName()
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getFileListing"></a>}}
+\if{latex}{\out{\hypertarget{method-getFileListing}{}}}
+\subsection{Method \code{getFileListing()}}{
+Returns collections file content as character vector.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$getFileListing(fullpath = TRUE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{fullPath}}{Checking if TRUE.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arvadosFile$getFileListing()
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getSizeInBytes"></a>}}
+\if{latex}{\out{\hypertarget{method-getSizeInBytes}{}}}
+\subsection{Method \code{getSizeInBytes()}}{
+Returns collections content size in bytes.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$getSizeInBytes()}\if{html}{\out{</div>}}
+}
+
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arvadosFile$getSizeInBytes()
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get"></a>}}
+\if{latex}{\out{\hypertarget{method-get}{}}}
+\subsection{Method \code{get()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$get(fileLikeObjectName)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getFirst"></a>}}
+\if{latex}{\out{\hypertarget{method-getFirst}{}}}
+\subsection{Method \code{getFirst()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$getFirst()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getCollection"></a>}}
+\if{latex}{\out{\hypertarget{method-getCollection}{}}}
+\subsection{Method \code{getCollection()}}{
+Returns collection UUID.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$getCollection()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-setCollection"></a>}}
+\if{latex}{\out{\hypertarget{method-setCollection}{}}}
+\subsection{Method \code{setCollection()}}{
+Sets new collection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$setCollection(collection, setRecursively = TRUE)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getRelativePath"></a>}}
+\if{latex}{\out{\hypertarget{method-getRelativePath}{}}}
+\subsection{Method \code{getRelativePath()}}{
+Returns file path relative to the root.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$getRelativePath()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getParent"></a>}}
+\if{latex}{\out{\hypertarget{method-getParent}{}}}
+\subsection{Method \code{getParent()}}{
+Returns project UUID.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$getParent()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-setParent"></a>}}
+\if{latex}{\out{\hypertarget{method-setParent}{}}}
+\subsection{Method \code{setParent()}}{
+Sets project collection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$setParent(newParent)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-read"></a>}}
+\if{latex}{\out{\hypertarget{method-read}{}}}
+\subsection{Method \code{read()}}{
+Read file content.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$read(contentType = "raw", offset = 0, length = 0)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{contentType}}{Type of content. Possible is "text", "raw".}
+
+\item{\code{offset}}{Describes the location of a piece of data compared to another location}
+
+\item{\code{length}}{Length of content}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+fileContent <- arvadosFile$read("text")
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-connection"></a>}}
+\if{latex}{\out{\hypertarget{method-connection}{}}}
+\subsection{Method \code{connection()}}{
+Get connection opened in "read" or "write" mode.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$connection(rw)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{rw}}{Type of connection.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+arvConnection <- arvadosFile$connection("w")
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-flush"></a>}}
+\if{latex}{\out{\hypertarget{method-flush}{}}}
+\subsection{Method \code{flush()}}{
+Write connections content to a file or override current content of the file.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$flush()}\if{html}{\out{</div>}}
+}
+
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+myFile$write("This is new file content")
+arvadosFile$flush()
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-write"></a>}}
+\if{latex}{\out{\hypertarget{method-write}{}}}
+\subsection{Method \code{write()}}{
+Write to file or override current content of the file.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$write(content, contentType = "text/html")}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{content}}{File to write.}
+
+\item{\code{contentType}}{Type of content. Possible is "text", "raw".}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{collection <- Collection$new(arv, collectionUUID)
+arvadosFile <- collection$get(fileName)
+myFile$write("This is new file content")
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-move"></a>}}
+\if{latex}{\out{\hypertarget{method-move}{}}}
+\subsection{Method \code{move()}}{
+Moves file to a new location inside collection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$move(destination)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{destination}}{Path to new folder.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arvadosFile$move(newPath)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-copy"></a>}}
+\if{latex}{\out{\hypertarget{method-copy}{}}}
+\subsection{Method \code{copy()}}{
+Copies file to a new location inside collection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$copy(destination)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{destination}}{Path to new folder.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arvadosFile$copy("NewName.format")
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-duplicate"></a>}}
+\if{latex}{\out{\hypertarget{method-duplicate}{}}}
+\subsection{Method \code{duplicate()}}{
+Duplicate file and gives it a new name.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$duplicate(newName = NULL)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{newName}}{New name for duplicated file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}
diff --git a/sdk/R/man/ArvadosR.Rd b/sdk/R/man/ArvadosR.Rd
new file mode 100644
index 000000000..def3927b0
--- /dev/null
+++ b/sdk/R/man/ArvadosR.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ArvadosR.R
+\name{ArvadosR}
+\alias{ArvadosR}
+\title{ArvadosR}
+\description{
+\if{html}{\figure{dax.png}{options: style='float: right' alt='logo' width='120'}}
+
+Arvados is an open source platform for managing, processing, and sharing genomic and other large scientific and biomedical data. With Arvados, bioinformaticians run and scale compute-intensive workflows, developers create biomedical applications, and IT administrators manage large compute and storage resources.
+}
+\seealso{
+\itemize{
+\item \code{\link{https://github.com/arvados/arvados/blob/main/README.md}}
+\item \code{\link{https://github.com/arvados/arvados/tree/main/sdk/R}}}
+}
+\author{
+\itemize{
+\item Lucas Di Pentima
+\item Ward Vandewege
+\item Peter Amstutz
+\item Fuad Muhic}
+}
diff --git a/sdk/R/man/Collection.Rd b/sdk/R/man/Collection.Rd
index fbe603866..5fbf1c1a1 100644
--- a/sdk/R/man/Collection.Rd
+++ b/sdk/R/man/Collection.Rd
@@ -1,49 +1,431 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Collection.R
-\name{Collection}
-\alias{Collection}
-\title{Collection}
-\description{
-Collection class provides interface for working with Arvados collections.
-}
-\section{Usage}{
-
-\preformatted{collection = Collection$new(arv, uuid)}
-}
-
-\section{Arguments}{
-
-\describe{
- \item{arv}{Arvados object.}
- \item{uuid}{UUID of a collection.}
-}
-}
-
-\section{Methods}{
-
-\describe{
- \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.}
- \item{create(files)}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
- \item{remove(fileNames)}{Remove one or more files from the collection.}
- \item{move(content, destination)}{Moves ArvadosFile or Subcollection to another location in the collection.}
- \item{copy(content, destination)}{Copies ArvadosFile or Subcollection to another location in the collection.}
- \item{getFileListing()}{Returns collections file content as character vector.}
- \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
-}
-}
-
-\examples{
-\dontrun{
-arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
-collection <- Collection$new(arv, "uuid")
-
-createdFiles <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
-
-collection$remove("location/to/my/file.cpp")
-
-collection$move("folder/file.cpp", "file.cpp")
-
-arvadosFile <- collection$get("location/to/my/file.cpp")
-arvadosSubcollection <- collection$get("location/to/my/directory/")
-}
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Collection.R
+\name{Collection}
+\alias{Collection}
+\title{R6 Class Representing Arvados Collection}
+\description{
+Collection class provides interface for working with Arvados collections,
+for exaplme actions like creating, updating, moving or removing are possible.
+}
+\examples{
+
+## ------------------------------------------------
+## Method `Collection$new`
+## ------------------------------------------------
+
+collection <- Collection$new(arv, CollectionUUID)
+
+## ------------------------------------------------
+## Method `Collection$readArvFile`
+## ------------------------------------------------
+
+collection <- Collection$new(arv, collectionUUID)
+readFile <- collection$readArvFile(arvadosFile, istable = 'yes') # table
+readFile <- collection$readArvFile(arvadosFile, istable = 'no') # text
+readFile <- collection$readArvFile(arvadosFile) # xlsx, csv, tsv, rds, rdata
+readFile <- collection$readArvFile(arvadosFile, fileclass = 'lala') # fasta
+readFile <- collection$readArvFile(arvadosFile, Ncol= 4, Nrow = 32) # binary, only numbers
+readFile <- collection$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text
+
+## ------------------------------------------------
+## Method `Collection$writeFile`
+## ------------------------------------------------
+
+collection <- Collection$new(arv, collectionUUID)
+writeFile <- collection$writeFile("myoutput.csv", file, istable = NULL) # csv
+writeFile <- collection$writeFile("myoutput.fasta", file, istable = NULL) # fasta
+writeFile <- collection$writeFile("myoutputtable.txt", file, istable = "yes") # txt table
+writeFile <- collection$writeFile("myoutputtext.txt", file, istable = "no") # txt text
+writeFile <- collection$writeFile("myoutputbinary.dat", file) # binary
+writeFile <- collection$writeFile("myoutputxlsx.xlsx", file) # xlsx
+
+## ------------------------------------------------
+## Method `Collection$create`
+## ------------------------------------------------
+
+collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))
+
+## ------------------------------------------------
+## Method `Collection$remove`
+## ------------------------------------------------
+
+collection$remove(fileName.format)
+
+## ------------------------------------------------
+## Method `Collection$move`
+## ------------------------------------------------
+
+collection$move("fileName.format", path)
+
+## ------------------------------------------------
+## Method `Collection$copy`
+## ------------------------------------------------
+
+copied <- collection$copy("oldName.format", "newName.format")
+
+## ------------------------------------------------
+## Method `Collection$refresh`
+## ------------------------------------------------
+
+collection$refresh()
+
+## ------------------------------------------------
+## Method `Collection$getFileListing`
+## ------------------------------------------------
+
+list <- collection$getFileListing()
+
+## ------------------------------------------------
+## Method `Collection$get`
+## ------------------------------------------------
+
+arvadosFile <- collection$get(fileName)
+}
+\seealso{
+\code{\link{https://github.com/arvados/arvados/tree/main/sdk/R}}
+}
+\section{Public fields}{
+\if{html}{\out{<div class="r6-fields">}}
+\describe{
+\item{\code{uuid}}{Autentic for Collection UUID.}
+}
+\if{html}{\out{</div>}}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{Collection$new()}}
+\item \href{#method-add}{\code{Collection$add()}}
+\item \href{#method-readArvFile}{\code{Collection$readArvFile()}}
+\item \href{#method-writeFile}{\code{Collection$writeFile()}}
+\item \href{#method-create}{\code{Collection$create()}}
+\item \href{#method-remove}{\code{Collection$remove()}}
+\item \href{#method-move}{\code{Collection$move()}}
+\item \href{#method-copy}{\code{Collection$copy()}}
+\item \href{#method-refresh}{\code{Collection$refresh()}}
+\item \href{#method-getFileListing}{\code{Collection$getFileListing()}}
+\item \href{#method-get}{\code{Collection$get()}}
+\item \href{#method-getRESTService}{\code{Collection$getRESTService()}}
+\item \href{#method-setRESTService}{\code{Collection$setRESTService()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-new"></a>}}
+\if{latex}{\out{\hypertarget{method-new}{}}}
+\subsection{Method \code{new()}}{
+Initialize new enviroment.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$new(api, uuid)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{api}}{Arvados enviroment.}
+
+\item{\code{uuid}}{The UUID Autentic for Collection UUID.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Returns}{
+A new `Collection` object.
