Merge branch 'master' of git.curoverse.com:arvados into 13609-r-sdk-copy
authorFuad Muhic <fmuhic@capeannenterprises.com>
Thu, 26 Jul 2018 15:18:24 +0000 (17:18 +0200)
committerFuad Muhic <fmuhic@capeannenterprises.com>
Thu, 26 Jul 2018 15:18:24 +0000 (17:18 +0200)
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

20 files changed:
sdk/R/R/Arvados.R
sdk/R/R/ArvadosFile.R
sdk/R/R/Collection.R
sdk/R/R/CollectionTree.R
sdk/R/R/HttpRequest.R
sdk/R/R/RESTService.R
sdk/R/R/Subcollection.R
sdk/R/R/zzz.R
sdk/R/README.Rmd
sdk/R/man/Arvados.Rd
sdk/R/man/ArvadosFile.Rd
sdk/R/man/Collection.Rd
sdk/R/man/Subcollection.Rd
sdk/R/man/users.merge.Rd [new file with mode: 0644]
sdk/R/tests/testthat/fakes/FakeHttpRequest.R
sdk/R/tests/testthat/fakes/FakeRESTService.R
sdk/R/tests/testthat/test-ArvadosFile.R
sdk/R/tests/testthat/test-Collection.R
sdk/R/tests/testthat/test-RESTService.R
sdk/R/tests/testthat/test-Subcollection.R

index 4b65546912393b52b4e05a4d1ecd21b83f44bd28..744cb3c296163906be8be5858e0713e8d43aa44e 100644 (file)
@@ -1,11 +1,7 @@
-# Copyright (C) The Arvados Authors. All rights reserved.
-#
-# SPDX-License-Identifier: Apache-2.0
-
 #' 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.
@@ -13,9 +9,9 @@
 NULL
 
 #' users.create
-#'
+#' 
 #' users.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$users.create(user, ensure_unique_name = "false")
 #' @param user User object.
 #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
@@ -24,9 +20,9 @@ NULL
 NULL
 
 #' users.update
-#'
+#' 
 #' users.update is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$users.update(user, uuid)
 #' @param user User object.
 #' @param uuid The UUID of the User in question.
@@ -35,9 +31,9 @@ NULL
 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.
@@ -45,93 +41,106 @@ NULL
 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
+#' @param uuid 
 #' @return User object.
 #' @name users.activate
 NULL
 
 #' users.setup
-#'
+#' 
 #' users.setup is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$users.setup(user = NULL, openid_prefix = NULL,
 #'     repo_name = NULL, vm_uuid = NULL, send_notification_email = "false")
-#' @param user
-#' @param openid_prefix
-#' @param repo_name
-#' @param vm_uuid
-#' @param send_notification_email
+#' @param user 
+#' @param openid_prefix 
+#' @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
+#' @param uuid 
 #' @return User object.
 #' @name users.unsetup
 NULL
 
 #' users.update_uuid
-#'
+#' 
 #' users.update_uuid is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$users.update_uuid(uuid, new_uuid)
-#' @param uuid
-#' @param new_uuid
+#' @param uuid 
+#' @param new_uuid 
 #' @return User object.
 #' @name users.update_uuid
 NULL
 
+#' users.merge
+#' 
+#' users.merge is a method defined in Arvados class.
+#' 
+#' @usage arv$users.merge(new_owner_uuid,
+#'     new_user_token, redirect_to_new_user = NULL)
+#' @param new_owner_uuid 
+#' @param new_user_token 
+#' @param redirect_to_new_user 
+#' @return User object.
+#' @name users.merge
+NULL
+
 #' users.list
-#'
+#' 
 #' users.list is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$users.list(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
 #'     count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return UserList object.
 #' @name users.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.
@@ -139,9 +148,9 @@ NULL
 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")
 #' @param apiClientAuthorization ApiClientAuthorization object.
@@ -151,9 +160,9 @@ NULL
 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.
@@ -163,9 +172,9 @@ NULL
 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.
@@ -173,50 +182,50 @@ NULL
 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
+#' @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")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return ApiClientAuthorizationList object.
 #' @name api_client_authorizations.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.
@@ -224,9 +233,9 @@ NULL
 NULL
 
 #' containers.create
-#'
+#' 
 #' containers.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$containers.create(container,
 #'     ensure_unique_name = "false")
 #' @param container Container object.
@@ -236,9 +245,9 @@ NULL
 NULL
 
 #' containers.update
-#'
+#' 
 #' containers.update is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$containers.update(container,
 #'     uuid)
 #' @param container Container object.
@@ -248,9 +257,9 @@ NULL
 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.
@@ -258,78 +267,78 @@ NULL
 NULL
 
 #' containers.auth
-#'
+#' 
 #' containers.auth is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$containers.auth(uuid)
-#' @param 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
+#' @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
+#' @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
+#' @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")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return ContainerList object.
 #' @name containers.list
 NULL
 
 #' api_clients.get
-#'
+#' 
 #' 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.
@@ -337,9 +346,9 @@ NULL
 NULL
 
 #' api_clients.create
-#'
+#' 
 #' api_clients.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$api_clients.create(apiclient,
 #'     ensure_unique_name = "false")
 #' @param apiClient ApiClient object.
@@ -349,9 +358,9 @@ NULL
 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.
@@ -361,9 +370,9 @@ NULL
 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.
@@ -371,93 +380,29 @@ NULL
 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")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return ApiClientList object.
 #' @name api_clients.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")
-#' @param authorizedKey AuthorizedKey object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @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$authorized_keys.list(filters = NULL,
-#'     where = NULL, order = NULL, select = NULL,
-#'     distinct = NULL, limit = "100", offset = "0",
-#'     count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @return AuthorizedKeyList object.
-#' @name authorized_keys.list
-NULL
-
 #' container_requests.get
-#'
+#' 
 #' container_requests.get is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$container_requests.get(uuid)
 #' @param uuid The UUID of the ContainerRequest in question.
 #' @return ContainerRequest object.
@@ -465,9 +410,9 @@ NULL
 NULL
 
 #' container_requests.create
-#'
+#' 
 #' container_requests.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$container_requests.create(containerrequest,
 #'     ensure_unique_name = "false")
 #' @param containerRequest ContainerRequest object.
@@ -477,9 +422,9 @@ NULL
 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.
@@ -489,9 +434,9 @@ NULL
 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.
@@ -499,29 +444,93 @@ NULL
 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")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return ContainerRequestList object.
 #' @name container_requests.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")
+#' @param authorizedKey AuthorizedKey object.
+#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
+#' @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$authorized_keys.list(filters = NULL,
+#'     where = NULL, order = NULL, select = NULL,
+#'     distinct = NULL, limit = "100", offset = "0",
+#'     count = "exact")
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
+#' @return AuthorizedKeyList object.
+#' @name authorized_keys.list
+NULL
+
 #' collections.get
-#'
+#' 
 #' collections.get is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$collections.get(uuid)
 #' @param uuid The UUID of the Collection in question.
 #' @return Collection object.
@@ -529,9 +538,9 @@ NULL
 NULL
 
 #' collections.create
-#'
+#' 
 #' collections.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$collections.create(collection,
 #'     ensure_unique_name = "false")
 #' @param collection Collection object.
@@ -541,9 +550,9 @@ NULL
 NULL
 
 #' collections.update
-#'
+#' 
 #' collections.update is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$collections.update(collection,
 #'     uuid)
 #' @param collection Collection object.
@@ -553,9 +562,9 @@ NULL
 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.
@@ -563,70 +572,70 @@ NULL
 NULL
 
 #' collections.provenance
-#'
+#' 
 #' collections.provenance is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$collections.provenance(uuid)
-#' @param 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
+#' @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
+#' @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
+#' @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", include_trash = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @param include_trash Include collections whose is_trashed attribute is true.
 #' @return CollectionList object.
 #' @name collections.list
 NULL
 
 #' humans.get
-#'
+#' 
 #' humans.get is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$humans.get(uuid)
 #' @param uuid The UUID of the Human in question.
 #' @return Human object.
@@ -634,9 +643,9 @@ NULL
 NULL
 
 #' humans.create
-#'
+#' 
 #' humans.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$humans.create(human, ensure_unique_name = "false")
 #' @param human Human object.
 #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
@@ -645,9 +654,9 @@ NULL
 NULL
 
 #' humans.update
-#'
+#' 
 #' humans.update is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$humans.update(human, uuid)
 #' @param human Human object.
 #' @param uuid The UUID of the Human in question.
@@ -656,9 +665,9 @@ NULL
 NULL
 
 #' humans.delete
-#'
+#' 
 #' humans.delete is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$humans.delete(uuid)
 #' @param uuid The UUID of the Human in question.
 #' @return Human object.
@@ -666,29 +675,29 @@ NULL
 NULL
 
 #' humans.list
-#'
+#' 
 #' humans.list is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$humans.list(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
 #'     count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return HumanList object.
 #' @name humans.list
 NULL
 
 #' job_tasks.get
-#'
+#' 
 #' job_tasks.get is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$job_tasks.get(uuid)
 #' @param uuid The UUID of the JobTask in question.
 #' @return JobTask object.
@@ -696,9 +705,9 @@ NULL
 NULL
 
 #' job_tasks.create
-#'
+#' 
 #' job_tasks.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$job_tasks.create(jobtask, ensure_unique_name = "false")
 #' @param jobTask JobTask object.
 #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
@@ -707,9 +716,9 @@ NULL
 NULL
 
 #' job_tasks.update
-#'
+#' 
 #' job_tasks.update is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$job_tasks.update(jobtask, uuid)
 #' @param jobTask JobTask object.
 #' @param uuid The UUID of the JobTask in question.
@@ -718,9 +727,9 @@ NULL
 NULL
 
 #' job_tasks.delete
-#'
+#' 
 #' job_tasks.delete is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$job_tasks.delete(uuid)
 #' @param uuid The UUID of the JobTask in question.
 #' @return JobTask object.
@@ -728,128 +737,56 @@ NULL
 NULL
 
 #' job_tasks.list
-#'
+#' 
 #' job_tasks.list is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$job_tasks.list(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
 #'     count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return JobTaskList object.
 #' @name job_tasks.list
 NULL
 
-#' links.get
-#'
-#' links.get is a method defined in Arvados class.
-#'
-#' @usage arv$links.get(uuid)
-#' @param uuid The UUID of the Link in question.
-#' @return Link object.
-#' @name links.get
+#' jobs.get
+#' 
+#' jobs.get is a method defined in Arvados class.
+#' 
+#' @usage arv$jobs.get(uuid)
+#' @param uuid The UUID of the Job in question.
+#' @return Job object.
+#' @name jobs.get
 NULL
 
-#' links.create
-#'
-#' links.create is a method defined in Arvados class.
-#'
-#' @usage arv$links.create(link, ensure_unique_name = "false")
-#' @param link Link object.
+#' jobs.create
+#' 
+#' jobs.create is a method defined in Arvados class.
+#' 
+#' @usage arv$jobs.create(job, ensure_unique_name = "false",
+#'     find_or_create = "false", filters = NULL,
+#'     minimum_script_version = NULL, exclude_script_versions = NULL)
+#' @param job Job object.
 #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @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$links.list(filters = NULL,
-#'     where = NULL, order = NULL, select = NULL,
-#'     distinct = NULL, limit = "100", offset = "0",
-#'     count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @return LinkList object.
-#' @name links.list
-NULL
-
-#' links.get_permissions
-#'
-#' links.get_permissions is a method defined in Arvados class.
-#'
-#' @usage arv$links.get_permissions(uuid)
-#' @param uuid
-#' @return Link object.
-#' @name links.get_permissions
-NULL
-
-#' jobs.get
-#'
-#' jobs.get is a method defined in Arvados class.
-#'
-#' @usage arv$jobs.get(uuid)
-#' @param uuid The UUID of the Job in question.
-#' @return Job object.
-#' @name jobs.get
-NULL
-
-#' jobs.create
-#'
-#' jobs.create is a method defined in Arvados class.
-#'
-#' @usage arv$jobs.create(job, ensure_unique_name = "false",
-#'     find_or_create = "false", filters = NULL,
-#'     minimum_script_version = NULL, exclude_script_versions = NULL)
-#' @param job Job object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param find_or_create
-#' @param filters
-#' @param minimum_script_version
-#' @param exclude_script_versions
-#' @return Job object.
-#' @name jobs.create
+#' @param find_or_create 
+#' @param filters 
+#' @param minimum_script_version 
+#' @param exclude_script_versions 
+#' @return Job object.
+#' @name jobs.create
 NULL
 
 #' jobs.update
-#'
+#' 
 #' jobs.update is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$jobs.update(job, uuid)
 #' @param job Job object.
 #' @param uuid The UUID of the Job in question.
@@ -858,9 +795,9 @@ NULL
 NULL
 