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{collection <- Collection$new(arv, CollectionUUID)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add"></a>}}
+\if{latex}{\out{\hypertarget{method-add}{}}}
+\subsection{Method \code{add()}}{
+Adds ArvadosFile or Subcollection specified by content to the collection. Used only with ArvadosFile or Subcollection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$add(content, relativePath = "")}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{content}}{Content to be added.}
+
+\item{\code{relativePath}}{Path to add content.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-readArvFile"></a>}}
+\if{latex}{\out{\hypertarget{method-readArvFile}{}}}
+\subsection{Method \code{readArvFile()}}{
+Read file content.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$readArvFile(
+ file,
+ con,
+ sep = ",",
+ istable = NULL,
+ fileclass = "SeqFastadna",
+ Ncol = NULL,
+ Nrow = NULL,
+ wantedFunction = NULL
+)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{file}}{Name of the file.}
+
+\item{\code{sep}}{Separator used in reading tsv, csv file format.}
+
+\item{\code{istable}}{Used in reading txt file to check if the file is table or not.}
+
+\item{\code{fileclass}}{Used in reading fasta file to set file class.}
+
+\item{\code{Ncol}}{Used in reading binary file to set numbers of columns in data.frame.}
+
+\item{\code{Nrow}}{Used in reading binary file to set numbers of rows in data.frame size.}
+
+\item{\code{col}}{Collection from which the file is read.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{collection <- Collection$new(arv, collectionUUID)
+readFile <- collection$readArvFile(arvadosFile, istable = 'yes') # table
+readFile <- collection$readArvFile(arvadosFile, istable = 'no') # text
+readFile <- collection$readArvFile(arvadosFile) # xlsx, csv, tsv, rds, rdata
+readFile <- collection$readArvFile(arvadosFile, fileclass = 'lala') # fasta
+readFile <- collection$readArvFile(arvadosFile, Ncol= 4, Nrow = 32) # binary, only numbers
+readFile <- collection$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-writeFile"></a>}}
+\if{latex}{\out{\hypertarget{method-writeFile}{}}}
+\subsection{Method \code{writeFile()}}{
+Write file content
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$writeFile(name, file, istable = NULL, seqName = NULL)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{name}}{Name of the file.}
+
+\item{\code{file}}{File to be saved.}
+
+\item{\code{istable}}{Used in writing txt file to check if the file is table or not.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{collection <- Collection$new(arv, collectionUUID)
+writeFile <- collection$writeFile("myoutput.csv", file, istable = NULL) # csv
+writeFile <- collection$writeFile("myoutput.fasta", file, istable = NULL) # fasta
+writeFile <- collection$writeFile("myoutputtable.txt", file, istable = "yes") # txt table
+writeFile <- collection$writeFile("myoutputtext.txt", file, istable = "no") # txt text
+writeFile <- collection$writeFile("myoutputbinary.dat", file) # binary
+writeFile <- collection$writeFile("myoutputxlsx.xlsx", file) # xlsx
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-create"></a>}}
+\if{latex}{\out{\hypertarget{method-create}{}}}
+\subsection{Method \code{create()}}{
+Creates one or more ArvadosFiles and adds them to the collection at specified path.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$create(files)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{files}}{Content to be created.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-remove"></a>}}
+\if{latex}{\out{\hypertarget{method-remove}{}}}
+\subsection{Method \code{remove()}}{
+Remove one or more files from the collection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$remove(paths)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{paths}}{Content to be removed.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{collection$remove(fileName.format)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-move"></a>}}
+\if{latex}{\out{\hypertarget{method-move}{}}}
+\subsection{Method \code{move()}}{
+Moves ArvadosFile or Subcollection to another location in the collection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$move(content, destination)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{content}}{Content to be moved.}
+
+\item{\code{destination}}{Path to move content.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{collection$move("fileName.format", path)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-copy"></a>}}
+\if{latex}{\out{\hypertarget{method-copy}{}}}
+\subsection{Method \code{copy()}}{
+Copies ArvadosFile or Subcollection to another location in the collection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$copy(content, destination)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{content}}{Content to be moved.}
+
+\item{\code{destination}}{Path to move content.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{copied <- collection$copy("oldName.format", "newName.format")
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-refresh"></a>}}
+\if{latex}{\out{\hypertarget{method-refresh}{}}}
+\subsection{Method \code{refresh()}}{
+Refreshes the environment.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$refresh()}\if{html}{\out{</div>}}
+}
+
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{collection$refresh()
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getFileListing"></a>}}
+\if{latex}{\out{\hypertarget{method-getFileListing}{}}}
+\subsection{Method \code{getFileListing()}}{
+Returns collections file content as character vector.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$getFileListing()}\if{html}{\out{</div>}}
+}
+
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{list <- collection$getFileListing()
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get"></a>}}
+\if{latex}{\out{\hypertarget{method-get}{}}}
+\subsection{Method \code{get()}}{
+If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$get(relativePath)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{relativePath}}{Path from content is taken.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{arvadosFile <- collection$get(fileName)
+}
+\if{html}{\out{</div>}}
+
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getRESTService"></a>}}
+\if{latex}{\out{\hypertarget{method-getRESTService}{}}}
+\subsection{Method \code{getRESTService()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$getRESTService()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-setRESTService"></a>}}
+\if{latex}{\out{\hypertarget{method-setRESTService}{}}}
+\subsection{Method \code{setRESTService()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Collection$setRESTService(newRESTService)}\if{html}{\out{</div>}}
+}
+
+}
+}
diff --git a/sdk/R/man/Subcollection.Rd b/sdk/R/man/Subcollection.Rd
index 0b27a8bc4..1c9ec96e1 100644
--- a/sdk/R/man/Subcollection.Rd
+++ b/sdk/R/man/Subcollection.Rd
@@ -1,49 +1,250 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Subcollection.R
-\name{Subcollection}
-\alias{Subcollection}
-\title{Subcollection}
-\description{
-Subcollection class represents a folder inside Arvados collection.
-It is essentially a composite of arvadosFiles and other subcollections.
-}
-\section{Usage}{
-
-\preformatted{subcollection = Subcollection$new(name)}
-}
-
-\section{Arguments}{
-
-\describe{
- \item{name}{Name of the subcollection.}
-}
-}
-
-\section{Methods}{
-
-\describe{
- \item{getName()}{Returns name of the subcollection.}
- \item{getRelativePath()}{Returns subcollection path relative to the root.}
- \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the subcollection.}
- \item{remove(name)}{Removes ArvadosFile or Subcollection specified by name from the subcollection.}
- \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
- \item{getFileListing()}{Returns subcollections file content as character vector.}
- \item{getSizeInBytes()}{Returns subcollections content size in bytes.}
- \item{move(destination)}{Moves subcollection to a new location inside collection.}
- \item{copy(destination)}{Copies subcollection to a new location inside collection.}
-}
-}
-
-\examples{
-\dontrun{
-myFolder <- Subcollection$new("myFolder")
-myFile <- ArvadosFile$new("myFile")
-
-myFolder$add(myFile)
-myFolder$get("myFile")
-myFolder$remove("myFile")
-
-myFolder$move("newLocation/myFolder")
-myFolder$copy("newLocation/myFolder")
-}
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Subcollection.R
+\name{Subcollection}
+\alias{Subcollection}
+\title{R6 Class Representing a Subcollection}
+\description{
+Subcollection class represents a folder inside Arvados collection.
+It is essentially a composite of arvadosFiles and other subcollections.
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{Subcollection$new()}}
+\item \href{#method-getName}{\code{Subcollection$getName()}}
+\item \href{#method-getRelativePath}{\code{Subcollection$getRelativePath()}}
+\item \href{#method-add}{\code{Subcollection$add()}}
+\item \href{#method-remove}{\code{Subcollection$remove()}}
+\item \href{#method-getFileListing}{\code{Subcollection$getFileListing()}}
+\item \href{#method-getSizeInBytes}{\code{Subcollection$getSizeInBytes()}}
+\item \href{#method-move}{\code{Subcollection$move()}}
+\item \href{#method-copy}{\code{Subcollection$copy()}}
+\item \href{#method-duplicate}{\code{Subcollection$duplicate()}}
+\item \href{#method-get}{\code{Subcollection$get()}}
+\item \href{#method-getFirst}{\code{Subcollection$getFirst()}}
+\item \href{#method-setCollection}{\code{Subcollection$setCollection()}}
+\item \href{#method-getCollection}{\code{Subcollection$getCollection()}}
+\item \href{#method-getParent}{\code{Subcollection$getParent()}}
+\item \href{#method-setParent}{\code{Subcollection$setParent()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-new"></a>}}
+\if{latex}{\out{\hypertarget{method-new}{}}}
+\subsection{Method \code{new()}}{
+Initialize new enviroment.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$new(name)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{name}}{Name of the new enviroment.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Returns}{
+A new `Subcollection` object.
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getName"></a>}}
+\if{latex}{\out{\hypertarget{method-getName}{}}}
+\subsection{Method \code{getName()}}{
+Returns name of the file.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$getName()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getRelativePath"></a>}}
+\if{latex}{\out{\hypertarget{method-getRelativePath}{}}}
+\subsection{Method \code{getRelativePath()}}{
+Returns Subcollection's path relative to the root.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$getRelativePath()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-add"></a>}}
+\if{latex}{\out{\hypertarget{method-add}{}}}
+\subsection{Method \code{add()}}{
+Adds ArvadosFile or Subcollection specified by content to the Subcollection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$add(content)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{content}}{Content to be added.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-remove"></a>}}
+\if{latex}{\out{\hypertarget{method-remove}{}}}
+\subsection{Method \code{remove()}}{
+Removes ArvadosFile or Subcollection specified by name from the Subcollection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$remove(name)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{name}}{Name of the file to be removed.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getFileListing"></a>}}
+\if{latex}{\out{\hypertarget{method-getFileListing}{}}}
+\subsection{Method \code{getFileListing()}}{
+Returns Subcollections file content as character vector.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$getFileListing(fullPath = TRUE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{fullPath}}{Checking if the path to file exists.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getSizeInBytes"></a>}}
+\if{latex}{\out{\hypertarget{method-getSizeInBytes}{}}}
+\subsection{Method \code{getSizeInBytes()}}{
+Returns subcollections content size in bytes.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$getSizeInBytes()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-move"></a>}}
+\if{latex}{\out{\hypertarget{method-move}{}}}
+\subsection{Method \code{move()}}{
+Moves Subcollection to a new location inside collection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$move(destination)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{destination}}{Path to move the file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-copy"></a>}}
+\if{latex}{\out{\hypertarget{method-copy}{}}}
+\subsection{Method \code{copy()}}{
+Copies Subcollection to a new location inside collection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$copy(destination)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{destination}}{Path to copy the file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-duplicate"></a>}}
+\if{latex}{\out{\hypertarget{method-duplicate}{}}}
+\subsection{Method \code{duplicate()}}{
+Duplicate Subcollection and gives it a new name.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$duplicate(newName = NULL)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{newName}}{New name for duplicated file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-get"></a>}}
+\if{latex}{\out{\hypertarget{method-get}{}}}
+\subsection{Method \code{get()}}{
+If name is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$get(name)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{name}}{Name of the file.}
+}
+\if{html}{\out{</div>}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getFirst"></a>}}
+\if{latex}{\out{\hypertarget{method-getFirst}{}}}
+\subsection{Method \code{getFirst()}}{
+Returns files in Subcollection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$getFirst()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-setCollection"></a>}}
+\if{latex}{\out{\hypertarget{method-setCollection}{}}}
+\subsection{Method \code{setCollection()}}{
+Sets Collection by its UUID.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$setCollection(collection, setRecursively = TRUE)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getCollection"></a>}}
+\if{latex}{\out{\hypertarget{method-getCollection}{}}}
+\subsection{Method \code{getCollection()}}{
+Returns Collection of Subcollection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$getCollection()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-getParent"></a>}}
+\if{latex}{\out{\hypertarget{method-getParent}{}}}
+\subsection{Method \code{getParent()}}{
+Returns Collection UUID.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$getParent()}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-setParent"></a>}}
+\if{latex}{\out{\hypertarget{method-setParent}{}}}
+\subsection{Method \code{setParent()}}{
+Sets new Collection.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Subcollection$setParent(newParent)}\if{html}{\out{</div>}}
+}
+
+}
+}
diff --git a/sdk/R/man/api_client_authorizations.create.Rd b/sdk/R/man/api_client_authorizations.create.Rd
deleted file mode 100644
index e32241946..000000000
--- a/sdk/R/man/api_client_authorizations.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{api_client_authorizations.create}
-\alias{api_client_authorizations.create}
-\title{api_client_authorizations.create}
-\usage{
-arv$api_client_authorizations.create(apiclientauthorization,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{apiClientAuthorization}{ApiClientAuthorization object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-ApiClientAuthorization object.
-}
-\description{
-api_client_authorizations.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/api_client_authorizations.create_system_auth.Rd b/sdk/R/man/api_client_authorizations.create_system_auth.Rd
deleted file mode 100644
index 3eb172aab..000000000
--- a/sdk/R/man/api_client_authorizations.create_system_auth.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{api_client_authorizations.create_system_auth}
-\alias{api_client_authorizations.create_system_auth}
-\title{api_client_authorizations.create_system_auth}
-\usage{
-arv$api_client_authorizations.create_system_auth(api_client_id = NULL,
- scopes = NULL)
-}
-\arguments{
-\item{api_client_id}{}
-
-\item{scopes}{}
-}
-\value{
-ApiClientAuthorization object.