 #' jobs.delete
-#'
+#' 
 #' jobs.delete is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$jobs.delete(uuid)
 #' @param uuid The UUID of the Job in question.
 #' @return Job object.
@@ -868,77 +805,77 @@ NULL
 NULL
 
 #' jobs.queue
-#'
+#' 
 #' jobs.queue is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$jobs.queue(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
 #'     count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return Job object.
 #' @name jobs.queue
 NULL
 
 #' jobs.queue_size
-#'
+#' 
 #' jobs.queue_size is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$jobs.queue_size(NULL)
 #' @return Job object.
 #' @name jobs.queue_size
 NULL
 
 #' jobs.cancel
-#'
+#' 
 #' jobs.cancel is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$jobs.cancel(uuid)
-#' @param uuid
+#' @param uuid 
 #' @return Job object.
 #' @name jobs.cancel
 NULL
 
 #' jobs.lock
-#'
+#' 
 #' jobs.lock is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$jobs.lock(uuid)
-#' @param uuid
+#' @param uuid 
 #' @return Job object.
 #' @name jobs.lock
 NULL
 
 #' jobs.list
-#'
+#' 
 #' jobs.list is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$jobs.list(filters = NULL, where = NULL,
 #'     order = NULL, select = NULL, distinct = NULL,
 #'     limit = "100", offset = "0", count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return JobList object.
 #' @name jobs.list
 NULL
 
 #' keep_disks.get
-#'
+#' 
 #' keep_disks.get is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$keep_disks.get(uuid)
 #' @param uuid The UUID of the KeepDisk in question.
 #' @return KeepDisk object.
@@ -946,9 +883,9 @@ NULL
 NULL
 
 #' keep_disks.create
-#'
+#' 
 #' keep_disks.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$keep_disks.create(keepdisk,
 #'     ensure_unique_name = "false")
 #' @param keepDisk KeepDisk object.
@@ -958,9 +895,9 @@ NULL
 NULL
 
 #' keep_disks.update
-#'
+#' 
 #' keep_disks.update is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$keep_disks.update(keepdisk,
 #'     uuid)
 #' @param keepDisk KeepDisk object.
@@ -970,9 +907,9 @@ NULL
 NULL
 
 #' keep_disks.delete
-#'
+#' 
 #' keep_disks.delete is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$keep_disks.delete(uuid)
 #' @param uuid The UUID of the KeepDisk in question.
 #' @return KeepDisk object.
@@ -980,47 +917,195 @@ NULL
 NULL
 
 #' keep_disks.ping
-#'
+#' 
 #' keep_disks.ping is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$keep_disks.ping(uuid = NULL,
 #'     ping_secret, node_uuid = NULL, filesystem_uuid = NULL,
 #'     service_host = NULL, service_port, service_ssl_flag)
-#' @param uuid
-#' @param ping_secret
-#' @param node_uuid
-#' @param filesystem_uuid
-#' @param service_host
-#' @param service_port
-#' @param service_ssl_flag
+#' @param uuid 
+#' @param ping_secret 
+#' @param node_uuid 
+#' @param filesystem_uuid 
+#' @param service_host 
+#' @param service_port 
+#' @param service_ssl_flag 
 #' @return KeepDisk object.
 #' @name keep_disks.ping
 NULL
 
 #' keep_disks.list
-#'
+#' 
 #' keep_disks.list is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$keep_disks.list(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
 #'     count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return KeepDiskList object.
 #' @name keep_disks.list
 NULL
 
+#' nodes.get
+#' 
+#' nodes.get is a method defined in Arvados class.
+#' 
+#' @usage arv$nodes.get(uuid)
+#' @param uuid The UUID of the Node in question.
+#' @return Node object.
+#' @name nodes.get
+NULL
+
+#' nodes.create
+#' 
+#' nodes.create is a method defined in Arvados class.
+#' 
+#' @usage arv$nodes.create(node, ensure_unique_name = "false",
+#'     assign_slot = NULL)
+#' @param node Node object.
+#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
+#' @param assign_slot assign slot and hostname
+#' @return Node object.
+#' @name nodes.create
+NULL
+
+#' nodes.update
+#' 
+#' nodes.update is a method defined in Arvados class.
+#' 
+#' @usage arv$nodes.update(node, uuid, assign_slot = NULL)
+#' @param node Node object.
+#' @param uuid The UUID of the Node in question.
+#' @param assign_slot assign slot and hostname
+#' @return Node object.
+#' @name nodes.update
+NULL
+
+#' nodes.delete
+#' 
+#' nodes.delete is a method defined in Arvados class.
+#' 
+#' @usage arv$nodes.delete(uuid)
+#' @param uuid The UUID of the Node in question.
+#' @return Node object.
+#' @name nodes.delete
+NULL
+
+#' nodes.ping
+#' 
+#' nodes.ping is a method defined in Arvados class.
+#' 
+#' @usage arv$nodes.ping(uuid, ping_secret)
+#' @param uuid 
+#' @param ping_secret 
+#' @return Node object.
+#' @name nodes.ping
+NULL
+
+#' nodes.list
+#' 
+#' nodes.list is a method defined in Arvados class.
+#' 
+#' @usage arv$nodes.list(filters = NULL,
+#'     where = NULL, order = NULL, select = NULL,
+#'     distinct = NULL, limit = "100", offset = "0",
+#'     count = "exact")
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
+#' @return NodeList object.
+#' @name nodes.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")
+#' @param link Link object.
+#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
+#' @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$links.list(filters = NULL,
+#'     where = NULL, order = NULL, select = NULL,
+#'     distinct = NULL, limit = "100", offset = "0",
+#'     count = "exact")
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
+#' @return LinkList object.
+#' @name links.list
+NULL
+
+#' links.get_permissions
+#' 
+#' links.get_permissions is a method defined in Arvados class.
+#' 
+#' @usage arv$links.get_permissions(uuid)
+#' @param uuid 
+#' @return Link object.
+#' @name links.get_permissions
+NULL
+
 #' 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.
@@ -1028,9 +1113,9 @@ NULL
 NULL
 
 #' keep_services.create
-#'
+#' 
 #' keep_services.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$keep_services.create(keepservice,
 #'     ensure_unique_name = "false")
 #' @param keepService KeepService object.
@@ -1040,9 +1125,9 @@ NULL
 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.
@@ -1052,9 +1137,9 @@ NULL
 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.
@@ -1062,38 +1147,38 @@ NULL
 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")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return KeepServiceList object.
 #' @name keep_services.list
 NULL
 
 #' pipeline_templates.get
-#'
+#' 
 #' pipeline_templates.get is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$pipeline_templates.get(uuid)
 #' @param uuid The UUID of the PipelineTemplate in question.
 #' @return PipelineTemplate object.
@@ -1101,9 +1186,9 @@ NULL
 NULL
 
 #' pipeline_templates.create
-#'
+#' 
 #' pipeline_templates.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$pipeline_templates.create(pipelinetemplate,
 #'     ensure_unique_name = "false")
 #' @param pipelineTemplate PipelineTemplate object.
@@ -1113,9 +1198,9 @@ NULL
 NULL
 
 #' pipeline_templates.update
-#'
+#' 
 #' pipeline_templates.update is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$pipeline_templates.update(pipelinetemplate,
 #'     uuid)
 #' @param pipelineTemplate PipelineTemplate object.
@@ -1125,9 +1210,9 @@ NULL
 NULL
 
 #' pipeline_templates.delete
-#'
+#' 
 #' pipeline_templates.delete is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$pipeline_templates.delete(uuid)
 #' @param uuid The UUID of the PipelineTemplate in question.
 #' @return PipelineTemplate object.
@@ -1135,29 +1220,29 @@ NULL
 NULL
 
 #' pipeline_templates.list
-#'
+#' 
 #' pipeline_templates.list is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$pipeline_templates.list(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
 #'     count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return PipelineTemplateList object.
 #' @name pipeline_templates.list
 NULL
 
 #' pipeline_instances.get
-#'
+#' 
 #' pipeline_instances.get is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$pipeline_instances.get(uuid)
 #' @param uuid The UUID of the PipelineInstance in question.
 #' @return PipelineInstance object.
@@ -1165,9 +1250,9 @@ NULL
 NULL
 
 #' pipeline_instances.create
-#'
+#' 
 #' pipeline_instances.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$pipeline_instances.create(pipelineinstance,
 #'     ensure_unique_name = "false")
 #' @param pipelineInstance PipelineInstance object.
@@ -1177,9 +1262,9 @@ NULL
 NULL
 
 #' pipeline_instances.update
-#'
+#' 
 #' pipeline_instances.update is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$pipeline_instances.update(pipelineinstance,
 #'     uuid)
 #' @param pipelineInstance PipelineInstance object.
@@ -1189,9 +1274,9 @@ NULL
 NULL
 
 #' pipeline_instances.delete
-#'
+#' 
 #' pipeline_instances.delete is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$pipeline_instances.delete(uuid)
 #' @param uuid The UUID of the PipelineInstance in question.
 #' @return PipelineInstance object.
@@ -1199,115 +1284,39 @@ NULL
 NULL
 
 #' pipeline_instances.cancel
-#'
+#' 
 #' pipeline_instances.cancel is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$pipeline_instances.cancel(uuid)
-#' @param uuid
+#' @param uuid 
 #' @return PipelineInstance object.
 #' @name pipeline_instances.cancel
 NULL
 
 #' pipeline_instances.list
-#'
+#' 
 #' pipeline_instances.list is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$pipeline_instances.list(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
 #'     count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return PipelineInstanceList object.
 #' @name pipeline_instances.list
 NULL
 
-#' nodes.get
-#'
-#' nodes.get is a method defined in Arvados class.
-#'
-#' @usage arv$nodes.get(uuid)
-#' @param uuid The UUID of the Node in question.
-#' @return Node object.
-#' @name nodes.get
-NULL
-
-#' nodes.create
-#'
-#' nodes.create is a method defined in Arvados class.
-#'
-#' @usage arv$nodes.create(node, ensure_unique_name = "false",
-#'     assign_slot = NULL)
-#' @param node Node object.
-#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @param assign_slot assign slot and hostname
-#' @return Node object.
-#' @name nodes.create
-NULL
-
-#' nodes.update
-#'
-#' nodes.update is a method defined in Arvados class.
-#'
-#' @usage arv$nodes.update(node, uuid, assign_slot = NULL)
-#' @param node Node object.
-#' @param uuid The UUID of the Node in question.
-#' @param assign_slot assign slot and hostname
-#' @return Node object.
-#' @name nodes.update
-NULL
-
-#' nodes.delete
-#'
-#' nodes.delete is a method defined in Arvados class.
-#'
-#' @usage arv$nodes.delete(uuid)
-#' @param uuid The UUID of the Node in question.
-#' @return Node object.
-#' @name nodes.delete
-NULL
-
-#' nodes.ping
-#'
-#' nodes.ping is a method defined in Arvados class.
-#'
-#' @usage arv$nodes.ping(uuid, ping_secret)
-#' @param uuid
-#' @param ping_secret
-#' @return Node object.
-#' @name nodes.ping
-NULL
-
-#' nodes.list
-#'
-#' nodes.list is a method defined in Arvados class.
-#'
-#' @usage arv$nodes.list(filters = NULL,
-#'     where = NULL, order = NULL, select = NULL,
-#'     distinct = NULL, limit = "100", offset = "0",
-#'     count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
-#' @return NodeList object.
-#' @name nodes.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.
@@ -1315,9 +1324,9 @@ NULL
 NULL
 
 #' repositories.create
-#'
+#' 
 #' repositories.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$repositories.create(repository,
 #'     ensure_unique_name = "false")
 #' @param repository Repository object.
@@ -1327,9 +1336,9 @@ NULL
 NULL
 
 #' repositories.update
-#'
+#' 
 #' repositories.update is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$repositories.update(repository,
 #'     uuid)
 #' @param repository Repository object.
@@ -1339,9 +1348,9 @@ NULL
 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.
@@ -1349,38 +1358,38 @@ NULL
 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")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return RepositoryList object.
 #' @name repositories.list
 NULL
 
 #' specimens.get
-#'
+#' 
 #' specimens.get is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$specimens.get(uuid)
 #' @param uuid The UUID of the Specimen in question.
 #' @return Specimen object.
@@ -1388,9 +1397,9 @@ NULL
 NULL
 
 #' specimens.create
-#'
+#' 
 #' specimens.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$specimens.create(specimen,
 #'     ensure_unique_name = "false")
 #' @param specimen Specimen object.
@@ -1400,9 +1409,9 @@ NULL
 NULL
 
 #' specimens.update
-#'
+#' 
 #' specimens.update is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$specimens.update(specimen,
 #'     uuid)
 #' @param specimen Specimen object.
@@ -1412,9 +1421,9 @@ NULL
 NULL
 
 #' specimens.delete
-#'
+#' 
 #' specimens.delete is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$specimens.delete(uuid)
 #' @param uuid The UUID of the Specimen in question.
 #' @return Specimen object.
@@ -1422,29 +1431,29 @@ NULL
 NULL
 
 #' specimens.list
-#'
+#' 
 #' specimens.list is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$specimens.list(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
 #'     count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return SpecimenList object.
 #' @name specimens.list
 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.
@@ -1452,9 +1461,9 @@ NULL
 NULL
 
 #' logs.create
-#'
+#' 
 #' logs.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$logs.create(log, ensure_unique_name = "false")
 #' @param log Log object.
 #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
@@ -1463,9 +1472,9 @@ NULL
 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.
@@ -1474,9 +1483,9 @@ NULL
 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.
@@ -1484,28 +1493,28 @@ NULL
 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")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return LogList object.
 #' @name logs.list
 NULL
 
 #' traits.get
-#'
+#' 
 #' traits.get is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$traits.get(uuid)
 #' @param uuid The UUID of the Trait in question.
 #' @return Trait object.
@@ -1513,9 +1522,9 @@ NULL
 NULL
 
 #' traits.create
-#'
+#' 
 #' traits.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$traits.create(trait, ensure_unique_name = "false")
 #' @param trait Trait object.
 #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
@@ -1524,9 +1533,9 @@ NULL
 NULL
 
 #' traits.update
-#'
+#' 
 #' traits.update is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$traits.update(trait, uuid)
 #' @param trait Trait object.
 #' @param uuid The UUID of the Trait in question.
@@ -1535,9 +1544,9 @@ NULL
 NULL
 
 #' traits.delete
-#'
+#' 
 #' traits.delete is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$traits.delete(uuid)
 #' @param uuid The UUID of the Trait in question.
 #' @return Trait object.
@@ -1545,29 +1554,29 @@ NULL
 NULL
 
 #' traits.list
-#'
+#' 
 #' traits.list is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$traits.list(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
 #'     count = "exact")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return TraitList object.
 #' @name traits.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.
@@ -1575,9 +1584,9 @@ NULL
 NULL
 
 #' virtual_machines.create
-#'
+#' 
 #' virtual_machines.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$virtual_machines.create(virtualmachine,
 #'     ensure_unique_name = "false")
 #' @param virtualMachine VirtualMachine object.
@@ -1587,9 +1596,9 @@ NULL
 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.
@@ -1599,9 +1608,9 @@ NULL
 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.
@@ -1609,48 +1618,48 @@ NULL
 NULL
 
 #' virtual_machines.logins
-#'
+#' 
 #' virtual_machines.logins is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$virtual_machines.logins(uuid)
-#' @param 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")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @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.
@@ -1658,9 +1667,9 @@ NULL
 NULL
 
 #' workflows.create
-#'
+#' 
 #' workflows.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$workflows.create(workflow,
 #'     ensure_unique_name = "false")
 #' @param workflow Workflow object.
@@ -1670,9 +1679,9 @@ NULL
 NULL
 
 #' workflows.update
-#'
+#' 
 #' workflows.update is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$workflows.update(workflow,
 #'     uuid)
 #' @param workflow Workflow object.
@@ -1682,9 +1691,9 @@ NULL
 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.
@@ -1692,29 +1701,29 @@ NULL
 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")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @return WorkflowList object.
 #' @name workflows.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.
@@ -1722,9 +1731,9 @@ NULL
 NULL
 
 #' groups.create
-#'
+#' 
 #' groups.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$groups.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.
@@ -1733,9 +1742,9 @@ NULL
 NULL
 
 #' groups.update
-#'
+#' 
 #' groups.update is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$groups.update(group, uuid)
 #' @param group Group object.
 #' @param uuid The UUID of the Group in question.
@@ -1744,9 +1753,9 @@ NULL
 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.
@@ -1754,72 +1763,72 @@ NULL
 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",
 #'     include_trash = NULL, uuid = NULL, recursive = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @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 uuid 
 #' @param recursive Include contents from child groups recursively.
 #' @return Group object.
 #' @name groups.contents
 NULL
 
 #' groups.trash
-#'
+#' 
 #' groups.trash is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$groups.trash(uuid)
-#' @param 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
+#' @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", include_trash = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @param include_trash Include items whose is_trashed attribute is true.
 #' @return GroupList object.
 #' @name groups.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.
@@ -1827,9 +1836,9 @@ NULL
 NULL
 
 #' user_agreements.create
-#'
+#' 
 #' user_agreements.create is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$user_agreements.create(useragreement,
 #'     ensure_unique_name = "false")
 #' @param userAgreement UserAgreement object.
@@ -1839,9 +1848,9 @@ NULL
 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.
@@ -1851,9 +1860,9 @@ NULL
 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.
@@ -1861,56 +1870,56 @@ NULL
 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
 
 #' 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")
-#' @param filters
-#' @param where
-#' @param order
-#' @param select
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param select 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @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
 
 #' 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.
@@ -1918,9 +1927,9 @@ NULL
 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.
@@ -1929,9 +1938,9 @@ NULL
 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.
@@ -1940,9 +1949,9 @@ NULL
 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.
@@ -1950,22 +1959,22 @@ NULL
 NULL
 
 #' project.list
-#'
+#' 
 #' projects.list wrapps groups.list method by setting group_class attribute to "project".
-#'
+#' 
 #' @usage arv$projects.list(filters = NULL,
 #'     where = NULL, order = NULL, distinct = NULL,
 #'     limit = "100", offset = "0", count = "exact",
 #'     include_trash = NULL, uuid = NULL, recursive = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @param include_trash Include items whose is_trashed attribute is true.
-#' @param uuid
+#' @param uuid 
 #' @param recursive Include contents from child groups recursively.
 #' @return Group object.
 #' @name projects.list
@@ -2130,6 +2139,7 @@ NULL
 #'     \item{}{\code{\link{users.delete}}}
 #'     \item{}{\code{\link{users.get}}}
 #'     \item{}{\code{\link{users.list}}}
+#'     \item{}{\code{\link{users.merge}}}
 #'     \item{}{\code{\link{users.setup}}}
 #'     \item{}{\code{\link{users.system}}}
 #'     \item{}{\code{\link{users.unsetup}}}
@@ -2237,19 +2247,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("users/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
@@ -2257,23 +2267,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("users")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(user) > 0)
-                               body <- jsonlite::toJSON(list(user = user),
+                               body <- jsonlite::toJSON(list(user = user), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -2281,23 +2291,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("users/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(user) > 0)
-                               body <- jsonlite::toJSON(list(user = user),
+                               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
                },
 
@@ -2305,19 +2315,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("users/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -2325,19 +2335,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("users/current")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
@@ -2345,19 +2355,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("users/system")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
@@ -2365,19 +2375,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("users/${uuid}/activate")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -2386,21 +2396,21 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("users/setup")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(user = user, openid_prefix = openid_prefix,
                                                          repo_name = repo_name, vm_uuid = vm_uuid,
                                                          send_notification_email = send_notification_email)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -2408,19 +2418,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("users/${uuid}/unsetup")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -2428,19 +2438,41 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("users/${uuid}/update_uuid")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(new_uuid = new_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.merge = function(new_owner_uuid, new_user_token,
+                       redirect_to_new_user = NULL)
+               {
+                       endPoint <- stringr::str_interp("users/merge")
+                       url <- paste0(private$host, endPoint)
+                       headers <- list(Authorization = paste("OAuth2", private$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)
+                       
+                       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
                },
 
@@ -2450,21 +2482,21 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("users")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -2472,19 +2504,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -2493,23 +2525,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("api_client_authorizations")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(apiclientauthorization) > 0)
-                               body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization),
+                               body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -2517,23 +2549,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(apiclientauthorization) > 0)
-                               body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization),
+                               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
                },
 
@@ -2541,19 +2573,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("api_client_authorizations/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -2561,20 +2593,20 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
@@ -2582,19 +2614,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("api_client_authorizations/current")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
@@ -2605,21 +2637,21 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("api_client_authorizations")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -2627,19 +2659,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("containers/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -2647,23 +2679,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("containers")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(container) > 0)
-                               body <- jsonlite::toJSON(list(container = container),
+                               body <- jsonlite::toJSON(list(container = container), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -2671,23 +2703,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("containers/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(container) > 0)
-                               body <- jsonlite::toJSON(list(container = container),
+                               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
                },
 
@@ -2695,19 +2727,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("containers/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -2715,19 +2747,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("containers/${uuid}/auth")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -2735,19 +2767,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("containers/${uuid}/lock")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -2755,19 +2787,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("containers/${uuid}/unlock")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -2775,19 +2807,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -2795,19 +2827,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("containers/current")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
@@ -2818,21 +2850,21 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("containers")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -2840,19 +2872,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("api_clients/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -2860,23 +2892,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("api_clients")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(apiclient) > 0)
-                               body <- jsonlite::toJSON(list(apiclient = apiclient),
+                               body <- jsonlite::toJSON(list(apiclient = apiclient), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -2884,23 +2916,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("api_clients/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(apiclient) > 0)
-                               body <- jsonlite::toJSON(list(apiclient = apiclient),
+                               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
                },
 
@@ -2908,19 +2940,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("api_clients/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -2931,249 +2963,249 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("api_clients")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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)
+               container_requests.get = function(uuid)
                {
-                       endPoint <- stringr::str_interp("authorized_keys/${uuid}")
+                       endPoint <- stringr::str_interp("container_requests/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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,
+               container_requests.create = function(containerrequest,
                        ensure_unique_name = "false")
                {
-                       endPoint <- stringr::str_interp("authorized_keys")
+                       endPoint <- stringr::str_interp("container_requests")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
-                       if(length(authorizedkey) > 0)
-                               body <- jsonlite::toJSON(list(authorizedkey = authorizedkey),
+                       
+                       if(length(containerrequest) > 0)
+                               body <- jsonlite::toJSON(list(containerrequest = containerrequest), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
-               authorized_keys.update = function(authorizedkey, uuid)
+               container_requests.update = function(containerrequest, uuid)
                {
-                       endPoint <- stringr::str_interp("authorized_keys/${uuid}")
+                       endPoint <- stringr::str_interp("container_requests/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
-                       if(length(authorizedkey) > 0)
-                               body <- jsonlite::toJSON(list(authorizedkey = authorizedkey),
+                       
+                       if(length(containerrequest) > 0)
+                               body <- jsonlite::toJSON(list(containerrequest = containerrequest), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
-               authorized_keys.delete = function(uuid)
+               container_requests.delete = function(uuid)
                {
-                       endPoint <- stringr::str_interp("authorized_keys/${uuid}")
+                       endPoint <- stringr::str_interp("container_requests/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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,
+               container_requests.list = function(filters = NULL,
                        where = NULL, order = NULL, select = NULL,
                        distinct = NULL, limit = "100", offset = "0",
                        count = "exact")
                {
-                       endPoint <- stringr::str_interp("authorized_keys")
+                       endPoint <- stringr::str_interp("container_requests")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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)
+               authorized_keys.get = function(uuid)
                {
-                       endPoint <- stringr::str_interp("container_requests/${uuid}")
+                       endPoint <- stringr::str_interp("authorized_keys/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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,
+               authorized_keys.create = function(authorizedkey,
                        ensure_unique_name = "false")
                {
-                       endPoint <- stringr::str_interp("container_requests")
+                       endPoint <- stringr::str_interp("authorized_keys")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
-                       if(length(containerrequest) > 0)
-                               body <- jsonlite::toJSON(list(containerrequest = containerrequest),
+                       
+                       if(length(authorizedkey) > 0)
+                               body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
-               container_requests.update = function(containerrequest, uuid)
+               authorized_keys.update = function(authorizedkey, uuid)
                {
-                       endPoint <- stringr::str_interp("container_requests/${uuid}")
+                       endPoint <- stringr::str_interp("authorized_keys/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
-                       if(length(containerrequest) > 0)
-                               body <- jsonlite::toJSON(list(containerrequest = containerrequest),
+                       
+                       if(length(authorizedkey) > 0)
+                               body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
-               container_requests.delete = function(uuid)
+               authorized_keys.delete = function(uuid)
                {
-                       endPoint <- stringr::str_interp("container_requests/${uuid}")
+                       endPoint <- stringr::str_interp("authorized_keys/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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,
+               authorized_keys.list = function(filters = NULL,
                        where = NULL, order = NULL, select = NULL,
                        distinct = NULL, limit = "100", offset = "0",
                        count = "exact")
                {
-                       endPoint <- stringr::str_interp("container_requests")
+                       endPoint <- stringr::str_interp("authorized_keys")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -3181,19 +3213,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("collections/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -3201,23 +3233,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("collections")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(collection) > 0)
-                               body <- jsonlite::toJSON(list(collection = collection),
+                               body <- jsonlite::toJSON(list(collection = collection), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -3225,23 +3257,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("collections/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(collection) > 0)
-                               body <- jsonlite::toJSON(list(collection = collection),
+                               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
                },
 