-}
-\description{
-api_client_authorizations.create_system_auth is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/api_client_authorizations.current.Rd b/sdk/R/man/api_client_authorizations.current.Rd
deleted file mode 100644
index c28623788..000000000
--- a/sdk/R/man/api_client_authorizations.current.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{api_client_authorizations.current}
-\alias{api_client_authorizations.current}
-\title{api_client_authorizations.current}
-\usage{
-arv$api_client_authorizations.current(NULL)
-}
-\value{
-ApiClientAuthorization object.
-}
-\description{
-api_client_authorizations.current is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/api_client_authorizations.delete.Rd b/sdk/R/man/api_client_authorizations.delete.Rd
deleted file mode 100644
index 054cc7966..000000000
--- a/sdk/R/man/api_client_authorizations.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{api_client_authorizations.delete}
-\alias{api_client_authorizations.delete}
-\title{api_client_authorizations.delete}
-\usage{
-arv$api_client_authorizations.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the ApiClientAuthorization in question.}
-}
-\value{
-ApiClientAuthorization object.
-}
-\description{
-api_client_authorizations.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/api_client_authorizations.get.Rd b/sdk/R/man/api_client_authorizations.get.Rd
deleted file mode 100644
index 3f5b630a4..000000000
--- a/sdk/R/man/api_client_authorizations.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{api_client_authorizations.get}
-\alias{api_client_authorizations.get}
-\title{api_client_authorizations.get}
-\usage{
-arv$api_client_authorizations.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the ApiClientAuthorization in question.}
-}
-\value{
-ApiClientAuthorization object.
-}
-\description{
-api_client_authorizations.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/api_client_authorizations.list.Rd b/sdk/R/man/api_client_authorizations.list.Rd
deleted file mode 100644
index 7c8ae69cd..000000000
--- a/sdk/R/man/api_client_authorizations.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{api_client_authorizations.list}
-\alias{api_client_authorizations.list}
-\title{api_client_authorizations.list}
-\usage{
-arv$api_client_authorizations.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-ApiClientAuthorizationList object.
-}
-\description{
-api_client_authorizations.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/api_client_authorizations.update.Rd b/sdk/R/man/api_client_authorizations.update.Rd
deleted file mode 100644
index e6380ccdd..000000000
--- a/sdk/R/man/api_client_authorizations.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{api_client_authorizations.update}
-\alias{api_client_authorizations.update}
-\title{api_client_authorizations.update}
-\usage{
-arv$api_client_authorizations.update(apiclientauthorization,
- uuid)
-}
-\arguments{
-\item{apiClientAuthorization}{ApiClientAuthorization object.}
-
-\item{uuid}{The UUID of the ApiClientAuthorization in question.}
-}
-\value{
-ApiClientAuthorization object.
-}
-\description{
-api_client_authorizations.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/api_clients.create.Rd b/sdk/R/man/api_clients.create.Rd
deleted file mode 100644
index 260116897..000000000
--- a/sdk/R/man/api_clients.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{api_clients.create}
-\alias{api_clients.create}
-\title{api_clients.create}
-\usage{
-arv$api_clients.create(apiclient,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{apiClient}{ApiClient object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-ApiClient object.
-}
-\description{
-api_clients.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/api_clients.delete.Rd b/sdk/R/man/api_clients.delete.Rd
deleted file mode 100644
index 90eaa9911..000000000
--- a/sdk/R/man/api_clients.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{api_clients.delete}
-\alias{api_clients.delete}
-\title{api_clients.delete}
-\usage{
-arv$api_clients.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the ApiClient in question.}
-}
-\value{
-ApiClient object.
-}
-\description{
-api_clients.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/api_clients.get.Rd b/sdk/R/man/api_clients.get.Rd
deleted file mode 100644
index 4a1b6c06b..000000000
--- a/sdk/R/man/api_clients.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{api_clients.get}
-\alias{api_clients.get}
-\title{api_clients.get}
-\usage{
-arv$api_clients.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the ApiClient in question.}
-}
-\value{
-ApiClient object.
-}
-\description{
-api_clients.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/api_clients.list.Rd b/sdk/R/man/api_clients.list.Rd
deleted file mode 100644
index 0679c9c12..000000000
--- a/sdk/R/man/api_clients.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{api_clients.list}
-\alias{api_clients.list}
-\title{api_clients.list}
-\usage{
-arv$api_clients.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-ApiClientList object.
-}
-\description{
-api_clients.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/api_clients.update.Rd b/sdk/R/man/api_clients.update.Rd
deleted file mode 100644
index a37e53367..000000000
--- a/sdk/R/man/api_clients.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{api_clients.update}
-\alias{api_clients.update}
-\title{api_clients.update}
-\usage{
-arv$api_clients.update(apiclient,
- uuid)
-}
-\arguments{
-\item{apiClient}{ApiClient object.}
-
-\item{uuid}{The UUID of the ApiClient in question.}
-}
-\value{
-ApiClient object.
-}
-\description{
-api_clients.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/authorized_keys.create.Rd b/sdk/R/man/authorized_keys.create.Rd
deleted file mode 100644
index e0d226af3..000000000
--- a/sdk/R/man/authorized_keys.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{authorized_keys.create}
-\alias{authorized_keys.create}
-\title{authorized_keys.create}
-\usage{
-arv$authorized_keys.create(authorizedkey,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{authorizedKey}{AuthorizedKey object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-AuthorizedKey object.
-}
-\description{
-authorized_keys.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/authorized_keys.delete.Rd b/sdk/R/man/authorized_keys.delete.Rd
deleted file mode 100644
index db1f0e7c4..000000000
--- a/sdk/R/man/authorized_keys.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{authorized_keys.delete}
-\alias{authorized_keys.delete}
-\title{authorized_keys.delete}
-\usage{
-arv$authorized_keys.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the AuthorizedKey in question.}
-}
-\value{
-AuthorizedKey object.
-}
-\description{
-authorized_keys.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/authorized_keys.get.Rd b/sdk/R/man/authorized_keys.get.Rd
deleted file mode 100644
index 31a2dd3f3..000000000
--- a/sdk/R/man/authorized_keys.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{authorized_keys.get}
-\alias{authorized_keys.get}
-\title{authorized_keys.get}
-\usage{
-arv$authorized_keys.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the AuthorizedKey in question.}
-}
-\value{
-AuthorizedKey object.
-}
-\description{
-authorized_keys.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/authorized_keys.list.Rd b/sdk/R/man/authorized_keys.list.Rd
deleted file mode 100644
index cd19bc60c..000000000
--- a/sdk/R/man/authorized_keys.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{authorized_keys.list}
-\alias{authorized_keys.list}
-\title{authorized_keys.list}
-\usage{
-arv$authorized_keys.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-AuthorizedKeyList object.
-}
-\description{
-authorized_keys.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/authorized_keys.update.Rd b/sdk/R/man/authorized_keys.update.Rd
deleted file mode 100644
index 65d93d073..000000000
--- a/sdk/R/man/authorized_keys.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{authorized_keys.update}
-\alias{authorized_keys.update}
-\title{authorized_keys.update}
-\usage{
-arv$authorized_keys.update(authorizedkey,
- uuid)
-}
-\arguments{
-\item{authorizedKey}{AuthorizedKey object.}
-
-\item{uuid}{The UUID of the AuthorizedKey in question.}
-}
-\value{
-AuthorizedKey object.
-}
-\description{
-authorized_keys.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/collections.create.Rd b/sdk/R/man/collections.create.Rd
deleted file mode 100644
index af8e3984b..000000000
--- a/sdk/R/man/collections.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{collections.create}
-\alias{collections.create}
-\title{collections.create}
-\usage{
-arv$collections.create(collection,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{collection}{Collection object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-Collection object.
-}
-\description{
-collections.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/collections.delete.Rd b/sdk/R/man/collections.delete.Rd
deleted file mode 100644
index 28b3543e4..000000000
--- a/sdk/R/man/collections.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{collections.delete}
-\alias{collections.delete}
-\title{collections.delete}
-\usage{
-arv$collections.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Collection in question.}
-}
-\value{
-Collection object.
-}
-\description{
-collections.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/collections.get.Rd b/sdk/R/man/collections.get.Rd
deleted file mode 100644
index 3878aaf8c..000000000
--- a/sdk/R/man/collections.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{collections.get}
-\alias{collections.get}
-\title{collections.get}
-\usage{
-arv$collections.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Collection in question.}
-}
-\value{
-Collection object.
-}
-\description{
-collections.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/collections.list.Rd b/sdk/R/man/collections.list.Rd
deleted file mode 100644
index 87f6f78e3..000000000
--- a/sdk/R/man/collections.list.Rd
+++ /dev/null
@@ -1,36 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{collections.list}
-\alias{collections.list}
-\title{collections.list}
-\usage{
-arv$collections.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", include_trash = NULL)
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-
-\item{include_trash}{Include collections whose is_trashed attribute is true.}
-}
-\value{
-CollectionList object.
-}
-\description{
-collections.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/collections.provenance.Rd b/sdk/R/man/collections.provenance.Rd
deleted file mode 100644
index 001a7b47c..000000000
--- a/sdk/R/man/collections.provenance.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{collections.provenance}
-\alias{collections.provenance}
-\title{collections.provenance}
-\usage{
-arv$collections.provenance(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-Collection object.
-}
-\description{
-collections.provenance is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/collections.trash.Rd b/sdk/R/man/collections.trash.Rd
deleted file mode 100644
index 4862109b9..000000000
--- a/sdk/R/man/collections.trash.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{collections.trash}
-\alias{collections.trash}
-\title{collections.trash}
-\usage{
-arv$collections.trash(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-Collection object.
-}
-\description{
-collections.trash is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/collections.untrash.Rd b/sdk/R/man/collections.untrash.Rd
deleted file mode 100644
index c41bc3d90..000000000
--- a/sdk/R/man/collections.untrash.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{collections.untrash}
-\alias{collections.untrash}
-\title{collections.untrash}
-\usage{
-arv$collections.untrash(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-Collection object.
-}
-\description{
-collections.untrash is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/collections.update.Rd b/sdk/R/man/collections.update.Rd
deleted file mode 100644
index c9b201cb4..000000000
--- a/sdk/R/man/collections.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{collections.update}
-\alias{collections.update}
-\title{collections.update}
-\usage{
-arv$collections.update(collection,
- uuid)
-}
-\arguments{
-\item{collection}{Collection object.}
-
-\item{uuid}{The UUID of the Collection in question.}
-}
-\value{
-Collection object.
-}
-\description{
-collections.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/collections.used_by.Rd b/sdk/R/man/collections.used_by.Rd
deleted file mode 100644
index 53b8e493f..000000000
--- a/sdk/R/man/collections.used_by.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{collections.used_by}
-\alias{collections.used_by}
-\title{collections.used_by}
-\usage{
-arv$collections.used_by(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-Collection object.
-}
-\description{
-collections.used_by is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/container_requests.create.Rd b/sdk/R/man/container_requests.create.Rd
deleted file mode 100644
index e114d322e..000000000
--- a/sdk/R/man/container_requests.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{container_requests.create}
-\alias{container_requests.create}
-\title{container_requests.create}
-\usage{
-arv$container_requests.create(containerrequest,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{containerRequest}{ContainerRequest object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-ContainerRequest object.
-}
-\description{
-container_requests.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/container_requests.delete.Rd b/sdk/R/man/container_requests.delete.Rd
deleted file mode 100644
index 905739bcd..000000000
--- a/sdk/R/man/container_requests.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{container_requests.delete}
-\alias{container_requests.delete}
-\title{container_requests.delete}
-\usage{
-arv$container_requests.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the ContainerRequest in question.}
-}
-\value{
-ContainerRequest object.
-}
-\description{
-container_requests.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/container_requests.get.Rd b/sdk/R/man/container_requests.get.Rd
deleted file mode 100644
index 54fe5d4c1..000000000
--- a/sdk/R/man/container_requests.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{container_requests.get}
-\alias{container_requests.get}
-\title{container_requests.get}
-\usage{
-arv$container_requests.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the ContainerRequest in question.}
-}
-\value{
-ContainerRequest object.
-}
-\description{
-container_requests.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/container_requests.list.Rd b/sdk/R/man/container_requests.list.Rd
deleted file mode 100644
index 9c2412bee..000000000
--- a/sdk/R/man/container_requests.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{container_requests.list}
-\alias{container_requests.list}
-\title{container_requests.list}
-\usage{
-arv$container_requests.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-ContainerRequestList object.