@@ -3249,19 +3281,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("collections/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -3269,19 +3301,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("collections/${uuid}/provenance")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -3289,19 +3321,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("collections/${uuid}/used_by")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -3309,19 +3341,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("collections/${uuid}/trash")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -3329,19 +3361,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("collections/${uuid}/untrash")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -3352,22 +3384,22 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("collections")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count,
                                                          include_trash = include_trash)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -3375,19 +3407,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("humans/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -3395,23 +3427,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("humans")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(human) > 0)
-                               body <- jsonlite::toJSON(list(human = human),
+                               body <- jsonlite::toJSON(list(human = human), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -3419,23 +3451,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("humans/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(human) > 0)
-                               body <- jsonlite::toJSON(list(human = human),
+                               body <- jsonlite::toJSON(list(human = human), 
                                                         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
                },
 
@@ -3443,19 +3475,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("humans/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -3465,21 +3497,21 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("humans")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -3487,19 +3519,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("job_tasks/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -3507,23 +3539,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("job_tasks")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(jobtask) > 0)
-                               body <- jsonlite::toJSON(list(jobtask = jobtask),
+                               body <- jsonlite::toJSON(list(jobtask = jobtask), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -3531,23 +3563,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("job_tasks/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(jobtask) > 0)
-                               body <- jsonlite::toJSON(list(jobtask = jobtask),
+                               body <- jsonlite::toJSON(list(jobtask = jobtask), 
                                                         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
                },
 
@@ -3555,19 +3587,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("job_tasks/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -3578,1008 +3610,1008 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("job_tasks")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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)
+               jobs.get = function(uuid)
                {
-                       endPoint <- stringr::str_interp("links/${uuid}")
+                       endPoint <- stringr::str_interp("jobs/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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")
+               jobs.create = function(job, ensure_unique_name = "false",
+                       find_or_create = "false", filters = NULL,
+                       minimum_script_version = NULL, exclude_script_versions = NULL)
                {
-                       endPoint <- stringr::str_interp("links")
+                       endPoint <- stringr::str_interp("jobs")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
-                       queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
-                       if(length(link) > 0)
-                               body <- jsonlite::toJSON(list(link = link),
+                       queryArgs <- list(ensure_unique_name = ensure_unique_name,
+                                                         find_or_create = find_or_create, filters = filters,
+                                                         minimum_script_version = minimum_script_version,
+                                                         exclude_script_versions = exclude_script_versions)
+                       
+                       if(length(job) > 0)
+                               body <- jsonlite::toJSON(list(job = job), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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)
+               jobs.update = function(job, uuid)
                {
-                       endPoint <- stringr::str_interp("links/${uuid}")
+                       endPoint <- stringr::str_interp("jobs/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
-                       if(length(link) > 0)
-                               body <- jsonlite::toJSON(list(link = link),
+                       
+                       if(length(job) > 0)
+                               body <- jsonlite::toJSON(list(job = job), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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)
+               jobs.delete = function(uuid)
                {
-                       endPoint <- stringr::str_interp("links/${uuid}")
+                       endPoint <- stringr::str_interp("jobs/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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,
+               jobs.queue = function(filters = NULL, where = NULL,
                        order = NULL, select = NULL, distinct = NULL,
                        limit = "100", offset = "0", count = "exact")
                {
-                       endPoint <- stringr::str_interp("links")
+                       endPoint <- stringr::str_interp("jobs/queue")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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)
+               jobs.queue_size = function()
                {
-                       endPoint <- stringr::str_interp("permissions/${uuid}")
+                       endPoint <- stringr::str_interp("jobs/queue_size")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
-               jobs.get = function(uuid)
+               jobs.cancel = function(uuid)
                {
-                       endPoint <- stringr::str_interp("jobs/${uuid}")
+                       endPoint <- stringr::str_interp("jobs/${uuid}/cancel")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        body <- NULL
-
-                       response <- private$REST$http$exec("GET", url, headers, body,
+                       
+                       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
                },
 
-               jobs.create = function(job, ensure_unique_name = "false",
-                       find_or_create = "false", filters = NULL,
-                       minimum_script_version = NULL, exclude_script_versions = NULL)
+               jobs.lock = function(uuid)
                {
-                       endPoint <- stringr::str_interp("jobs")
+                       endPoint <- stringr::str_interp("jobs/${uuid}/lock")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
-                       queryArgs <- list(ensure_unique_name = ensure_unique_name,
-                                                         find_or_create = find_or_create, filters = filters,
-                                                         minimum_script_version = minimum_script_version,
-                                                         exclude_script_versions = exclude_script_versions)
-
-                       if(length(job) > 0)
-                               body <- jsonlite::toJSON(list(job = job),
-                                                        auto_unbox = TRUE)
-                       else
-                               body <- NULL
-
+                       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
                },
 
-               jobs.update = function(job, uuid)
+               jobs.list = function(filters = NULL, where = NULL,
+                       order = NULL, select = NULL, distinct = NULL,
+                       limit = "100", offset = "0", count = "exact")
                {
-                       endPoint <- stringr::str_interp("jobs/${uuid}")
+                       endPoint <- stringr::str_interp("jobs")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
-                       queryArgs <- NULL
-
-                       if(length(job) > 0)
-                               body <- jsonlite::toJSON(list(job = job),
-                                                        auto_unbox = TRUE)
-                       else
-                               body <- NULL
-
-                       response <- private$REST$http$exec("PUT", url, headers, body,
+                       queryArgs <- list(filters = filters, where = where,
+                                                         order = order, select = select, distinct = distinct,
+                                                         limit = limit, offset = offset, count = count)
+                       
+                       body <- NULL
+                       
+                       response <- private$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
                },
 
-               jobs.delete = function(uuid)
+               keep_disks.get = function(uuid)
                {
-                       endPoint <- stringr::str_interp("jobs/${uuid}")
+                       endPoint <- stringr::str_interp("keep_disks/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        body <- NULL
-
-                       response <- private$REST$http$exec("DELETE", url, headers, body,
+                       
+                       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
                },
 
-               jobs.queue = function(filters = NULL, where = NULL,
-                       order = NULL, select = NULL, distinct = NULL,
-                       limit = "100", offset = "0", count = "exact")
+               keep_disks.create = function(keepdisk, ensure_unique_name = "false")
                {
-                       endPoint <- stringr::str_interp("jobs/queue")
+                       endPoint <- stringr::str_interp("keep_disks")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
-                       queryArgs <- list(filters = filters, where = where,
-                                                         order = order, select = select, distinct = distinct,
-                                                         limit = limit, offset = offset, count = count)
-
-                       body <- NULL
-
-                       response <- private$REST$http$exec("GET", url, headers, body,
+                       queryArgs <- list(ensure_unique_name = ensure_unique_name)
+                       
+                       if(length(keepdisk) > 0)
+                               body <- jsonlite::toJSON(list(keepdisk = keepdisk), 
+                                                        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
                },
 
-               jobs.queue_size = function()
+               keep_disks.update = function(keepdisk, uuid)
                {
-                       endPoint <- stringr::str_interp("jobs/queue_size")
+                       endPoint <- stringr::str_interp("keep_disks/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
-                       body <- NULL
-
-                       response <- private$REST$http$exec("GET", url, headers, body,
+                       
+                       if(length(keepdisk) > 0)
+                               body <- jsonlite::toJSON(list(keepdisk = keepdisk), 
+                                                        auto_unbox = TRUE)
+                       else
+                               body <- NULL
+                       
+                       response <- private$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
                },
 
-               jobs.cancel = function(uuid)
+               keep_disks.delete = function(uuid)
                {
-                       endPoint <- stringr::str_interp("jobs/${uuid}/cancel")
+                       endPoint <- stringr::str_interp("keep_disks/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        body <- NULL
-
-                       response <- private$REST$http$exec("POST", url, headers, body,
+                       
+                       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
                },
 
-               jobs.lock = function(uuid)
+               keep_disks.ping = function(uuid = NULL, ping_secret,
+                       node_uuid = NULL, filesystem_uuid = NULL,
+                       service_host = NULL, service_port, service_ssl_flag)
                {
-                       endPoint <- stringr::str_interp("jobs/${uuid}/lock")
+                       endPoint <- stringr::str_interp("keep_disks/ping")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
-                       queryArgs <- NULL
-
+                       queryArgs <- list(uuid = uuid, ping_secret = ping_secret,
+                                                         node_uuid = node_uuid, filesystem_uuid = filesystem_uuid,
+                                                         service_host = service_host, service_port = service_port,
+                                                         service_ssl_flag = service_ssl_flag)
+                       
                        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
                },
 
-               jobs.list = function(filters = NULL, where = NULL,
-                       order = NULL, select = NULL, distinct = NULL,
-                       limit = "100", offset = "0", count = "exact")
+               keep_disks.list = function(filters = NULL,
+                       where = NULL, order = NULL, select = NULL,
+                       distinct = NULL, limit = "100", offset = "0",
+                       count = "exact")
                {
-                       endPoint <- stringr::str_interp("jobs")
+                       endPoint <- stringr::str_interp("keep_disks")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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_disks.get = function(uuid)
+               nodes.get = function(uuid)
                {
-                       endPoint <- stringr::str_interp("keep_disks/${uuid}")
+                       endPoint <- stringr::str_interp("nodes/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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_disks.create = function(keepdisk, ensure_unique_name = "false")
+               nodes.create = function(node, ensure_unique_name = "false",
+                       assign_slot = NULL)
                {
-                       endPoint <- stringr::str_interp("keep_disks")
+                       endPoint <- stringr::str_interp("nodes")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
-                       queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
-                       if(length(keepdisk) > 0)
-                               body <- jsonlite::toJSON(list(keepdisk = keepdisk),
+                       queryArgs <- list(ensure_unique_name = ensure_unique_name,
+                                                         assign_slot = assign_slot)
+                       
+                       if(length(node) > 0)
+                               body <- jsonlite::toJSON(list(node = node), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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_disks.update = function(keepdisk, uuid)
+               nodes.update = function(node, uuid, assign_slot = NULL)
                {
-                       endPoint <- stringr::str_interp("keep_disks/${uuid}")
+                       endPoint <- stringr::str_interp("nodes/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
-                       queryArgs <- NULL
-
-                       if(length(keepdisk) > 0)
-                               body <- jsonlite::toJSON(list(keepdisk = keepdisk),
+                       queryArgs <- list(assign_slot = assign_slot)
+                       
+                       if(length(node) > 0)
+                               body <- jsonlite::toJSON(list(node = node), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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_disks.delete = function(uuid)
+               nodes.delete = function(uuid)
                {
-                       endPoint <- stringr::str_interp("keep_disks/${uuid}")
+                       endPoint <- stringr::str_interp("nodes/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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_disks.ping = function(uuid = NULL, ping_secret,
-                       node_uuid = NULL, filesystem_uuid = NULL,
-                       service_host = NULL, service_port, service_ssl_flag)
+               nodes.ping = function(uuid, ping_secret)
                {
-                       endPoint <- stringr::str_interp("keep_disks/ping")
+                       endPoint <- stringr::str_interp("nodes/${uuid}/ping")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
-                       queryArgs <- list(uuid = uuid, ping_secret = ping_secret,
-                                                         node_uuid = node_uuid, filesystem_uuid = filesystem_uuid,
-                                                         service_host = service_host, service_port = service_port,
-                                                         service_ssl_flag = service_ssl_flag)
-
+                       queryArgs <- list(ping_secret = ping_secret)
+                       
                        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_disks.list = function(filters = NULL,
-                       where = NULL, order = NULL, select = NULL,
-                       distinct = NULL, limit = "100", offset = "0",
-                       count = "exact")
+               nodes.list = function(filters = NULL, where = NULL,
+                       order = NULL, select = NULL, distinct = NULL,
+                       limit = "100", offset = "0", count = "exact")
                {
-                       endPoint <- stringr::str_interp("keep_disks")
+                       endPoint <- stringr::str_interp("nodes")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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)
+               links.get = function(uuid)
                {
-                       endPoint <- stringr::str_interp("keep_services/${uuid}")
+                       endPoint <- stringr::str_interp("links/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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")
+               links.create = function(link, ensure_unique_name = "false")
                {
-                       endPoint <- stringr::str_interp("keep_services")
+                       endPoint <- stringr::str_interp("links")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
-                       if(length(keepservice) > 0)
-                               body <- jsonlite::toJSON(list(keepservice = keepservice),
+                       
+                       if(length(link) > 0)
+                               body <- jsonlite::toJSON(list(link = link), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
-               keep_services.update = function(keepservice, uuid)
+               links.update = function(link, uuid)
                {
-                       endPoint <- stringr::str_interp("keep_services/${uuid}")
+                       endPoint <- stringr::str_interp("links/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
-                       if(length(keepservice) > 0)
-                               body <- jsonlite::toJSON(list(keepservice = keepservice),
+                       
+                       if(length(link) > 0)
+                               body <- jsonlite::toJSON(list(link = link), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
-               keep_services.delete = function(uuid)
+               links.delete = function(uuid)
                {
-                       endPoint <- stringr::str_interp("keep_services/${uuid}")
+                       endPoint <- stringr::str_interp("links/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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()
+               links.list = function(filters = NULL, where = NULL,
+                       order = NULL, select = NULL, distinct = NULL,
+                       limit = "100", offset = "0", count = "exact")
                {
-                       endPoint <- stringr::str_interp("keep_services/accessible")
+                       endPoint <- stringr::str_interp("links")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
-                       queryArgs <- NULL
-
+                       queryArgs <- list(filters = filters, where = where,
+                                                         order = order, select = select, distinct = distinct,
+                                                         limit = limit, offset = offset, count = count)
+                       
                        body <- NULL
-
+                       
                        response <- private$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")
+               links.get_permissions = function(uuid)
                {
-                       endPoint <- stringr::str_interp("keep_services")
+                       endPoint <- stringr::str_interp("permissions/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
-                       queryArgs <- list(filters = filters, where = where,
-                                                         order = order, select = select, distinct = distinct,
-                                                         limit = limit, offset = offset, count = count)
-
+                       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
                },
 