-}
-\description{
-container_requests.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/container_requests.update.Rd b/sdk/R/man/container_requests.update.Rd
deleted file mode 100644
index 063417b3e..000000000
--- a/sdk/R/man/container_requests.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{container_requests.update}
-\alias{container_requests.update}
-\title{container_requests.update}
-\usage{
-arv$container_requests.update(containerrequest,
- uuid)
-}
-\arguments{
-\item{containerRequest}{ContainerRequest object.}
-
-\item{uuid}{The UUID of the ContainerRequest in question.}
-}
-\value{
-ContainerRequest object.
-}
-\description{
-container_requests.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/containers.auth.Rd b/sdk/R/man/containers.auth.Rd
deleted file mode 100644
index a594d2f19..000000000
--- a/sdk/R/man/containers.auth.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{containers.auth}
-\alias{containers.auth}
-\title{containers.auth}
-\usage{
-arv$containers.auth(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-Container object.
-}
-\description{
-containers.auth is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/containers.create.Rd b/sdk/R/man/containers.create.Rd
deleted file mode 100644
index 4ce25bb83..000000000
--- a/sdk/R/man/containers.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{containers.create}
-\alias{containers.create}
-\title{containers.create}
-\usage{
-arv$containers.create(container,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{container}{Container object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-Container object.
-}
-\description{
-containers.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/containers.current.Rd b/sdk/R/man/containers.current.Rd
deleted file mode 100644
index 0f6ad4eb9..000000000
--- a/sdk/R/man/containers.current.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{containers.current}
-\alias{containers.current}
-\title{containers.current}
-\usage{
-arv$containers.current(NULL)
-}
-\value{
-Container object.
-}
-\description{
-containers.current is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/containers.delete.Rd b/sdk/R/man/containers.delete.Rd
deleted file mode 100644
index e2e3cd7fc..000000000
--- a/sdk/R/man/containers.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{containers.delete}
-\alias{containers.delete}
-\title{containers.delete}
-\usage{
-arv$containers.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Container in question.}
-}
-\value{
-Container object.
-}
-\description{
-containers.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/containers.get.Rd b/sdk/R/man/containers.get.Rd
deleted file mode 100644
index 05d97d3d9..000000000
--- a/sdk/R/man/containers.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{containers.get}
-\alias{containers.get}
-\title{containers.get}
-\usage{
-arv$containers.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Container in question.}
-}
-\value{
-Container object.
-}
-\description{
-containers.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/containers.list.Rd b/sdk/R/man/containers.list.Rd
deleted file mode 100644
index d44579613..000000000
--- a/sdk/R/man/containers.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{containers.list}
-\alias{containers.list}
-\title{containers.list}
-\usage{
-arv$containers.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-ContainerList object.
-}
-\description{
-containers.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/containers.lock.Rd b/sdk/R/man/containers.lock.Rd
deleted file mode 100644
index 72bcdf0f8..000000000
--- a/sdk/R/man/containers.lock.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{containers.lock}
-\alias{containers.lock}
-\title{containers.lock}
-\usage{
-arv$containers.lock(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-Container object.
-}
-\description{
-containers.lock is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/containers.secret_mounts.Rd b/sdk/R/man/containers.secret_mounts.Rd
deleted file mode 100644
index d0f8444fa..000000000
--- a/sdk/R/man/containers.secret_mounts.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{containers.secret_mounts}
-\alias{containers.secret_mounts}
-\title{containers.secret_mounts}
-\usage{
-arv$containers.secret_mounts(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-Container object.
-}
-\description{
-containers.secret_mounts is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/containers.unlock.Rd b/sdk/R/man/containers.unlock.Rd
deleted file mode 100644
index 5c41f2059..000000000
--- a/sdk/R/man/containers.unlock.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{containers.unlock}
-\alias{containers.unlock}
-\title{containers.unlock}
-\usage{
-arv$containers.unlock(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-Container object.
-}
-\description{
-containers.unlock is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/containers.update.Rd b/sdk/R/man/containers.update.Rd
deleted file mode 100644
index 3a8572670..000000000
--- a/sdk/R/man/containers.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{containers.update}
-\alias{containers.update}
-\title{containers.update}
-\usage{
-arv$containers.update(container,
- uuid)
-}
-\arguments{
-\item{container}{Container object.}
-
-\item{uuid}{The UUID of the Container in question.}
-}
-\value{
-Container object.
-}
-\description{
-containers.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/figures/dax.png b/sdk/R/man/figures/dax.png
new file mode 100644
index 000000000..c511f0ec5
Binary files /dev/null and b/sdk/R/man/figures/dax.png differ
diff --git a/sdk/R/man/groups.contents.Rd b/sdk/R/man/groups.contents.Rd
deleted file mode 100644
index 26647df4f..000000000
--- a/sdk/R/man/groups.contents.Rd
+++ /dev/null
@@ -1,38 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{groups.contents}
-\alias{groups.contents}
-\title{groups.contents}
-\usage{
-arv$groups.contents(filters = NULL,
- where = NULL, order = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact",
- include_trash = NULL, uuid = NULL, recursive = NULL)
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-
-\item{include_trash}{Include items whose is_trashed attribute is true.}
-
-\item{uuid}{}
-
-\item{recursive}{Include contents from child groups recursively.}
-}
-\value{
-Group object.
-}
-\description{
-groups.contents is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/groups.create.Rd b/sdk/R/man/groups.create.Rd
deleted file mode 100644
index 871960362..000000000
--- a/sdk/R/man/groups.create.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{groups.create}
-\alias{groups.create}
-\title{groups.create}
-\usage{
-arv$groups.create(group, ensure_unique_name = "false")
-}
-\arguments{
-\item{group}{Group object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-Group object.
-}
-\description{
-groups.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/groups.delete.Rd b/sdk/R/man/groups.delete.Rd
deleted file mode 100644
index 1b4a0d9e6..000000000
--- a/sdk/R/man/groups.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{groups.delete}
-\alias{groups.delete}
-\title{groups.delete}
-\usage{
-arv$groups.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Group in question.}
-}
-\value{
-Group object.
-}
-\description{
-groups.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/groups.get.Rd b/sdk/R/man/groups.get.Rd
deleted file mode 100644
index 28a187259..000000000
--- a/sdk/R/man/groups.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{groups.get}
-\alias{groups.get}
-\title{groups.get}
-\usage{
-arv$groups.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Group in question.}
-}
-\value{
-Group object.
-}
-\description{
-groups.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/groups.list.Rd b/sdk/R/man/groups.list.Rd
deleted file mode 100644
index 7699f3ef4..000000000
--- a/sdk/R/man/groups.list.Rd
+++ /dev/null
@@ -1,36 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{groups.list}
-\alias{groups.list}
-\title{groups.list}
-\usage{
-arv$groups.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact", include_trash = NULL)
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-
-\item{include_trash}{Include items whose is_trashed attribute is true.}
-}
-\value{
-GroupList object.
-}
-\description{
-groups.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/groups.trash.Rd b/sdk/R/man/groups.trash.Rd
deleted file mode 100644
index c529618f7..000000000
--- a/sdk/R/man/groups.trash.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{groups.trash}
-\alias{groups.trash}
-\title{groups.trash}
-\usage{
-arv$groups.trash(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-Group object.
-}
-\description{
-groups.trash is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/groups.untrash.Rd b/sdk/R/man/groups.untrash.Rd
deleted file mode 100644
index 014190c8f..000000000
--- a/sdk/R/man/groups.untrash.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{groups.untrash}
-\alias{groups.untrash}
-\title{groups.untrash}
-\usage{
-arv$groups.untrash(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-Group object.
-}
-\description{
-groups.untrash is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/groups.update.Rd b/sdk/R/man/groups.update.Rd
deleted file mode 100644
index 47abde7a9..000000000
--- a/sdk/R/man/groups.update.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{groups.update}
-\alias{groups.update}
-\title{groups.update}
-\usage{
-arv$groups.update(group, uuid)
-}
-\arguments{
-\item{group}{Group object.}
-
-\item{uuid}{The UUID of the Group in question.}
-}
-\value{
-Group object.
-}
-\description{
-groups.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/humans.create.Rd b/sdk/R/man/humans.create.Rd
deleted file mode 100644
index 44c9aa308..000000000
--- a/sdk/R/man/humans.create.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{humans.create}
-\alias{humans.create}
-\title{humans.create}
-\usage{
-arv$humans.create(human, ensure_unique_name = "false")
-}
-\arguments{
-\item{human}{Human object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-Human object.
-}
-\description{
-humans.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/humans.delete.Rd b/sdk/R/man/humans.delete.Rd
deleted file mode 100644
index ae66b8eda..000000000
--- a/sdk/R/man/humans.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{humans.delete}
-\alias{humans.delete}
-\title{humans.delete}
-\usage{
-arv$humans.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Human in question.}
-}
-\value{
-Human object.
-}
-\description{
-humans.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/humans.get.Rd b/sdk/R/man/humans.get.Rd
deleted file mode 100644
index 820c562c3..000000000
--- a/sdk/R/man/humans.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{humans.get}
-\alias{humans.get}
-\title{humans.get}
-\usage{
-arv$humans.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Human in question.}
-}
-\value{
-Human object.
-}
-\description{
-humans.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/humans.list.Rd b/sdk/R/man/humans.list.Rd
deleted file mode 100644
index a8db4c7f6..000000000
--- a/sdk/R/man/humans.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{humans.list}
-\alias{humans.list}
-\title{humans.list}
-\usage{
-arv$humans.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-HumanList object.
-}
-\description{
-humans.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/humans.update.Rd b/sdk/R/man/humans.update.Rd
deleted file mode 100644
index 83956a25e..000000000
--- a/sdk/R/man/humans.update.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{humans.update}
-\alias{humans.update}
-\title{humans.update}
-\usage{
-arv$humans.update(human, uuid)
-}
-\arguments{
-\item{human}{Human object.}
-
-\item{uuid}{The UUID of the Human in question.}
-}
-\value{
-Human object.
-}
-\description{
-humans.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/job_tasks.create.Rd b/sdk/R/man/job_tasks.create.Rd
deleted file mode 100644
index 2da0b0c56..000000000
--- a/sdk/R/man/job_tasks.create.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{job_tasks.create}
-\alias{job_tasks.create}
-\title{job_tasks.create}
-\usage{
-arv$job_tasks.create(jobtask, ensure_unique_name = "false")
-}
-\arguments{
-\item{jobTask}{JobTask object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-JobTask object.
-}
-\description{
-job_tasks.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/job_tasks.delete.Rd b/sdk/R/man/job_tasks.delete.Rd
deleted file mode 100644
index b78a38e8d..000000000
--- a/sdk/R/man/job_tasks.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{job_tasks.delete}
-\alias{job_tasks.delete}
-\title{job_tasks.delete}
-\usage{
-arv$job_tasks.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the JobTask in question.}
-}
-\value{
-JobTask object.
-}
-\description{
-job_tasks.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/job_tasks.get.Rd b/sdk/R/man/job_tasks.get.Rd
deleted file mode 100644
index 07d205414..000000000
--- a/sdk/R/man/job_tasks.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{job_tasks.get}
-\alias{job_tasks.get}
-\title{job_tasks.get}
-\usage{
-arv$job_tasks.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the JobTask in question.}
-}
-\value{
-JobTask object.
-}
-\description{
-job_tasks.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/job_tasks.list.Rd b/sdk/R/man/job_tasks.list.Rd
deleted file mode 100644
index 51c4b4942..000000000
--- a/sdk/R/man/job_tasks.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{job_tasks.list}
-\alias{job_tasks.list}
-\title{job_tasks.list}
-\usage{
-arv$job_tasks.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-JobTaskList object.
-}
-\description{
-job_tasks.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/job_tasks.update.Rd b/sdk/R/man/job_tasks.update.Rd
deleted file mode 100644
index 42d10bd43..000000000
--- a/sdk/R/man/job_tasks.update.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{job_tasks.update}
-\alias{job_tasks.update}
-\title{job_tasks.update}
-\usage{
-arv$job_tasks.update(jobtask, uuid)
-}
-\arguments{
-\item{jobTask}{JobTask object.}
-
-\item{uuid}{The UUID of the JobTask in question.}
-}
-\value{
-JobTask object.
-}
-\description{
-job_tasks.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/jobs.cancel.Rd b/sdk/R/man/jobs.cancel.Rd
deleted file mode 100644
index 7399d28a8..000000000
--- a/sdk/R/man/jobs.cancel.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{jobs.cancel}
-\alias{jobs.cancel}
-\title{jobs.cancel}
-\usage{
-arv$jobs.cancel(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-Job object.