-               pipeline_templates.get = function(uuid)
+               keep_services.get = function(uuid)
                {
-                       endPoint <- stringr::str_interp("pipeline_templates/${uuid}")
+                       endPoint <- stringr::str_interp("keep_services/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
-               pipeline_templates.create = function(pipelinetemplate,
+               keep_services.create = function(keepservice,
                        ensure_unique_name = "false")
                {
-                       endPoint <- stringr::str_interp("pipeline_templates")
+                       endPoint <- stringr::str_interp("keep_services")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
-                       if(length(pipelinetemplate) > 0)
-                               body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate),
+                       
+                       if(length(keepservice) > 0)
+                               body <- jsonlite::toJSON(list(keepservice = keepservice), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
-               pipeline_templates.update = function(pipelinetemplate, uuid)
+               keep_services.update = function(keepservice, uuid)
                {
-                       endPoint <- stringr::str_interp("pipeline_templates/${uuid}")
+                       endPoint <- stringr::str_interp("keep_services/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
-                       if(length(pipelinetemplate) > 0)
-                               body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate),
+                       
+                       if(length(keepservice) > 0)
+                               body <- jsonlite::toJSON(list(keepservice = keepservice), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
-               pipeline_templates.delete = function(uuid)
+               keep_services.delete = function(uuid)
                {
-                       endPoint <- stringr::str_interp("pipeline_templates/${uuid}")
+                       endPoint <- stringr::str_interp("keep_services/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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$host, endPoint)
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
-               pipeline_templates.list = function(filters = NULL,
+               keep_services.list = function(filters = NULL,
                        where = NULL, order = NULL, select = NULL,
                        distinct = NULL, limit = "100", offset = "0",
                        count = "exact")
                {
-                       endPoint <- stringr::str_interp("pipeline_templates")
+                       endPoint <- stringr::str_interp("keep_services")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
-               pipeline_instances.get = function(uuid)
+               pipeline_templates.get = function(uuid)
                {
-                       endPoint <- stringr::str_interp("pipeline_instances/${uuid}")
+                       endPoint <- stringr::str_interp("pipeline_templates/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
-               pipeline_instances.create = function(pipelineinstance,
+               pipeline_templates.create = function(pipelinetemplate,
                        ensure_unique_name = "false")
                {
-                       endPoint <- stringr::str_interp("pipeline_instances")
+                       endPoint <- stringr::str_interp("pipeline_templates")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
-                       if(length(pipelineinstance) > 0)
-                               body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance),
+                       
+                       if(length(pipelinetemplate) > 0)
+                               body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
-               pipeline_instances.update = function(pipelineinstance, uuid)
+               pipeline_templates.update = function(pipelinetemplate, uuid)
                {
-                       endPoint <- stringr::str_interp("pipeline_instances/${uuid}")
+                       endPoint <- stringr::str_interp("pipeline_templates/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
-                       if(length(pipelineinstance) > 0)
-                               body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance),
+                       
+                       if(length(pipelinetemplate) > 0)
+                               body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
-               pipeline_instances.delete = function(uuid)
+               pipeline_templates.delete = function(uuid)
                {
-                       endPoint <- stringr::str_interp("pipeline_instances/${uuid}")
+                       endPoint <- stringr::str_interp("pipeline_templates/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
-               },
-
-               pipeline_instances.cancel = function(uuid)
-               {
-                       endPoint <- stringr::str_interp("pipeline_instances/${uuid}/cancel")
-                       url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
-               pipeline_instances.list = function(filters = NULL,
+               pipeline_templates.list = function(filters = NULL,
                        where = NULL, order = NULL, select = NULL,
                        distinct = NULL, limit = "100", offset = "0",
                        count = "exact")
                {
-                       endPoint <- stringr::str_interp("pipeline_instances")
+                       endPoint <- stringr::str_interp("pipeline_templates")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
-               nodes.get = function(uuid)
+               pipeline_instances.get = function(uuid)
                {
-                       endPoint <- stringr::str_interp("nodes/${uuid}")
+                       endPoint <- stringr::str_interp("pipeline_instances/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
-               nodes.create = function(node, ensure_unique_name = "false",
-                       assign_slot = NULL)
+               pipeline_instances.create = function(pipelineinstance,
+                       ensure_unique_name = "false")
                {
-                       endPoint <- stringr::str_interp("nodes")
+                       endPoint <- stringr::str_interp("pipeline_instances")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
-                       queryArgs <- list(ensure_unique_name = ensure_unique_name,
-                                                         assign_slot = assign_slot)
-
-                       if(length(node) > 0)
-                               body <- jsonlite::toJSON(list(node = node),
+                       queryArgs <- list(ensure_unique_name = ensure_unique_name)
+                       
+                       if(length(pipelineinstance) > 0)
+                               body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
-               nodes.update = function(node, uuid, assign_slot = NULL)
+               pipeline_instances.update = function(pipelineinstance, uuid)
                {
-                       endPoint <- stringr::str_interp("nodes/${uuid}")
+                       endPoint <- stringr::str_interp("pipeline_instances/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
-                       queryArgs <- list(assign_slot = assign_slot)
-
-                       if(length(node) > 0)
-                               body <- jsonlite::toJSON(list(node = node),
+                       queryArgs <- NULL
+                       
+                       if(length(pipelineinstance) > 0)
+                               body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
-               nodes.delete = function(uuid)
+               pipeline_instances.delete = function(uuid)
                {
-                       endPoint <- stringr::str_interp("nodes/${uuid}")
+                       endPoint <- stringr::str_interp("pipeline_instances/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
-               nodes.ping = function(uuid, ping_secret)
+               pipeline_instances.cancel = function(uuid)
                {
-                       endPoint <- stringr::str_interp("nodes/${uuid}/ping")
+                       endPoint <- stringr::str_interp("pipeline_instances/${uuid}/cancel")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
-                       queryArgs <- list(ping_secret = ping_secret)
-
+                       queryArgs <- NULL
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
-               nodes.list = function(filters = NULL, where = NULL,
-                       order = NULL, select = NULL, distinct = NULL,
-                       limit = "100", offset = "0", count = "exact")
+               pipeline_instances.list = function(filters = NULL,
+                       where = NULL, order = NULL, select = NULL,
+                       distinct = NULL, limit = "100", offset = "0",
+                       count = "exact")
                {
-                       endPoint <- stringr::str_interp("nodes")
+                       endPoint <- stringr::str_interp("pipeline_instances")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -4587,19 +4619,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("repositories/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -4607,23 +4639,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("repositories")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(repository) > 0)
-                               body <- jsonlite::toJSON(list(repository = repository),
+                               body <- jsonlite::toJSON(list(repository = repository), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -4631,23 +4663,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("repositories/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(repository) > 0)
-                               body <- jsonlite::toJSON(list(repository = repository),
+                               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
                },
 
@@ -4655,19 +4687,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("repositories/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -4675,19 +4707,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("repositories/get_all_permissions")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
@@ -4698,21 +4730,21 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("repositories")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -4720,19 +4752,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("specimens/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -4740,23 +4772,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("specimens")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(specimen) > 0)
-                               body <- jsonlite::toJSON(list(specimen = specimen),
+                               body <- jsonlite::toJSON(list(specimen = specimen), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -4764,23 +4796,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("specimens/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(specimen) > 0)
-                               body <- jsonlite::toJSON(list(specimen = specimen),
+                               body <- jsonlite::toJSON(list(specimen = specimen), 
                                                         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
                },
 
@@ -4788,19 +4820,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("specimens/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -4811,21 +4843,21 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("specimens")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -4833,19 +4865,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("logs/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -4853,23 +4885,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("logs")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(log) > 0)
-                               body <- jsonlite::toJSON(list(log = log),
+                               body <- jsonlite::toJSON(list(log = log), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -4877,23 +4909,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("logs/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(log) > 0)
-                               body <- jsonlite::toJSON(list(log = log),
+                               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
                },
 
@@ -4901,19 +4933,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("logs/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -4923,21 +4955,21 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("logs")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -4945,19 +4977,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("traits/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -4965,23 +4997,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("traits")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(trait) > 0)
-                               body <- jsonlite::toJSON(list(trait = trait),
+                               body <- jsonlite::toJSON(list(trait = trait), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -4989,23 +5021,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("traits/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(trait) > 0)
-                               body <- jsonlite::toJSON(list(trait = trait),
+                               body <- jsonlite::toJSON(list(trait = trait), 
                                                         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
                },
 
@@ -5013,19 +5045,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("traits/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -5035,21 +5067,21 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("traits")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -5057,19 +5089,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("virtual_machines/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -5078,23 +5110,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("virtual_machines")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(virtualmachine) > 0)
-                               body <- jsonlite::toJSON(list(virtualmachine = virtualmachine),
+                               body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -5102,23 +5134,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("virtual_machines/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(virtualmachine) > 0)
-                               body <- jsonlite::toJSON(list(virtualmachine = virtualmachine),
+                               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
                },
 
@@ -5126,19 +5158,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("virtual_machines/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -5146,19 +5178,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("virtual_machines/${uuid}/logins")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -5166,19 +5198,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("virtual_machines/get_all_logins")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
@@ -5189,21 +5221,21 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("virtual_machines")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -5211,19 +5243,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("workflows/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -5231,23 +5263,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("workflows")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(workflow) > 0)
-                               body <- jsonlite::toJSON(list(workflow = workflow),
+                               body <- jsonlite::toJSON(list(workflow = workflow), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -5255,23 +5287,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("workflows/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(workflow) > 0)
-                               body <- jsonlite::toJSON(list(workflow = workflow),
+                               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
                },
 
@@ -5279,19 +5311,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("workflows/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -5302,21 +5334,21 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("workflows")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -5324,19 +5356,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("groups/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -5344,23 +5376,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("groups")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(group) > 0)
-                               body <- jsonlite::toJSON(list(group = group),
+                               body <- jsonlite::toJSON(list(group = group), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -5368,23 +5400,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("groups/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(group) > 0)
-                               body <- jsonlite::toJSON(list(group = group),
+                               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
                },
 
@@ -5392,19 +5424,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("groups/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -5415,22 +5447,22 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("groups/contents")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, distinct = distinct, limit = limit,
                                                          offset = offset, count = count, include_trash = include_trash,
                                                          uuid = uuid, recursive = recursive)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -5438,19 +5470,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("groups/${uuid}/trash")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -5458,19 +5490,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("groups/${uuid}/untrash")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -5481,22 +5513,22 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("groups")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count,
                                                          include_trash = include_trash)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -5504,19 +5536,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("user_agreements/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -5525,23 +5557,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("user_agreements")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(useragreement) > 0)
-                               body <- jsonlite::toJSON(list(useragreement = useragreement),
+                               body <- jsonlite::toJSON(list(useragreement = useragreement), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -5549,23 +5581,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("user_agreements/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
-
+                       
                        if(length(useragreement) > 0)
-                               body <- jsonlite::toJSON(list(useragreement = useragreement),
+                               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
                },
 
@@ -5573,19 +5605,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("user_agreements/${uuid}")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$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
                },
 
@@ -5593,19 +5625,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("user_agreements/signatures")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
@@ -5613,19 +5645,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("user_agreements/sign")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
@@ -5636,21 +5668,21 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("user_agreements")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -5658,19 +5690,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("user_agreements/new")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", 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
                },
 
index 1071302892690a659370d41afaa4336316678362..70bb4450eccca6efd453002dc7a0962c904fb0d0 100644 (file)
@@ -26,7 +26,8 @@ source("./R/util.R")
 #'   \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(newLocation)}{Moves file to a new location inside collection.}
+#'   \item{move(destination)}{Moves file to a new location inside collection.}
+#'   \item{copy(destination)}{Copies file to a new location inside collection.}
 #' }
 #'
 #' @name ArvadosFile
@@ -49,6 +50,7 @@ source("./R/util.R")
 #' mytable <- read.table(arvConnection)
 #'
 #' myFile$move("newFolder/myFile")
+#' myFile$copy("newFolder/myFile")
 #' }
 NULL
 
@@ -83,7 +85,6 @@ ArvadosFile <- R6::R6Class(
 
             fileSize <- REST$getResourceSize(self$getRelativePath(),
                                              private$collection$uuid)
-
             fileSize
         },
 
@@ -99,7 +100,7 @@ ArvadosFile <- R6::R6Class(
 
         getCollection = function() private$collection,
 
-        setCollection = function(collection)
+        setCollection = function(collection, setRecursively = TRUE)
         {
             private$collection <- collection
         },
@@ -176,20 +177,18 @@ ArvadosFile <- R6::R6Class(
             writeResult
         },
 
-        move = function(newLocation)
+        move = function(destination)
         {
             if(is.null(private$collection))
-                stop("ArvadosFile doesn't belong to any collection")
+                stop("ArvadosFile doesn't belong to any collection.")
 
-            newLocation <- trimFromEnd(newLocation, "/")
-            nameAndPath <- splitToPathAndName(newLocation)
+            destination <- trimFromEnd(destination, "/")
+            nameAndPath <- splitToPathAndName(destination)
 
             newParent <- private$collection$get(nameAndPath$path)
 
             if(is.null(newParent))
-            {
-                stop("Unable to get destination subcollection")
-            }
+                stop("Unable to get destination subcollection.")
 
             childWithSameName <- newParent$get(nameAndPath$name)
 
@@ -202,11 +201,50 @@ ArvadosFile <- R6::R6Class(
                       private$collection$uuid)
 
             private$dettachFromCurrentParent()
-            private$attachToNewParent(newParent)
+            private$attachToNewParent(self, newParent)
 
+            private$parent <- newParent
             private$name <- nameAndPath$name
 
-            "Content moved successfully."
+            self
+        },
+
+        copy = function(destination)
+        {
+            if(is.null(private$collection))
+                stop("ArvadosFile doesn't belong to any collection.")
+
+            destination <- trimFromEnd(destination, "/")
+            nameAndPath <- splitToPathAndName(destination)
+
+            newParent <- private$collection$get(nameAndPath$path)
+
+            if(is.null(newParent))
+                stop("Unable to get destination subcollection.")
+
+            childWithSameName <- newParent$get(nameAndPath$name)
+
+            if(!is.null(childWithSameName))
+                stop("Destination already contains content with same name.")
+
+            REST <- private$collection$getRESTService()
+            REST$copy(self$getRelativePath(),
+                      paste0(newParent$getRelativePath(), "/", nameAndPath$name),
+                      private$collection$uuid)
+
+            newFile <- self$duplicate(nameAndPath$name)
+            newFile$setCollection(self$getCollection())
+            private$attachToNewParent(newFile, newParent)
+            newFile$setParent(newParent)
+
+            newFile
+        },
+
+        duplicate = function(newName = NULL)
+        {
+            name <- if(!is.null(newName)) newName else private$name
+            newFile <- ArvadosFile$new(name)
+            newFile
         }
     ),
 
@@ -218,30 +256,29 @@ ArvadosFile <- R6::R6Class(
         collection = NULL,
         buffer     = NULL,
 
-        attachToNewParent = function(newParent)
+        attachToNewParent = function(content, newParent)
         {
-            #Note: We temporary set parents collection to NULL. This will ensure that
-            #      add method doesn't post file on REST.
+            # We temporary set parents collection to NULL. This will ensure that
+            # add method doesn't post this file on REST.
+            # 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$getCollection()
+            content$setCollection(NULL, setRecursively = FALSE)
             newParent$setCollection(NULL, setRecursively = FALSE)
-
-            newParent$add(self)
-
+            newParent$add(content)
+            content$setCollection(parentsCollection, setRecursively = FALSE)
             newParent$setCollection(parentsCollection, setRecursively = FALSE)
-
-            private$parent <- newParent
         },
 
         dettachFromCurrentParent = function()
         {
-            #Note: We temporary set parents collection to NULL. This will ensure that
-            #      remove method doesn't remove this subcollection from REST.
+            # We temporary set parents collection to NULL. This will ensure that
+            # remove method doesn't remove this file from REST.
             parent <- private$parent
             parentsCollection <- parent$getCollection()
             parent$setCollection(NULL, setRecursively = FALSE)
-
             parent$remove(private$name)
-
             parent$setCollection(parentsCollection, setRecursively = FALSE)
         }
     ),
@@ -267,8 +304,8 @@ print.ArvadosFile = function(x, ...)
         relativePath <- paste0("/", relativePath)
     }
 
-    cat(paste0("Type:          ", "\"", "ArvadosFile",         "\""), sep = "\n")
-    cat(paste0("Name:          ", "\"", x$getName(),           "\""), sep = "\n")
-    cat(paste0("Relative path: ", "\"", relativePath,          "\""), sep = "\n")
-    cat(paste0("Collection:    ", "\"", collection,            "\""), sep = "\n")
+    cat(paste0("Type:          ", "\"", "ArvadosFile", "\""), sep = "\n")
+    cat(paste0("Name:          ", "\"", x$getName(),   "\""), sep = "\n")
+    cat(paste0("Relative path: ", "\"", relativePath,  "\""), sep = "\n")
+    cat(paste0("Collection:    ", "\"", collection,    "\""), sep = "\n")
 }
index 833b833c80f367ef59d4ca82ef78784e278cf73d..8869d7be67846b449200fe2c675936dd1c4133db 100644 (file)
@@ -23,9 +23,10 @@ source("./R/util.R")
 #' @section Methods:
 #' \describe{
 #'   \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.}
-#'   \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
+#'   \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, newLocation)}{Moves ArvadosFile or Subcollection to another location in 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.}
 #' }
@@ -36,9 +37,6 @@ source("./R/util.R")
 #' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
 #' collection <- Collection$new(arv, "uuid")
 #'
-#' newFile <- ArvadosFile$new("myFile")
-#' collection$add(newFile, "myFolder")
-#'
 #' createdFiles <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
 #'
 #' collection$remove("location/to/my/file.cpp")
@@ -58,23 +56,17 @@ Collection <- R6::R6Class(
     public = list(
 
                uuid = NULL,
-        # api  = NULL,
 
                initialize = function(api, uuid)
         {
-            # self$api <- api
             private$REST <- api$getRESTService()
-
             self$uuid <- uuid
-
-            private$fileContent <- private$REST$getCollectionContent(uuid)
-            private$tree <- CollectionTree$new(private$fileContent, self)
         },
 
         add = function(content, relativePath = "")
         {
             if(is.null(private$tree))
-                private$genereateCollectionTreeStructure()
+                private$generateCollectionTreeStructure()
 
             if(relativePath == ""  ||
                relativePath == "." ||
@@ -94,6 +86,9 @@ Collection <- R6::R6Class(
             if("ArvadosFile"   %in% class(content) ||
                "Subcollection" %in% class(content))
             {
+                if(!is.null(content$getCollection()))
+                    stop("Content already belongs to a collection.")
+
                 if(content$getName() == "")
                     stop("Content has invalid name.")
 
@@ -108,50 +103,32 @@ Collection <- R6::R6Class(
             }
         },
 
-        create = function(fileNames, relativePath = "")
+        create = function(files)
         {
             if(is.null(private$tree))
-                private$genereateCollectionTreeStructure()
-
-            if(relativePath == ""  ||
-               relativePath == "." ||
-               relativePath == "./")
-            {
-                subcollection <- private$tree$getTree()
-            }
-            else
-            {
-                relativePath  <- trimFromEnd(relativePath, "/")
-                subcollection <- self$get(relativePath)
-            }
-
-            if(is.null(subcollection))
-                stop(paste("Subcollection", relativePath, "doesn't exist."))
+                private$generateCollectionTreeStructure()
 
-            if(is.character(fileNames))
+            if(is.character(files))
             {
-                arvadosFiles <- NULL
-                sapply(fileNames, function(fileName)
+                sapply(files, function(file)
                 {
-                    childWithSameName <- subcollection$get(fileName)
+                    childWithSameName <- self$get(file)
                     if(!is.null(childWithSameName))
                         stop("Destination already contains file with same name.")
 
-                    newFile <- ArvadosFile$new(fileName)
-                    subcollection$add(newFile)
+                    newTreeBranch <- private$tree$createBranch(file)
+                    private$tree$addBranch(private$tree$getTree(), newTreeBranch)
 
-                    arvadosFiles <<- c(arvadosFiles, newFile)
+                    private$REST$create(file, self$uuid)
+                    newTreeBranch$setCollection(self)
                 })
 
-                if(length(arvadosFiles) == 1)
-                    return(arvadosFiles[[1]])
-                else
-                    return(arvadosFiles)
+                "Created"
             }
             else
             {
                 stop(paste0("Expected character vector, got ",
-                            paste0("(", paste0(class(fileNames), collapse = ", "), ")"),
+                            paste0("(", paste0(class(files), collapse = ", "), ")"),
                             "."))
             }
         },
@@ -159,7 +136,7 @@ Collection <- R6::R6Class(
         remove = function(paths)
         {
             if(is.null(private$tree))
-                private$genereateCollectionTreeStructure()
+                private$generateCollectionTreeStructure()
 
             if(is.character(paths))
             {
@@ -189,10 +166,10 @@ Collection <- R6::R6Class(
             }
         },
 
-        move = function(content, newLocation)
+        move = function(content, destination)
         {
             if(is.null(private$tree))
-                private$genereateCollectionTreeStructure()
+                private$generateCollectionTreeStructure()
 
             content <- trimFromEnd(content, "/")
 
@@ -201,13 +178,37 @@ Collection <- R6::R6Class(
             if(is.null(elementToMove))
                 stop("Content you want to move doesn't exist in the collection.")
 