-}
-\description{
-jobs.cancel is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/jobs.create.Rd b/sdk/R/man/jobs.create.Rd
deleted file mode 100644
index 4c4d61ae7..000000000
--- a/sdk/R/man/jobs.create.Rd
+++ /dev/null
@@ -1,29 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{jobs.create}
-\alias{jobs.create}
-\title{jobs.create}
-\usage{
-arv$jobs.create(job, ensure_unique_name = "false",
- find_or_create = "false", filters = NULL,
- minimum_script_version = NULL, exclude_script_versions = NULL)
-}
-\arguments{
-\item{job}{Job object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-
-\item{find_or_create}{}
-
-\item{filters}{}
-
-\item{minimum_script_version}{}
-
-\item{exclude_script_versions}{}
-}
-\value{
-Job object.
-}
-\description{
-jobs.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/jobs.delete.Rd b/sdk/R/man/jobs.delete.Rd
deleted file mode 100644
index 7f756084a..000000000
--- a/sdk/R/man/jobs.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{jobs.delete}
-\alias{jobs.delete}
-\title{jobs.delete}
-\usage{
-arv$jobs.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Job in question.}
-}
-\value{
-Job object.
-}
-\description{
-jobs.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/jobs.get.Rd b/sdk/R/man/jobs.get.Rd
deleted file mode 100644
index 072b613e1..000000000
--- a/sdk/R/man/jobs.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{jobs.get}
-\alias{jobs.get}
-\title{jobs.get}
-\usage{
-arv$jobs.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Job in question.}
-}
-\value{
-Job object.
-}
-\description{
-jobs.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/jobs.list.Rd b/sdk/R/man/jobs.list.Rd
deleted file mode 100644
index 53055f587..000000000
--- a/sdk/R/man/jobs.list.Rd
+++ /dev/null
@@ -1,33 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{jobs.list}
-\alias{jobs.list}
-\title{jobs.list}
-\usage{
-arv$jobs.list(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-JobList object.
-}
-\description{
-jobs.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/jobs.lock.Rd b/sdk/R/man/jobs.lock.Rd
deleted file mode 100644
index 3c2e23280..000000000
--- a/sdk/R/man/jobs.lock.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{jobs.lock}
-\alias{jobs.lock}
-\title{jobs.lock}
-\usage{
-arv$jobs.lock(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-Job object.
-}
-\description{
-jobs.lock is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/jobs.queue.Rd b/sdk/R/man/jobs.queue.Rd
deleted file mode 100644
index a9deaa971..000000000
--- a/sdk/R/man/jobs.queue.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{jobs.queue}
-\alias{jobs.queue}
-\title{jobs.queue}
-\usage{
-arv$jobs.queue(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-Job object.
-}
-\description{
-jobs.queue is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/jobs.queue_size.Rd b/sdk/R/man/jobs.queue_size.Rd
deleted file mode 100644
index 21858204b..000000000
--- a/sdk/R/man/jobs.queue_size.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{jobs.queue_size}
-\alias{jobs.queue_size}
-\title{jobs.queue_size}
-\usage{
-arv$jobs.queue_size(NULL)
-}
-\value{
-Job object.
-}
-\description{
-jobs.queue_size is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/jobs.update.Rd b/sdk/R/man/jobs.update.Rd
deleted file mode 100644
index 666d7fd7f..000000000
--- a/sdk/R/man/jobs.update.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{jobs.update}
-\alias{jobs.update}
-\title{jobs.update}
-\usage{
-arv$jobs.update(job, uuid)
-}
-\arguments{
-\item{job}{Job object.}
-
-\item{uuid}{The UUID of the Job in question.}
-}
-\value{
-Job object.
-}
-\description{
-jobs.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/keep_disks.create.Rd b/sdk/R/man/keep_disks.create.Rd
deleted file mode 100644
index 524c5b642..000000000
--- a/sdk/R/man/keep_disks.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{keep_disks.create}
-\alias{keep_disks.create}
-\title{keep_disks.create}
-\usage{
-arv$keep_disks.create(keepdisk,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{keepDisk}{KeepDisk object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-KeepDisk object.
-}
-\description{
-keep_disks.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/keep_disks.delete.Rd b/sdk/R/man/keep_disks.delete.Rd
deleted file mode 100644
index 80f39f314..000000000
--- a/sdk/R/man/keep_disks.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{keep_disks.delete}
-\alias{keep_disks.delete}
-\title{keep_disks.delete}
-\usage{
-arv$keep_disks.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the KeepDisk in question.}
-}
-\value{
-KeepDisk object.
-}
-\description{
-keep_disks.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/keep_disks.get.Rd b/sdk/R/man/keep_disks.get.Rd
deleted file mode 100644
index 1b511fe1f..000000000
--- a/sdk/R/man/keep_disks.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{keep_disks.get}
-\alias{keep_disks.get}
-\title{keep_disks.get}
-\usage{
-arv$keep_disks.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the KeepDisk in question.}
-}
-\value{
-KeepDisk object.
-}
-\description{
-keep_disks.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/keep_disks.list.Rd b/sdk/R/man/keep_disks.list.Rd
deleted file mode 100644
index fdb599f70..000000000
--- a/sdk/R/man/keep_disks.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{keep_disks.list}
-\alias{keep_disks.list}
-\title{keep_disks.list}
-\usage{
-arv$keep_disks.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-KeepDiskList object.
-}
-\description{
-keep_disks.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/keep_disks.ping.Rd b/sdk/R/man/keep_disks.ping.Rd
deleted file mode 100644
index 6ae55955f..000000000
--- a/sdk/R/man/keep_disks.ping.Rd
+++ /dev/null
@@ -1,31 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{keep_disks.ping}
-\alias{keep_disks.ping}
-\title{keep_disks.ping}
-\usage{
-arv$keep_disks.ping(uuid = NULL,
- ping_secret, node_uuid = NULL, filesystem_uuid = NULL,
- service_host = NULL, service_port, service_ssl_flag)
-}
-\arguments{
-\item{uuid}{}
-
-\item{ping_secret}{}
-
-\item{node_uuid}{}
-
-\item{filesystem_uuid}{}
-
-\item{service_host}{}
-
-\item{service_port}{}
-
-\item{service_ssl_flag}{}
-}
-\value{
-KeepDisk object.
-}
-\description{
-keep_disks.ping is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/keep_disks.update.Rd b/sdk/R/man/keep_disks.update.Rd
deleted file mode 100644
index 1ca3363ce..000000000
--- a/sdk/R/man/keep_disks.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{keep_disks.update}
-\alias{keep_disks.update}
-\title{keep_disks.update}
-\usage{
-arv$keep_disks.update(keepdisk,
- uuid)
-}
-\arguments{
-\item{keepDisk}{KeepDisk object.}
-
-\item{uuid}{The UUID of the KeepDisk in question.}
-}
-\value{
-KeepDisk object.
-}
-\description{
-keep_disks.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/keep_services.accessible.Rd b/sdk/R/man/keep_services.accessible.Rd
deleted file mode 100644
index 3caae2f24..000000000
--- a/sdk/R/man/keep_services.accessible.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{keep_services.accessible}
-\alias{keep_services.accessible}
-\title{keep_services.accessible}
-\usage{
-arv$keep_services.accessible(NULL)
-}
-\value{
-KeepService object.
-}
-\description{
-keep_services.accessible is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/keep_services.create.Rd b/sdk/R/man/keep_services.create.Rd
deleted file mode 100644
index 59c43ab82..000000000
--- a/sdk/R/man/keep_services.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{keep_services.create}
-\alias{keep_services.create}
-\title{keep_services.create}
-\usage{
-arv$keep_services.create(keepservice,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{keepService}{KeepService object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-KeepService object.
-}
-\description{
-keep_services.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/keep_services.delete.Rd b/sdk/R/man/keep_services.delete.Rd
deleted file mode 100644
index 726771e79..000000000
--- a/sdk/R/man/keep_services.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{keep_services.delete}
-\alias{keep_services.delete}
-\title{keep_services.delete}
-\usage{
-arv$keep_services.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the KeepService in question.}
-}
-\value{
-KeepService object.
-}
-\description{
-keep_services.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/keep_services.get.Rd b/sdk/R/man/keep_services.get.Rd
deleted file mode 100644
index 065cf8465..000000000
--- a/sdk/R/man/keep_services.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{keep_services.get}
-\alias{keep_services.get}
-\title{keep_services.get}
-\usage{
-arv$keep_services.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the KeepService in question.}
-}
-\value{
-KeepService object.
-}
-\description{
-keep_services.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/keep_services.list.Rd b/sdk/R/man/keep_services.list.Rd
deleted file mode 100644
index 22aa3aa10..000000000
--- a/sdk/R/man/keep_services.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{keep_services.list}
-\alias{keep_services.list}
-\title{keep_services.list}
-\usage{
-arv$keep_services.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-KeepServiceList object.
-}
-\description{
-keep_services.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/keep_services.update.Rd b/sdk/R/man/keep_services.update.Rd
deleted file mode 100644
index 2680a5c76..000000000
--- a/sdk/R/man/keep_services.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{keep_services.update}
-\alias{keep_services.update}
-\title{keep_services.update}
-\usage{
-arv$keep_services.update(keepservice,
- uuid)
-}
-\arguments{
-\item{keepService}{KeepService object.}
-
-\item{uuid}{The UUID of the KeepService in question.}
-}
-\value{
-KeepService object.
-}
-\description{
-keep_services.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/links.create.Rd b/sdk/R/man/links.create.Rd
deleted file mode 100644
index 06b012e3a..000000000
--- a/sdk/R/man/links.create.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{links.create}
-\alias{links.create}
-\title{links.create}
-\usage{
-arv$links.create(link, ensure_unique_name = "false")
-}
-\arguments{
-\item{link}{Link object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-Link object.
-}
-\description{
-links.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/links.delete.Rd b/sdk/R/man/links.delete.Rd
deleted file mode 100644
index 3a78b7f22..000000000
--- a/sdk/R/man/links.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{links.delete}
-\alias{links.delete}
-\title{links.delete}
-\usage{
-arv$links.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Link in question.}
-}
-\value{
-Link object.
-}
-\description{
-links.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/links.get.Rd b/sdk/R/man/links.get.Rd
deleted file mode 100644
index bf2627126..000000000
--- a/sdk/R/man/links.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{links.get}
-\alias{links.get}
-\title{links.get}
-\usage{
-arv$links.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Link in question.}
-}
-\value{
-Link object.
-}
-\description{
-links.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/links.get_permissions.Rd b/sdk/R/man/links.get_permissions.Rd
deleted file mode 100644
index 982dbb969..000000000
--- a/sdk/R/man/links.get_permissions.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{links.get_permissions}
-\alias{links.get_permissions}
-\title{links.get_permissions}
-\usage{
-arv$links.get_permissions(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-Link object.
-}
-\description{
-links.get_permissions is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/links.list.Rd b/sdk/R/man/links.list.Rd
deleted file mode 100644
index 540fdc168..000000000
--- a/sdk/R/man/links.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{links.list}
-\alias{links.list}
-\title{links.list}
-\usage{
-arv$links.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-LinkList object.
-}
-\description{
-links.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/links.update.Rd b/sdk/R/man/links.update.Rd
deleted file mode 100644
index 398b6fd03..000000000
--- a/sdk/R/man/links.update.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{links.update}
-\alias{links.update}
-\title{links.update}
-\usage{
-arv$links.update(link, uuid)
-}
-\arguments{
-\item{link}{Link object.}
-
-\item{uuid}{The UUID of the Link in question.}
-}
-\value{
-Link object.
-}
-\description{
-links.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/listAll.Rd b/sdk/R/man/listAll.Rd
index 2084b476f..b9a5c5d17 100644
--- a/sdk/R/man/listAll.Rd
+++ b/sdk/R/man/listAll.Rd
@@ -1,22 +1,22 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/util.R
-\name{listAll}
-\alias{listAll}
-\title{listAll}
-\usage{
-listAll(fn, ...)
-}
-\arguments{
-\item{fn}{Arvados method used to retrieve items from REST service.}
-
-\item{...}{Optional arguments which will be pased to fn .}
-}
-\description{
-List all resources even if the number of items is greater than maximum API limit.
-}
-\examples{
-\dontrun{
-arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
-cl <- listAll(arv$collections.list, filters = list(list("name", "like", "test\%"))
-}
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/util.R
+\name{listAll}
+\alias{listAll}
+\title{listAll}
+\usage{
+listAll(fn, ...)
+}
+\arguments{
+\item{fn}{Arvados method used to retrieve items from REST service.}
+
+\item{...}{Optional arguments which will be pased to fn .}
+}
+\description{
+List all resources even if the number of items is greater than maximum API limit.
+}
+\examples{
+\dontrun{
+arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
+cl <- listAll(arv$collections.list, filters = list(list("name", "like", "test\%"))
+}
+}
diff --git a/sdk/R/man/logs.create.Rd b/sdk/R/man/logs.create.Rd
deleted file mode 100644
index a575e5fb8..000000000
--- a/sdk/R/man/logs.create.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{logs.create}
-\alias{logs.create}
-\title{logs.create}
-\usage{
-arv$logs.create(log, ensure_unique_name = "false")
-}
-\arguments{
-\item{log}{Log object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-Log object.
-}
-\description{
-logs.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/logs.delete.Rd b/sdk/R/man/logs.delete.Rd
deleted file mode 100644
index 63d6a0bb6..000000000
--- a/sdk/R/man/logs.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{logs.delete}
-\alias{logs.delete}
-\title{logs.delete}
-\usage{
-arv$logs.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Log in question.}
-}
-\value{
-Log object.
-}
-\description{
-logs.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/logs.get.Rd b/sdk/R/man/logs.get.Rd
deleted file mode 100644
index d3053d1af..000000000
--- a/sdk/R/man/logs.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{logs.get}
-\alias{logs.get}
-\title{logs.get}
-\usage{
-arv$logs.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Log in question.}
-}
-\value{
-Log object.
-}
-\description{
-logs.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/logs.list.Rd b/sdk/R/man/logs.list.Rd
deleted file mode 100644
index 58dbdb71e..000000000
--- a/sdk/R/man/logs.list.Rd
+++ /dev/null
@@ -1,33 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{logs.list}
-\alias{logs.list}
-\title{logs.list}
-\usage{
-arv$logs.list(filters = NULL, where = NULL,
- order = NULL, select = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-LogList object.
-}
-\description{
-logs.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/logs.update.Rd b/sdk/R/man/logs.update.Rd
deleted file mode 100644
index efd670c27..000000000
--- a/sdk/R/man/logs.update.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{logs.update}
-\alias{logs.update}
-\title{logs.update}
-\usage{
-arv$logs.update(log, uuid)
-}
-\arguments{
-\item{log}{Log object.}
-
-\item{uuid}{The UUID of the Log in question.}
-}
-\value{
-Log object.
-}
-\description{
-logs.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/nodes.create.Rd b/sdk/R/man/nodes.create.Rd
deleted file mode 100644
index eb73e6915..000000000
--- a/sdk/R/man/nodes.create.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{nodes.create}
-\alias{nodes.create}
-\title{nodes.create}
-\usage{
-arv$nodes.create(node, ensure_unique_name = "false",
- assign_slot = NULL)
-}
-\arguments{
-\item{node}{Node object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-
-\item{assign_slot}{assign slot and hostname}
-}
-\value{
-Node object.
-}
-\description{
-nodes.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/nodes.delete.Rd b/sdk/R/man/nodes.delete.Rd
deleted file mode 100644
index 0591dedcc..000000000
--- a/sdk/R/man/nodes.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{nodes.delete}
-\alias{nodes.delete}
-\title{nodes.delete}
-\usage{
-arv$nodes.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Node in question.}
-}
-\value{
-Node object.
-}
-\description{
-nodes.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/nodes.get.Rd b/sdk/R/man/nodes.get.Rd
deleted file mode 100644
index dcd7b1209..000000000
--- a/sdk/R/man/nodes.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{nodes.get}
-\alias{nodes.get}
-\title{nodes.get}
-\usage{
-arv$nodes.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Node in question.}
-}
-\value{
-Node object.
-}
-\description{
-nodes.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/nodes.list.Rd b/sdk/R/man/nodes.list.Rd
deleted file mode 100644
index 7ccfad6d9..000000000
--- a/sdk/R/man/nodes.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{nodes.list}
-\alias{nodes.list}
-\title{nodes.list}
-\usage{
-arv$nodes.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-NodeList object.
-}
-\description{
-nodes.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/nodes.ping.Rd b/sdk/R/man/nodes.ping.Rd
deleted file mode 100644
index e77d2b5b8..000000000
--- a/sdk/R/man/nodes.ping.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{nodes.ping}
-\alias{nodes.ping}
-\title{nodes.ping}
-\usage{
-arv$nodes.ping(uuid, ping_secret)
-}
-\arguments{
-\item{uuid}{}
-
-\item{ping_secret}{}
-}
-\value{
-Node object.
-}
-\description{
-nodes.ping is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/nodes.update.Rd b/sdk/R/man/nodes.update.Rd
deleted file mode 100644
index f87245f9d..000000000
--- a/sdk/R/man/nodes.update.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{nodes.update}
-\alias{nodes.update}
-\title{nodes.update}
-\usage{
-arv$nodes.update(node, uuid, assign_slot = NULL)
-}
-\arguments{
-\item{node}{Node object.}
-
-\item{uuid}{The UUID of the Node in question.}
-
-\item{assign_slot}{assign slot and hostname}
-}
-\value{
-Node object.
-}
-\description{
-nodes.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/pipeline_instances.cancel.Rd b/sdk/R/man/pipeline_instances.cancel.Rd
deleted file mode 100644
index 026de816f..000000000
--- a/sdk/R/man/pipeline_instances.cancel.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{pipeline_instances.cancel}
-\alias{pipeline_instances.cancel}
-\title{pipeline_instances.cancel}
-\usage{
-arv$pipeline_instances.cancel(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-PipelineInstance object.
-}
-\description{
-pipeline_instances.cancel is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/pipeline_instances.create.Rd b/sdk/R/man/pipeline_instances.create.Rd
deleted file mode 100644
index 9ee5586c8..000000000
--- a/sdk/R/man/pipeline_instances.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{pipeline_instances.create}
-\alias{pipeline_instances.create}
-\title{pipeline_instances.create}
-\usage{
-arv$pipeline_instances.create(pipelineinstance,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{pipelineInstance}{PipelineInstance object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-PipelineInstance object.
-}
-\description{
-pipeline_instances.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/pipeline_instances.delete.Rd b/sdk/R/man/pipeline_instances.delete.Rd
deleted file mode 100644
index 7297da5bd..000000000
--- a/sdk/R/man/pipeline_instances.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{pipeline_instances.delete}
-\alias{pipeline_instances.delete}
-\title{pipeline_instances.delete}
-\usage{
-arv$pipeline_instances.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the PipelineInstance in question.}
-}
-\value{
-PipelineInstance object.
-}
-\description{
-pipeline_instances.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/pipeline_instances.get.Rd b/sdk/R/man/pipeline_instances.get.Rd
deleted file mode 100644
index e500df589..000000000
--- a/sdk/R/man/pipeline_instances.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{pipeline_instances.get}
-\alias{pipeline_instances.get}
-\title{pipeline_instances.get}
-\usage{
-arv$pipeline_instances.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the PipelineInstance in question.}
-}
-\value{
-PipelineInstance object.
-}
-\description{
-pipeline_instances.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/pipeline_instances.list.Rd b/sdk/R/man/pipeline_instances.list.Rd
deleted file mode 100644
index 407f94446..000000000
--- a/sdk/R/man/pipeline_instances.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{pipeline_instances.list}
-\alias{pipeline_instances.list}
-\title{pipeline_instances.list}
-\usage{
-arv$pipeline_instances.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-PipelineInstanceList object.
-}
-\description{
-pipeline_instances.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/pipeline_instances.update.Rd b/sdk/R/man/pipeline_instances.update.Rd
deleted file mode 100644
index 4a6666004..000000000
--- a/sdk/R/man/pipeline_instances.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{pipeline_instances.update}
-\alias{pipeline_instances.update}
-\title{pipeline_instances.update}
-\usage{
-arv$pipeline_instances.update(pipelineinstance,
- uuid)
-}
-\arguments{
-\item{pipelineInstance}{PipelineInstance object.}
-
-\item{uuid}{The UUID of the PipelineInstance in question.}
-}
-\value{
-PipelineInstance object.
-}
-\description{
-pipeline_instances.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/pipeline_templates.create.Rd b/sdk/R/man/pipeline_templates.create.Rd
deleted file mode 100644
index afb1e5870..000000000
--- a/sdk/R/man/pipeline_templates.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{pipeline_templates.create}
-\alias{pipeline_templates.create}
-\title{pipeline_templates.create}
-\usage{
-arv$pipeline_templates.create(pipelinetemplate,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{pipelineTemplate}{PipelineTemplate object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-PipelineTemplate object.
-}
-\description{
-pipeline_templates.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/pipeline_templates.delete.Rd b/sdk/R/man/pipeline_templates.delete.Rd
deleted file mode 100644
index c74d88b05..000000000
--- a/sdk/R/man/pipeline_templates.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{pipeline_templates.delete}
-\alias{pipeline_templates.delete}
-\title{pipeline_templates.delete}
-\usage{
-arv$pipeline_templates.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the PipelineTemplate in question.}
-}
-\value{
-PipelineTemplate object.
-}
-\description{
-pipeline_templates.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/pipeline_templates.get.Rd b/sdk/R/man/pipeline_templates.get.Rd
deleted file mode 100644
index 48ef73950..000000000
--- a/sdk/R/man/pipeline_templates.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{pipeline_templates.get}
-\alias{pipeline_templates.get}
-\title{pipeline_templates.get}
-\usage{
-arv$pipeline_templates.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the PipelineTemplate in question.}
-}
-\value{
-PipelineTemplate object.
-}
-\description{
-pipeline_templates.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/pipeline_templates.list.Rd b/sdk/R/man/pipeline_templates.list.Rd
deleted file mode 100644
index c6c7413d5..000000000
--- a/sdk/R/man/pipeline_templates.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{pipeline_templates.list}
-\alias{pipeline_templates.list}
-\title{pipeline_templates.list}
-\usage{
-arv$pipeline_templates.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-PipelineTemplateList object.
-}
-\description{
-pipeline_templates.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/pipeline_templates.update.Rd b/sdk/R/man/pipeline_templates.update.Rd
deleted file mode 100644
index 25e02bfad..000000000
--- a/sdk/R/man/pipeline_templates.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{pipeline_templates.update}
-\alias{pipeline_templates.update}
-\title{pipeline_templates.update}
-\usage{
-arv$pipeline_templates.update(pipelinetemplate,
- uuid)
-}
-\arguments{
-\item{pipelineTemplate}{PipelineTemplate object.}
-
-\item{uuid}{The UUID of the PipelineTemplate in question.}
-}
-\value{
-PipelineTemplate object.
-}
-\description{
-pipeline_templates.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/print.ArvadosFile.Rd b/sdk/R/man/print.ArvadosFile.Rd
index 566ec8b20..43f734121 100644
--- a/sdk/R/man/print.ArvadosFile.Rd
+++ b/sdk/R/man/print.ArvadosFile.Rd
@@ -1,16 +1,16 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ArvadosFile.R
-\name{print.ArvadosFile}
-\alias{print.ArvadosFile}
-\title{print.ArvadosFile}
-\usage{
-\method{print}{ArvadosFile}(x, ...)
-}
-\arguments{
-\item{x}{Instance of ArvadosFile class}
-
-\item{...}{Optional arguments.}
-}
-\description{
-Custom print function for ArvadosFile class
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ArvadosFile.R
+\name{print.ArvadosFile}
+\alias{print.ArvadosFile}
+\title{print.ArvadosFile}
+\usage{
+\method{print}{ArvadosFile}(x, ...)
+}
+\arguments{
+\item{x}{Instance of ArvadosFile class}
+
+\item{...}{Optional arguments.}
+}
+\description{
+Custom print function for ArvadosFile class
+}
diff --git a/sdk/R/man/print.Collection.Rd b/sdk/R/man/print.Collection.Rd
index 885238370..3de4bd541 100644
--- a/sdk/R/man/print.Collection.Rd
+++ b/sdk/R/man/print.Collection.Rd
@@ -1,16 +1,16 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Collection.R
-\name{print.Collection}
-\alias{print.Collection}
-\title{print.Collection}
-\usage{
-\method{print}{Collection}(x, ...)
-}
-\arguments{
-\item{x}{Instance of Collection class}
-
-\item{...}{Optional arguments.}
-}
-\description{
-Custom print function for Collection class
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Collection.R
+\name{print.Collection}
+\alias{print.Collection}
+\title{print.Collection}
+\usage{
+\method{print}{Collection}(x, ...)