-            elementToMove$move(newLocation)
+            elementToMove$move(destination)
+        },
+
+        copy = function(content, destination)
+        {
+            if(is.null(private$tree))
+                private$generateCollectionTreeStructure()
+
+            content <- trimFromEnd(content, "/")
+
+            elementToCopy <- self$get(content)
+
+            if(is.null(elementToCopy))
+                stop("Content you want to copy doesn't exist in the collection.")
+
+            elementToCopy$copy(destination)
+        },
+
+        refresh = function()
+        {
+            if(!is.null(private$tree))
+            {
+                private$tree$getTree()$setCollection(NULL, setRecursively = TRUE)
+                private$tree <- NULL
+            }
         },
 
         getFileListing = function()
         {
             if(is.null(private$tree))
-                private$genereateCollectionTreeStructure()
+                private$generateCollectionTreeStructure()
 
             content <- private$REST$getCollectionContent(self$uuid)
             content[order(tolower(content))]
@@ -216,32 +217,11 @@ Collection <- R6::R6Class(
         get = function(relativePath)
         {
             if(is.null(private$tree))
-                private$genereateCollectionTreeStructure()
+                private$generateCollectionTreeStructure()
 
             private$tree$getElement(relativePath)
         },
 
-               toJSON = function()
-        {
-                       fields <- sapply(private$classFields, function(field)
-                       {
-                               self[[field]]
-                       }, USE.NAMES = TRUE)
-
-                       jsonlite::toJSON(list("collection" =
-                     Filter(Negate(is.null), fields)), auto_unbox = TRUE)
-               },
-
-               isEmpty = function() {
-                       fields <- sapply(private$classFields,
-                                        function(field) self[[field]])
-
-                       if(any(sapply(fields, function(field) !is.null(field) && field != "")))
-                               FALSE
-                       else
-                               TRUE
-               },
-
         getRESTService = function() private$REST,
         setRESTService = function(newRESTService) private$REST <- newRESTService
     ),
@@ -251,9 +231,8 @@ Collection <- R6::R6Class(
         REST        = NULL,
         tree        = NULL,
         fileContent = NULL,
-        classFields = NULL,
 
-        genereateCollectionTreeStructure = function()
+        generateCollectionTreeStructure = function()
         {
             if(is.null(self$uuid))
                 stop("Collection uuid is not defined.")
index 8b2f8876b0f91a0d86e148f81f1d29d87ab2f479..5f7a29455ae4a58aaae6792f6dd1eb26ae30ae4e 100644 (file)
@@ -15,55 +15,16 @@ CollectionTree <- R6::R6Class(
         initialize = function(fileContent, collection)
         {
             self$pathsList <- fileContent
-
-            treeBranches <- sapply(fileContent, function(filePath)
-            {
-                splitPath <- unlist(strsplit(filePath, "/", fixed = TRUE))
-                branch <- private$createBranch(splitPath)
-            })
-
+            treeBranches <- sapply(fileContent, function(filePath) self$createBranch(filePath))
             root <- Subcollection$new("")
-
-            sapply(treeBranches, function(branch)
-            {
-                private$addBranch(root, branch)
-            })
-
+            sapply(treeBranches, function(branch) self$addBranch(root, branch))
             root$setCollection(collection)
             private$tree <- root
         },
 
-        getElement = function(relativePath)
-        {
-            relativePath <- trimFromStart(relativePath, "./")
-            relativePath <- trimFromEnd(relativePath, "/")
-
-            if(endsWith(relativePath, "/"))
-                relativePath <- substr(relativePath, 0, nchar(relativePath) - 1)
-
-            splitPath <- unlist(strsplit(relativePath, "/", fixed = TRUE))
-            returnElement <- private$tree
-
-            for(pathFragment in splitPath)
-            {
-                returnElement <- returnElement$get(pathFragment)
-
-                if(is.null(returnElement))
-                    return(NULL)
-            }
-
-            returnElement
-        },
-
-        getTree = function() private$tree
-    ),
-
-    private = list(
-
-        tree = NULL,
-
-        createBranch = function(splitPath)
+        createBranch = function(filePath)
         {
+            splitPath <- unlist(strsplit(filePath, "/", fixed = TRUE))
             branch <- NULL
             lastElementIndex <- length(splitPath)
 
@@ -90,7 +51,11 @@ CollectionTree <- R6::R6Class(
 
             if(is.null(child))
             {
+                # Make sure we are don't make any REST call while adding child
+                collection <- container$getCollection()
+                container$setCollection(NULL, setRecursively = FALSE)
                 container$add(node)
+                container$setCollection(collection, setRecursively = FALSE)
             }
             else
             {
@@ -100,14 +65,41 @@ CollectionTree <- R6::R6Class(
                 # If we encounter that same name again we know
                 # it's a folder so we need to replace ArvadosFile with Subcollection.
                 if("ArvadosFile" %in% class(child))
-                {
                     child = private$replaceFileWithSubcollection(child)
-                }
 
-                private$addBranch(child, node$getFirst())
+                self$addBranch(child, node$getFirst())
             }
         },
 
+        getElement = function(relativePath)
+        {
+            relativePath <- trimFromStart(relativePath, "./")
+            relativePath <- trimFromEnd(relativePath, "/")
+
+            if(endsWith(relativePath, "/"))
+                relativePath <- substr(relativePath, 0, nchar(relativePath) - 1)
+
+            splitPath <- unlist(strsplit(relativePath, "/", fixed = TRUE))
+            returnElement <- private$tree
+
+            for(pathFragment in splitPath)
+            {
+                returnElement <- returnElement$get(pathFragment)
+
+                if(is.null(returnElement))
+                    return(NULL)
+            }
+
+            returnElement
+        },
+
+        getTree = function() private$tree
+    ),
+
+    private = list(
+
+        tree = NULL,
+
         replaceFileWithSubcollection = function(arvadosFile)
         {
             subcollection <- Subcollection$new(arvadosFile$getName())
index 4595fef662c1c9422af13dc0222a10bd9a9df48a..07defca90f4c99e8be9f8a73f7412f398ab1a701 100644 (file)
@@ -16,7 +16,7 @@ HttpRequest <- R6::R6Class(
         initialize = function()
         {
             self$validContentTypes <- c("text", "raw")
-            self$validVerbs <- c("GET", "POST", "PUT", "DELETE", "PROPFIND", "MOVE")
+            self$validVerbs <- c("GET", "POST", "PUT", "DELETE", "PROPFIND", "MOVE", "COPY")
         },
 
         exec = function(verb, url, headers = NULL, body = NULL, queryParams = NULL,
index 867665299f49899909167c4fd838bc9ae1371dd8..78b2c35e32fa117190f033075e1ea5ee2a3805e3 100644 (file)
@@ -81,10 +81,10 @@ RESTService <- R6::R6Class(
         {
             collectionURL <- paste0(self$getWebDavHostName(), "c=", uuid, "/")
             fromURL <- paste0(collectionURL, from)
-            toURL <- paste0(collectionURL, to)
+            toURL <- paste0(collectionURL, trimFromStart(to, "/"))
 
             headers <- list("Authorization" = paste("OAuth2", self$token),
-                           "Destination" = toURL)
+                            "Destination" = toURL)
 
             serverResponse <- self$http$exec("MOVE", fromURL, headers,
                                              retryTimes = self$numRetries)
@@ -95,6 +95,24 @@ RESTService <- R6::R6Class(
             serverResponse
         },
 
+        copy = function(from, to, uuid)
+        {
+            collectionURL <- paste0(self$getWebDavHostName(), "c=", uuid, "/")
+            fromURL <- paste0(collectionURL, from)
+            toURL <- paste0(collectionURL, trimFromStart(to, "/"))
+
+            headers <- list("Authorization" = paste("OAuth2", self$token),
+                            "Destination" = toURL)
+
+            serverResponse <- self$http$exec("COPY", fromURL, headers,
+                                             retryTimes = self$numRetries)
+
+            if(serverResponse$status_code < 200 || serverResponse$status_code >= 300)
+                stop(paste("Server code:", serverResponse$status_code))
+
+            serverResponse
+        },
+
         getCollectionContent = function(uuid)
         {
             collectionURL <- URLencode(paste0(self$getWebDavHostName(),
index 45fe34347903192bed1d8618e14aceedf73a18f2..17a9ef3ee3ba6180546763da637a8824905d66dc 100644 (file)
@@ -26,7 +26,8 @@ source("./R/util.R")
 #'   \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
 #'   \item{getFileListing()}{Returns subcollections file content as character vector.}
 #'   \item{getSizeInBytes()}{Returns subcollections content size in bytes.}
-#'   \item{move(newLocation)}{Moves subcollection to a new location inside collection.}
+#'   \item{move(destination)}{Moves subcollection to a new location inside collection.}
+#'   \item{copy(destination)}{Copies subcollection to a new location inside collection.}
 #' }
 #'
 #' @name Subcollection
@@ -40,6 +41,7 @@ source("./R/util.R")
 #' myFolder$remove("myFile")
 #'
 #' myFolder$move("newLocation/myFolder")
+#' myFolder$copy("newLocation/myFolder")
 #' }
 NULL
 
@@ -77,6 +79,9 @@ Subcollection <- R6::R6Class(
             if("ArvadosFile"   %in% class(content) ||
                "Subcollection" %in% class(content))
             {
+                if(!is.null(content$getCollection()))
+                    stop("Content already belongs to a collection.")
+
                 if(content$getName() == "")
                     stop("Content has invalid name.")
 
@@ -161,20 +166,18 @@ Subcollection <- R6::R6Class(
             return(sum(fileSizes))
         },
 
-        move = function(newLocation)
+        move = function(destination)
         {
             if(is.null(private$collection))
-                stop("Subcollection doesn't belong to any collection")
+                stop("Subcollection doesn't belong to any collection.")
 
-            newLocation <- trimFromEnd(newLocation, "/")
-            nameAndPath <- splitToPathAndName(newLocation)
+            destination <- trimFromEnd(destination, "/")
+            nameAndPath <- splitToPathAndName(destination)
 
             newParent <- private$collection$get(nameAndPath$path)
 
             if(is.null(newParent))
-            {
-                stop("Unable to get destination subcollection")
-            }
+                stop("Unable to get destination subcollection.")
 
             childWithSameName <- newParent$get(nameAndPath$name)
 
@@ -187,11 +190,53 @@ Subcollection <- R6::R6Class(
                       private$collection$uuid)
 
             private$dettachFromCurrentParent()
-            private$attachToNewParent(newParent)
+            private$attachToNewParent(self, newParent)
 
+            private$parent <- newParent
             private$name <- nameAndPath$name
 
-            "Content moved successfully."
+            self
+        },
+
+        copy = function(destination)
+        {
+            if(is.null(private$collection))
+                stop("Subcollection doesn't belong to any collection.")
+
+            destination <- trimFromEnd(destination, "/")
+            nameAndPath <- splitToPathAndName(destination)
+
+            newParent <- private$collection$get(nameAndPath$path)
+
+            if(is.null(newParent) || !("Subcollection" %in% class(newParent)))
+                stop("Unable to get destination subcollection.")
+
+            childWithSameName <- newParent$get(nameAndPath$name)
+
+            if(!is.null(childWithSameName))
+                stop("Destination already contains content with same name.")
+
+            REST <- private$collection$getRESTService()
+            REST$copy(self$getRelativePath(),
+                      paste0(newParent$getRelativePath(), "/", nameAndPath$name),
+                      private$collection$uuid)
+
+            newContent <- self$duplicate(nameAndPath$name)
+            newContent$setCollection(self$getCollection(), setRecursively = TRUE)
+            newContent$setParent(newParent)
+            private$attachToNewParent(newContent, newParent)
+
+            newContent
+        },
+
+        duplicate = function(newName = NULL)
+        {
+            name <- if(!is.null(newName)) newName else private$name
+            root <- Subcollection$new(name)
+            for(child in private$children)
+                root$add(child$duplicate())
+
+            root
         },
 
         get = function(name)
@@ -254,30 +299,29 @@ Subcollection <- R6::R6Class(
             }
         },
 
-        attachToNewParent = function(newParent)
+        attachToNewParent = function(content, newParent)
         {
-            #Note: We temporary set parents collection to NULL. This will ensure that
-            #      add method doesn't post file on REST.
+            # We temporary set parents collection to NULL. This will ensure that
+            # add method doesn't post this subcollection to REST.
+            # 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$getCollection()
+            content$setCollection(NULL, setRecursively = FALSE)
             newParent$setCollection(NULL, setRecursively = FALSE)
-
-            newParent$add(self)
-
+            newParent$add(content)
+            content$setCollection(parentsCollection, setRecursively = FALSE)
             newParent$setCollection(parentsCollection, setRecursively = FALSE)
-
-            private$parent <- newParent
         },
 
         dettachFromCurrentParent = function()
         {
-            #Note: We temporary set parents collection to NULL. This will ensure that
-            #      remove method doesn't remove this subcollection from REST.
+            # We temporary set parents collection to NULL. This will ensure that
+            # remove method doesn't remove this subcollection from REST.
             parent <- private$parent
             parentsCollection <- parent$getCollection()
             parent$setCollection(NULL, setRecursively = FALSE)
-
             parent$remove(private$name)
-
             parent$setCollection(parentsCollection, setRecursively = FALSE)
         },
 
index c98f803e5ea8e123b4e058b8256850668b5ae068..fa0cda45bfc65dfefb2c681eabee5c3668e822d9 100644 (file)
@@ -1,3 +1,7 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
 .onLoad <- function(libName, pkgName)
 {
     minAllowedRVersion <- "3.3.0"
index be34b2fdb1dabd3531ca74e696a8240528418520..7ea226fd0931d61a2c8c2e92f8d892f3406918b3 100644 (file)
@@ -186,31 +186,16 @@ size <- arvadosSubcollection$getSizeInBytes()
 * Create new file in a collection:
 
 ```{r}
-collection$create(fileNames, optionalRelativePath)
+collection$create(files)
 ```
 
     Example:
 
 ```{r}
-mainFile <- collection$create("main.cpp", "cpp/src/")
-fileList <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
+mainFile <- collection$create("cpp/src/main.cpp")
+fileList <- collection$create(c("cpp/src/main.cpp", "cpp/src/util.h"))
 ```
 