+}
+\arguments{
+\item{x}{Instance of Collection class}
+
+\item{...}{Optional arguments.}
+}
+\description{
+Custom print function for Collection class
+}
diff --git a/sdk/R/man/print.Subcollection.Rd b/sdk/R/man/print.Subcollection.Rd
index 621350f60..3bc62c090 100644
--- a/sdk/R/man/print.Subcollection.Rd
+++ b/sdk/R/man/print.Subcollection.Rd
@@ -1,16 +1,16 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Subcollection.R
-\name{print.Subcollection}
-\alias{print.Subcollection}
-\title{print.Subcollection}
-\usage{
-\method{print}{Subcollection}(x, ...)
-}
-\arguments{
-\item{x}{Instance of Subcollection class}
-
-\item{...}{Optional arguments.}
-}
-\description{
-Custom print function for Subcollection class
-}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Subcollection.R
+\name{print.Subcollection}
+\alias{print.Subcollection}
+\title{print.Subcollection}
+\usage{
+\method{print}{Subcollection}(x, ...)
+}
+\arguments{
+\item{x}{Instance of Subcollection class}
+
+\item{...}{Optional arguments.}
+}
+\description{
+Custom print function for Subcollection class
+}
diff --git a/sdk/R/man/projects.create.Rd b/sdk/R/man/projects.create.Rd
deleted file mode 100644
index 66b1f2ab6..000000000
--- a/sdk/R/man/projects.create.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{projects.create}
-\alias{projects.create}
-\title{project.create}
-\usage{
-arv$projects.create(group, ensure_unique_name = "false")
-}
-\arguments{
-\item{group}{Group object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-Group object.
-}
-\description{
-projects.create wrapps groups.create method by setting group_class attribute to "project".
-}
diff --git a/sdk/R/man/projects.delete.Rd b/sdk/R/man/projects.delete.Rd
deleted file mode 100644
index 7170792ed..000000000
--- a/sdk/R/man/projects.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{projects.delete}
-\alias{projects.delete}
-\title{project.delete}
-\usage{
-arv$project.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Group in question.}
-}
-\value{
-Group object.
-}
-\description{
-projects.delete is equivalent to groups.delete method.
-}
diff --git a/sdk/R/man/projects.get.Rd b/sdk/R/man/projects.get.Rd
deleted file mode 100644
index 193937878..000000000
--- a/sdk/R/man/projects.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{projects.get}
-\alias{projects.get}
-\title{project.get}
-\usage{
-arv$projects.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Group in question.}
-}
-\value{
-Group object.
-}
-\description{
-projects.get is equivalent to groups.get method.
-}
diff --git a/sdk/R/man/projects.list.Rd b/sdk/R/man/projects.list.Rd
deleted file mode 100644
index ff4c1c9ed..000000000
--- a/sdk/R/man/projects.list.Rd
+++ /dev/null
@@ -1,38 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{projects.list}
-\alias{projects.list}
-\title{project.list}
-\usage{
-arv$projects.list(filters = NULL,
- where = NULL, order = NULL, distinct = NULL,
- limit = "100", offset = "0", count = "exact",
- include_trash = NULL, uuid = NULL, recursive = NULL)
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-
-\item{include_trash}{Include items whose is_trashed attribute is true.}
-
-\item{uuid}{}
-
-\item{recursive}{Include contents from child groups recursively.}
-}
-\value{
-Group object.
-}
-\description{
-projects.list wrapps groups.list method by setting group_class attribute to "project".
-}
diff --git a/sdk/R/man/projects.update.Rd b/sdk/R/man/projects.update.Rd
deleted file mode 100644
index 824c5b53f..000000000
--- a/sdk/R/man/projects.update.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{projects.update}
-\alias{projects.update}
-\title{project.update}
-\usage{
-arv$projects.update(group, uuid)
-}
-\arguments{
-\item{group}{Group object.}
-
-\item{uuid}{The UUID of the Group in question.}
-}
-\value{
-Group object.
-}
-\description{
-projects.update wrapps groups.update method by setting group_class attribute to "project".
-}
diff --git a/sdk/R/man/repositories.create.Rd b/sdk/R/man/repositories.create.Rd
deleted file mode 100644
index 1603604f3..000000000
--- a/sdk/R/man/repositories.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{repositories.create}
-\alias{repositories.create}
-\title{repositories.create}
-\usage{
-arv$repositories.create(repository,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{repository}{Repository object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-Repository object.
-}
-\description{
-repositories.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/repositories.delete.Rd b/sdk/R/man/repositories.delete.Rd
deleted file mode 100644
index 36fac73ac..000000000
--- a/sdk/R/man/repositories.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{repositories.delete}
-\alias{repositories.delete}
-\title{repositories.delete}
-\usage{
-arv$repositories.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Repository in question.}
-}
-\value{
-Repository object.
-}
-\description{
-repositories.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/repositories.get.Rd b/sdk/R/man/repositories.get.Rd
deleted file mode 100644
index b855b76d8..000000000
--- a/sdk/R/man/repositories.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{repositories.get}
-\alias{repositories.get}
-\title{repositories.get}
-\usage{
-arv$repositories.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Repository in question.}
-}
-\value{
-Repository object.
-}
-\description{
-repositories.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/repositories.get_all_permissions.Rd b/sdk/R/man/repositories.get_all_permissions.Rd
deleted file mode 100644
index f16dbd1d9..000000000
--- a/sdk/R/man/repositories.get_all_permissions.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{repositories.get_all_permissions}
-\alias{repositories.get_all_permissions}
-\title{repositories.get_all_permissions}
-\usage{
-arv$repositories.get_all_permissions(NULL)
-}
-\value{
-Repository object.
-}
-\description{
-repositories.get_all_permissions is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/repositories.list.Rd b/sdk/R/man/repositories.list.Rd
deleted file mode 100644
index d1f4772e7..000000000
--- a/sdk/R/man/repositories.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{repositories.list}
-\alias{repositories.list}
-\title{repositories.list}
-\usage{
-arv$repositories.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-RepositoryList object.
-}
-\description{
-repositories.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/repositories.update.Rd b/sdk/R/man/repositories.update.Rd
deleted file mode 100644
index 1be4b6148..000000000
--- a/sdk/R/man/repositories.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{repositories.update}
-\alias{repositories.update}
-\title{repositories.update}
-\usage{
-arv$repositories.update(repository,
- uuid)
-}
-\arguments{
-\item{repository}{Repository object.}
-
-\item{uuid}{The UUID of the Repository in question.}
-}
-\value{
-Repository object.
-}
-\description{
-repositories.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/specimens.create.Rd b/sdk/R/man/specimens.create.Rd
deleted file mode 100644
index 12344f29f..000000000
--- a/sdk/R/man/specimens.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{specimens.create}
-\alias{specimens.create}
-\title{specimens.create}
-\usage{
-arv$specimens.create(specimen,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{specimen}{Specimen object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-Specimen object.
-}
-\description{
-specimens.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/specimens.delete.Rd b/sdk/R/man/specimens.delete.Rd
deleted file mode 100644
index 8ed2d397a..000000000
--- a/sdk/R/man/specimens.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{specimens.delete}
-\alias{specimens.delete}
-\title{specimens.delete}
-\usage{
-arv$specimens.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Specimen in question.}
-}
-\value{
-Specimen object.
-}
-\description{
-specimens.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/specimens.get.Rd b/sdk/R/man/specimens.get.Rd
deleted file mode 100644
index e757056a2..000000000
--- a/sdk/R/man/specimens.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{specimens.get}
-\alias{specimens.get}
-\title{specimens.get}
-\usage{
-arv$specimens.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Specimen in question.}
-}
-\value{
-Specimen object.
-}
-\description{
-specimens.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/specimens.list.Rd b/sdk/R/man/specimens.list.Rd
deleted file mode 100644
index 4e07f4ab2..000000000
--- a/sdk/R/man/specimens.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{specimens.list}
-\alias{specimens.list}
-\title{specimens.list}
-\usage{
-arv$specimens.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-SpecimenList object.
-}
-\description{
-specimens.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/specimens.update.Rd b/sdk/R/man/specimens.update.Rd
deleted file mode 100644
index 73a901087..000000000
--- a/sdk/R/man/specimens.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{specimens.update}
-\alias{specimens.update}
-\title{specimens.update}
-\usage{
-arv$specimens.update(specimen,
- uuid)
-}
-\arguments{
-\item{specimen}{Specimen object.}
-
-\item{uuid}{The UUID of the Specimen in question.}
-}
-\value{
-Specimen object.
-}
-\description{
-specimens.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/traits.create.Rd b/sdk/R/man/traits.create.Rd
deleted file mode 100644
index bf6e0c1e1..000000000
--- a/sdk/R/man/traits.create.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{traits.create}
-\alias{traits.create}
-\title{traits.create}
-\usage{
-arv$traits.create(trait, ensure_unique_name = "false")
-}
-\arguments{
-\item{trait}{Trait object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-Trait object.
-}
-\description{
-traits.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/traits.delete.Rd b/sdk/R/man/traits.delete.Rd
deleted file mode 100644
index 9ab957002..000000000
--- a/sdk/R/man/traits.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{traits.delete}
-\alias{traits.delete}
-\title{traits.delete}
-\usage{
-arv$traits.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Trait in question.}
-}
-\value{
-Trait object.
-}
-\description{
-traits.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/traits.get.Rd b/sdk/R/man/traits.get.Rd
deleted file mode 100644
index 7d2bac56b..000000000
--- a/sdk/R/man/traits.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{traits.get}
-\alias{traits.get}
-\title{traits.get}
-\usage{
-arv$traits.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Trait in question.}
-}
-\value{
-Trait object.
-}
-\description{
-traits.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/traits.list.Rd b/sdk/R/man/traits.list.Rd
deleted file mode 100644
index e91b92994..000000000
--- a/sdk/R/man/traits.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{traits.list}
-\alias{traits.list}
-\title{traits.list}
-\usage{
-arv$traits.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-TraitList object.
-}
-\description{
-traits.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/traits.update.Rd b/sdk/R/man/traits.update.Rd
deleted file mode 100644
index f59443422..000000000
--- a/sdk/R/man/traits.update.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{traits.update}
-\alias{traits.update}
-\title{traits.update}
-\usage{
-arv$traits.update(trait, uuid)
-}
-\arguments{
-\item{trait}{Trait object.}
-
-\item{uuid}{The UUID of the Trait in question.}
-}
-\value{
-Trait object.
-}
-\description{
-traits.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/user_agreements.create.Rd b/sdk/R/man/user_agreements.create.Rd
deleted file mode 100644
index 79913057c..000000000
--- a/sdk/R/man/user_agreements.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{user_agreements.create}
-\alias{user_agreements.create}
-\title{user_agreements.create}
-\usage{
-arv$user_agreements.create(useragreement,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{userAgreement}{UserAgreement object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-UserAgreement object.
-}
-\description{
-user_agreements.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/user_agreements.delete.Rd b/sdk/R/man/user_agreements.delete.Rd
deleted file mode 100644
index 30c9bf80b..000000000
--- a/sdk/R/man/user_agreements.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{user_agreements.delete}
-\alias{user_agreements.delete}
-\title{user_agreements.delete}
-\usage{
-arv$user_agreements.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the UserAgreement in question.}
-}
-\value{
-UserAgreement object.
-}
-\description{
-user_agreements.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/user_agreements.get.Rd b/sdk/R/man/user_agreements.get.Rd
deleted file mode 100644
index 63116059e..000000000
--- a/sdk/R/man/user_agreements.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{user_agreements.get}
-\alias{user_agreements.get}
-\title{user_agreements.get}
-\usage{
-arv$user_agreements.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the UserAgreement in question.}
-}
-\value{
-UserAgreement object.
-}
-\description{
-user_agreements.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/user_agreements.list.Rd b/sdk/R/man/user_agreements.list.Rd
deleted file mode 100644
index 5e6986189..000000000
--- a/sdk/R/man/user_agreements.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{user_agreements.list}
-\alias{user_agreements.list}
-\title{user_agreements.list}
-\usage{
-arv$user_agreements.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-UserAgreementList object.
-}
-\description{
-user_agreements.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/user_agreements.new.Rd b/sdk/R/man/user_agreements.new.Rd
deleted file mode 100644
index c213cb425..000000000
--- a/sdk/R/man/user_agreements.new.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{user_agreements.new}
-\alias{user_agreements.new}
-\title{user_agreements.new}
-\usage{
-arv$user_agreements.new(NULL)
-}
-\value{
-UserAgreement object.
-}
-\description{
-user_agreements.new is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/user_agreements.sign.Rd b/sdk/R/man/user_agreements.sign.Rd
deleted file mode 100644
index 98116106b..000000000
--- a/sdk/R/man/user_agreements.sign.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{user_agreements.sign}
-\alias{user_agreements.sign}
-\title{user_agreements.sign}
-\usage{
-arv$user_agreements.sign(NULL)
-}
-\value{
-UserAgreement object.
-}
-\description{
-user_agreements.sign is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/user_agreements.signatures.Rd b/sdk/R/man/user_agreements.signatures.Rd
deleted file mode 100644
index d889579bb..000000000
--- a/sdk/R/man/user_agreements.signatures.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{user_agreements.signatures}
-\alias{user_agreements.signatures}
-\title{user_agreements.signatures}
-\usage{
-arv$user_agreements.signatures(NULL)
-}
-\value{
-UserAgreement object.
-}
-\description{
-user_agreements.signatures is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/user_agreements.update.Rd b/sdk/R/man/user_agreements.update.Rd
deleted file mode 100644
index 578e17954..000000000
--- a/sdk/R/man/user_agreements.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{user_agreements.update}
-\alias{user_agreements.update}
-\title{user_agreements.update}
-\usage{
-arv$user_agreements.update(useragreement,
- uuid)
-}
-\arguments{
-\item{userAgreement}{UserAgreement object.}
-
-\item{uuid}{The UUID of the UserAgreement in question.}
-}
-\value{
-UserAgreement object.
-}
-\description{
-user_agreements.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/users.activate.Rd b/sdk/R/man/users.activate.Rd
deleted file mode 100644
index 201caf4c8..000000000
--- a/sdk/R/man/users.activate.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{users.activate}
-\alias{users.activate}
-\title{users.activate}
-\usage{
-arv$users.activate(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-User object.
-}
-\description{
-users.activate is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/users.create.Rd b/sdk/R/man/users.create.Rd
deleted file mode 100644
index 1805c66d2..000000000
--- a/sdk/R/man/users.create.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{users.create}
-\alias{users.create}
-\title{users.create}
-\usage{
-arv$users.create(user, ensure_unique_name = "false")
-}
-\arguments{
-\item{user}{User object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-User object.
-}
-\description{
-users.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/users.current.Rd b/sdk/R/man/users.current.Rd
deleted file mode 100644
index 4e8af94fb..000000000
--- a/sdk/R/man/users.current.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{users.current}
-\alias{users.current}
-\title{users.current}
-\usage{
-arv$users.current(NULL)
-}
-\value{
-User object.
-}
-\description{
-users.current is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/users.delete.Rd b/sdk/R/man/users.delete.Rd
deleted file mode 100644
index df9e23880..000000000
--- a/sdk/R/man/users.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{users.delete}
-\alias{users.delete}
-\title{users.delete}
-\usage{
-arv$users.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the User in question.}
-}
-\value{
-User object.
-}
-\description{
-users.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/users.get.Rd b/sdk/R/man/users.get.Rd
deleted file mode 100644
index ec2b284ee..000000000
--- a/sdk/R/man/users.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{users.get}
-\alias{users.get}
-\title{users.get}
-\usage{
-arv$users.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the User in question.}
-}
-\value{
-User object.
-}
-\description{
-users.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/users.list.Rd b/sdk/R/man/users.list.Rd
deleted file mode 100644
index 71319433b..000000000
--- a/sdk/R/man/users.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{users.list}
-\alias{users.list}
-\title{users.list}
-\usage{
-arv$users.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-UserList object.
-}
-\description{
-users.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/users.merge.Rd b/sdk/R/man/users.merge.Rd
deleted file mode 100644
index a539591a6..000000000
--- a/sdk/R/man/users.merge.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{users.merge}
-\alias{users.merge}
-\title{users.merge}
-\usage{
-arv$users.merge(new_owner_uuid,
- new_user_token, redirect_to_new_user = NULL)
-}
-\arguments{
-\item{new_owner_uuid}{}
-
-\item{new_user_token}{}
-
-\item{redirect_to_new_user}{}
-}
-\value{
-User object.
-}
-\description{
-users.merge is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/users.setup.Rd b/sdk/R/man/users.setup.Rd
deleted file mode 100644
index 869403d3e..000000000
--- a/sdk/R/man/users.setup.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{users.setup}
-\alias{users.setup}
-\title{users.setup}
-\usage{
-arv$users.setup(user = NULL, openid_prefix = NULL,
- repo_name = NULL, vm_uuid = NULL, send_notification_email = "false")
-}
-\arguments{
-\item{user}{}
-
-\item{openid_prefix}{}
-
-\item{repo_name}{}
-
-\item{vm_uuid}{}
-
-\item{send_notification_email}{}
-}
-\value{
-User object.
-}
-\description{
-users.setup is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/users.system.Rd b/sdk/R/man/users.system.Rd
deleted file mode 100644
index c321c23cd..000000000
--- a/sdk/R/man/users.system.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{users.system}
-\alias{users.system}
-\title{users.system}
-\usage{
-arv$users.system(NULL)
-}
-\value{
-User object.
-}
-\description{
-users.system is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/users.unsetup.Rd b/sdk/R/man/users.unsetup.Rd
deleted file mode 100644
index 85de6f978..000000000
--- a/sdk/R/man/users.unsetup.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{users.unsetup}
-\alias{users.unsetup}
-\title{users.unsetup}
-\usage{
-arv$users.unsetup(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-User object.
-}
-\description{
-users.unsetup is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/users.update.Rd b/sdk/R/man/users.update.Rd
deleted file mode 100644
index fcd9c71c7..000000000
--- a/sdk/R/man/users.update.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{users.update}
-\alias{users.update}
-\title{users.update}
-\usage{
-arv$users.update(user, uuid)
-}
-\arguments{
-\item{user}{User object.}
-
-\item{uuid}{The UUID of the User in question.}
-}
-\value{
-User object.
-}
-\description{
-users.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/virtual_machines.create.Rd b/sdk/R/man/virtual_machines.create.Rd
deleted file mode 100644
index 689a0f989..000000000
--- a/sdk/R/man/virtual_machines.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{virtual_machines.create}
-\alias{virtual_machines.create}
-\title{virtual_machines.create}
-\usage{
-arv$virtual_machines.create(virtualmachine,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{virtualMachine}{VirtualMachine object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-VirtualMachine object.
-}
-\description{
-virtual_machines.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/virtual_machines.delete.Rd b/sdk/R/man/virtual_machines.delete.Rd
deleted file mode 100644
index c513833db..000000000
--- a/sdk/R/man/virtual_machines.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{virtual_machines.delete}
-\alias{virtual_machines.delete}
-\title{virtual_machines.delete}
-\usage{
-arv$virtual_machines.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the VirtualMachine in question.}
-}
-\value{
-VirtualMachine object.
-}
-\description{
-virtual_machines.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/virtual_machines.get.Rd b/sdk/R/man/virtual_machines.get.Rd
deleted file mode 100644
index 3e56e17ea..000000000
--- a/sdk/R/man/virtual_machines.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{virtual_machines.get}
-\alias{virtual_machines.get}
-\title{virtual_machines.get}
-\usage{
-arv$virtual_machines.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the VirtualMachine in question.}
-}
-\value{
-VirtualMachine object.
-}
-\description{
-virtual_machines.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/virtual_machines.get_all_logins.Rd b/sdk/R/man/virtual_machines.get_all_logins.Rd
deleted file mode 100644
index b2af1e492..000000000
--- a/sdk/R/man/virtual_machines.get_all_logins.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{virtual_machines.get_all_logins}
-\alias{virtual_machines.get_all_logins}
-\title{virtual_machines.get_all_logins}
-\usage{
-arv$virtual_machines.get_all_logins(NULL)
-}
-\value{
-VirtualMachine object.
-}
-\description{
-virtual_machines.get_all_logins is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/virtual_machines.list.Rd b/sdk/R/man/virtual_machines.list.Rd
deleted file mode 100644
index 42ed58b0e..000000000
--- a/sdk/R/man/virtual_machines.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{virtual_machines.list}
-\alias{virtual_machines.list}
-\title{virtual_machines.list}
-\usage{
-arv$virtual_machines.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-VirtualMachineList object.
-}
-\description{
-virtual_machines.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/virtual_machines.logins.Rd b/sdk/R/man/virtual_machines.logins.Rd
deleted file mode 100644
index 7e25110aa..000000000
--- a/sdk/R/man/virtual_machines.logins.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{virtual_machines.logins}
-\alias{virtual_machines.logins}
-\title{virtual_machines.logins}
-\usage{
-arv$virtual_machines.logins(uuid)
-}
-\arguments{
-\item{uuid}{}
-}
-\value{
-VirtualMachine object.
-}
-\description{
-virtual_machines.logins is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/virtual_machines.update.Rd b/sdk/R/man/virtual_machines.update.Rd
deleted file mode 100644
index d1a07eb33..000000000
--- a/sdk/R/man/virtual_machines.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{virtual_machines.update}
-\alias{virtual_machines.update}
-\title{virtual_machines.update}
-\usage{
-arv$virtual_machines.update(virtualmachine,
- uuid)
-}
-\arguments{
-\item{virtualMachine}{VirtualMachine object.}
-
-\item{uuid}{The UUID of the VirtualMachine in question.}
-}
-\value{
-VirtualMachine object.
-}
-\description{
-virtual_machines.update is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/workflows.create.Rd b/sdk/R/man/workflows.create.Rd
deleted file mode 100644
index 8a84e0046..000000000
--- a/sdk/R/man/workflows.create.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{workflows.create}
-\alias{workflows.create}
-\title{workflows.create}
-\usage{
-arv$workflows.create(workflow,
- ensure_unique_name = "false")
-}
-\arguments{
-\item{workflow}{Workflow object.}
-
-\item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
-}
-\value{
-Workflow object.
-}
-\description{
-workflows.create is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/workflows.delete.Rd b/sdk/R/man/workflows.delete.Rd
deleted file mode 100644
index 96a561e36..000000000
--- a/sdk/R/man/workflows.delete.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{workflows.delete}
-\alias{workflows.delete}
-\title{workflows.delete}
-\usage{
-arv$workflows.delete(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Workflow in question.}
-}
-\value{
-Workflow object.
-}
-\description{
-workflows.delete is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/workflows.get.Rd b/sdk/R/man/workflows.get.Rd
deleted file mode 100644
index 8a8c3a8bd..000000000
--- a/sdk/R/man/workflows.get.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{workflows.get}
-\alias{workflows.get}
-\title{workflows.get}
-\usage{
-arv$workflows.get(uuid)
-}
-\arguments{
-\item{uuid}{The UUID of the Workflow in question.}
-}
-\value{
-Workflow object.
-}
-\description{
-workflows.get is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/workflows.list.Rd b/sdk/R/man/workflows.list.Rd
deleted file mode 100644
index e24b74d03..000000000
--- a/sdk/R/man/workflows.list.Rd
+++ /dev/null
@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{workflows.list}
-\alias{workflows.list}
-\title{workflows.list}
-\usage{
-arv$workflows.list(filters = NULL,
- where = NULL, order = NULL, select = NULL,
- distinct = NULL, limit = "100", offset = "0",
- count = "exact")
-}
-\arguments{
-\item{filters}{}
-
-\item{where}{}
-
-\item{order}{}
-
-\item{select}{}
-
-\item{distinct}{}
-
-\item{limit}{}
-
-\item{offset}{}
-
-\item{count}{}
-}
-\value{
-WorkflowList object.
-}
-\description{
-workflows.list is a method defined in Arvados class.
-}
diff --git a/sdk/R/man/workflows.update.Rd b/sdk/R/man/workflows.update.Rd
deleted file mode 100644
index d3f6186a0..000000000
--- a/sdk/R/man/workflows.update.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/Arvados.R
-\name{workflows.update}
-\alias{workflows.update}
-\title{workflows.update}
-\usage{
-arv$workflows.update(workflow,
- uuid)
-}
-\arguments{
-\item{workflow}{Workflow object.}
-
-\item{uuid}{The UUID of the Workflow in question.}
-}
-\value{
-Workflow object.
-}
-\description{
-workflows.update is a method defined in Arvados class.
-}
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