-* Add existing ArvadosFile or Subcollection to a collection:
-
-```{r}
-folder <- Subcollection$new("src")
-file   <- ArvadosFile$new("main.cpp")
-folder$add(file)
-```
-
-```{r}
-collection$add(folder, "cpp")
-```
-
-This examples will add file "main.cpp" in "./cpp/src/" folder if folder exists.
-If subcollection contains more files or folders they will be added recursively.
-
 * Delete file from a collection:
 
 ```{r}
@@ -259,6 +244,28 @@ 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 inside collection:
+
+Directley 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:
index 95a2e5561fa9ce21b1d5bd236489595b8c2c034d..51f98d81dcd4de28b9e5faca303ee87a5da7a58d 100644 (file)
@@ -166,6 +166,7 @@ Arvados class gives users ability to access Arvados REST API.
        \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}}}
index b7840dc16ff4cbbd15dd7383b9fcde0c59416606..514e9e846df958548bacefa670b35e69814d0767 100644 (file)
@@ -29,7 +29,8 @@ ArvadosFile class represents a file inside Arvados collection.
   \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(newLocation)}{Moves file to a new location inside collection.}
+  \item{move(destination)}{Moves file to a new location inside collection.}
+  \item{copy(destination)}{Copies file to a new location inside collection.}
 }
 }
 
@@ -40,7 +41,7 @@ myFile <- ArvadosFile$new("myFile")
 myFile$write("This is new file content")
 fileContent <- myFile$read()
 fileContent <- myFile$read("text")
-fileContent <- myFile$read("raw", offset = 8, length = 4) 
+fileContent <- myFile$read("raw", offset = 8, length = 4)
 
 #Write a table:
 arvConnection <- myFile$connection("w")
@@ -52,5 +53,6 @@ arvConnection <- myFile$connection("r")
 mytable <- read.table(arvConnection)
 
 myFile$move("newFolder/myFile")
+myFile$copy("newFolder/myFile")
 }
 }
index 8cf29a2ea56d19cc32307cdab3c0a488537ac295..fbe6038664447df230ba77295f17d5df97274d29 100644 (file)
@@ -23,9 +23,10 @@ Collection class provides interface for working with Arvados collections.
 
 \describe{
   \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.}
-  \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
+  \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, newLocation)}{Moves ArvadosFile or Subcollection to another location in 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.}
 }
@@ -36,9 +37,6 @@ Collection class provides interface for working with Arvados collections.
 arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
 collection <- Collection$new(arv, "uuid")
 
-newFile <- ArvadosFile$new("myFile")
-collection$add(newFile, "myFolder")
-
 createdFiles <- collection$create(c("main.cpp", lib.dll), "cpp/src/")
 
 collection$remove("location/to/my/file.cpp")
index df0970b30fd4ef843b595f8db52efbafd9b140a4..0b27a8bc4389d134b5f360bf012cd17d7934d77f 100644 (file)
@@ -5,7 +5,7 @@
 \title{Subcollection}
 \description{
 Subcollection class represents a folder inside Arvados collection.
-It is essentially a composite of ArvadosFiles and other Subcollections.
+It is essentially a composite of arvadosFiles and other subcollections.
 }
 \section{Usage}{
 
@@ -29,7 +29,8 @@ It is essentially a composite of ArvadosFiles and other Subcollections.
   \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(newLocation)}{Moves subcollection to a new location inside collection.}
+  \item{move(destination)}{Moves subcollection to a new location inside collection.}
+  \item{copy(destination)}{Copies subcollection to a new location inside collection.}
 }
 }
 
@@ -43,5 +44,6 @@ myFolder$get("myFile")
 myFolder$remove("myFile")
 
 myFolder$move("newLocation/myFolder")
+myFolder$copy("newLocation/myFolder")
 }
 }
diff --git a/sdk/R/man/users.merge.Rd b/sdk/R/man/users.merge.Rd
new file mode 100644 (file)
index 0000000..a539591
--- /dev/null
@@ -0,0 +1,22 @@
+% 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.
+}
index 2ebcda2e4d671dc91cef9ca6ca0cdcb6a2707e18..7734e0d9284d6bde09b478ab30171e687ea75a2c 100644 (file)
@@ -27,6 +27,7 @@ FakeHttpRequest <- R6::R6Class(
         numberOfPUTRequests        = NULL,
         numberOfPOSTRequests       = NULL,
         numberOfMOVERequests       = NULL,
+        numberOfCOPYRequests       = NULL,
         numberOfgetConnectionCalls = NULL,
 
         initialize = function(expectedURL      = NULL,
@@ -57,6 +58,7 @@ FakeHttpRequest <- R6::R6Class(
             self$numberOfPUTRequests    <- 0
             self$numberOfPOSTRequests   <- 0
             self$numberOfMOVERequests   <- 0
+            self$numberOfCOPYRequests   <- 0
 
             self$numberOfgetConnectionCalls <- 0
 
@@ -81,6 +83,8 @@ FakeHttpRequest <- R6::R6Class(
                 self$numberOfDELETERequests <- self$numberOfDELETERequests + 1
             else if(verb == "MOVE")
                 self$numberOfMOVERequests <- self$numberOfMOVERequests + 1
+            else if(verb == "COPY")
+                self$numberOfCOPYRequests <- self$numberOfCOPYRequests + 1
             else if(verb == "PROPFIND")
             {
                 return(self$content)
index 048013f566a3c737188dc04f876bee6d9ae8dd90..a91da04fd1295edf5332b54b61da47ab2ea4687d 100644 (file)
@@ -18,6 +18,7 @@ FakeRESTService <- R6::R6Class(
         createCallCount               = NULL,
         deleteCallCount               = NULL,
         moveCallCount                 = NULL,
+        copyCallCount                 = NULL,
         getCollectionContentCallCount = NULL,
         getResourceSizeCallCount      = NULL,
         readCallCount                 = NULL,
@@ -31,7 +32,7 @@ FakeRESTService <- R6::R6Class(
         collectionContent = NULL,
         returnContent     = NULL,
 
-        initialize = function(collectionContent = NULL, returnContent = NULL, 
+        initialize = function(collectionContent = NULL, returnContent = NULL,
                               expectedFilterContent = NULL)
         {
             self$getResourceCallCount    <- 0
@@ -44,6 +45,7 @@ FakeRESTService <- R6::R6Class(
             self$createCallCount               <- 0
             self$deleteCallCount               <- 0
             self$moveCallCount                 <- 0
+            self$copyCallCount                 <- 0
             self$getCollectionContentCallCount <- 0
             self$getResourceSizeCallCount      <- 0
             self$readCallCount                 <- 0
@@ -135,6 +137,12 @@ FakeRESTService <- R6::R6Class(
             self$returnContent
         },
 
+        copy = function(from, to, uuid)
+        {
+            self$copyCallCount <- self$copyCallCount + 1
+            self$returnContent
+        },
+
         getCollectionContent = function(uuid)
         {
             self$getCollectionContentCallCount <- self$getCollectionContentCallCount + 1
@@ -146,7 +154,7 @@ FakeRESTService <- R6::R6Class(
             self$getResourceSizeCallCount <- self$getResourceSizeCallCount + 1
             self$returnContent
         },
-        
+
         read = function(relativePath, uuid, contentType = "text", offset = 0, length = 0)
         {
             self$readCallCount <- self$readCallCount + 1
index 1f559e999c52be207317b1f9f6f17332ab287ac0..e3457c993f7c88cee4a963ca7006a90c6078f478 100644 (file)
@@ -81,7 +81,6 @@ test_that("read raises exception if file doesn't belong to a collection", {
 
 test_that("read raises exception offset or length is negative number", {
 
-
     collectionContent <- c("animal", "animal/fish")
     fakeREST <- FakeRESTService$new(collectionContent)
 
@@ -156,7 +155,6 @@ test_that(paste("connection returns textConnection opened",
 
 test_that("flush sends data stored in a connection to a REST server", {
 
-
     collectionContent <- c("animal", "animal/fish")
     fakeREST <- FakeRESTService$new(collectionContent)
 
@@ -204,13 +202,12 @@ test_that(paste("move raises exception if arvados file",
     animal <- ArvadosFile$new("animal")
 
     expect_that(animal$move("new/location"),
-                throws_error("ArvadosFile doesn't belong to any collection"))
+                throws_error("ArvadosFile doesn't belong to any collection."))
 })
 
 test_that(paste("move raises exception if newLocationInCollection",
                 "parameter is invalid"), {
 
-
     collectionContent <- c("animal",
                            "animal/fish",
                            "animal/dog",
@@ -226,7 +223,7 @@ test_that(paste("move raises exception if newLocationInCollection",
     dog <- collection$get("animal/dog")
 
     expect_that(dog$move("objects/dog"),
-                throws_error("Unable to get destination subcollection"))
+                throws_error("Unable to get destination subcollection."))
 })
 
 test_that("move raises exception if new location contains content with the same name", {
@@ -252,7 +249,6 @@ test_that("move raises exception if new location contains content with the same
 
 test_that("move moves arvados file inside collection tree", {
 
-
     collectionContent <- c("animal",
                            "animal/fish",
                            "animal/dog",
@@ -273,3 +269,85 @@ test_that("move moves arvados file inside collection tree", {
     expect_that(dogIsNullOnOldLocation, is_true())
     expect_that(dogExistsOnNewLocation, is_true())
 })
+
+test_that(paste("copy raises exception if arvados file",
+                "doesn't belong to any collection"), {
+
+    animal <- ArvadosFile$new("animal")
+
+    expect_that(animal$copy("new/location"),
+                throws_error("ArvadosFile doesn't belong to any collection."))
+})
+
+test_that(paste("copy raises exception if location parameter is invalid"), {
+
+    collectionContent <- c("animal",
+                           "animal/fish",
+                           "animal/dog",
+                           "animal/fish/shark",
+                           "ball")
+
+    fakeREST <- FakeRESTService$new(collectionContent)
+
+    api <- Arvados$new("myToken", "myHostName")
+    api$setRESTService(fakeREST)
+
+    collection <- Collection$new(api, "myUUID")
+    dog <- collection$get("animal/dog")
+
+    expect_that(dog$copy("objects/dog"),
+                throws_error("Unable to get destination subcollection."))
+})
+
+test_that("copy raises exception if new location contains content with the same name", {
+
+
+    collectionContent <- c("animal",
+                           "animal/fish",
+                           "animal/dog",
+                           "animal/fish/shark",
+                           "dog")
+
+    fakeREST <- FakeRESTService$new(collectionContent)
+
+    api <- Arvados$new("myToken", "myHostName")
+    api$setRESTService(fakeREST)
+    collection <- Collection$new(api, "myUUID")
+    dog <- collection$get("animal/dog")
+
+    expect_that(dog$copy("dog"),
+                throws_error("Destination already contains content with same name."))
+
+})
+
+test_that("copy copies arvados file inside collection tree", {
+
+    collectionContent <- c("animal",
+                           "animal/fish",
+                           "animal/dog",
+                           "animal/fish/shark",
+                           "ball")
+
+    fakeREST <- FakeRESTService$new(collectionContent)
+
+    api <- Arvados$new("myToken", "myHostName")
+    api$setRESTService(fakeREST)
+    collection <- Collection$new(api, "myUUID")
+    dog <- collection$get("animal/dog")
+
+    dog$copy("dog")
+    dogExistsOnOldLocation <- !is.null(collection$get("animal/dog"))
+    dogExistsOnNewLocation <- !is.null(collection$get("dog"))
+
+    expect_that(dogExistsOnOldLocation, is_true())
+    expect_that(dogExistsOnNewLocation, is_true())
+})
+
+test_that("duplicate performs deep cloning of Arvados file", {
+    arvFile <- ArvadosFile$new("foo")
+    newFile1 <- arvFile$duplicate()
+    newFile2 <- arvFile$duplicate("bar")
+
+    expect_that(newFile1$getFileListing(), equals(arvFile$getFileListing()))
+    expect_that(newFile2$getFileListing(), equals(c("bar")))
+})
index af5fabeb73c82c99cfee67e935a1ebfa8e61fd2c..636359ae21a7b196d406ec2b16ee8839e0921f9e 100644 (file)
@@ -104,37 +104,15 @@ test_that("create raises exception if passed argumet is not character vector", {
                              fixed = TRUE))
 })
 
-test_that("create raises exception if relative path is not valid", {
-
-    collectionContent <- c("animal",
-                           "animal/fish",
-                           "ball")
-
-    fakeREST <- FakeRESTService$new(collectionContent)
-
-    api <- Arvados$new("myToken", "myHostName")
-    api$setRESTService(fakeREST)
-    collection <- Collection$new(api, "myUUID")
-
-    newPen <- ArvadosFile$new("pen")
-
-    expect_that(collection$create(newPen, "objects"),
-                throws_error("Subcollection objects doesn't exist.",
-                              fixed = TRUE))
-})
-
 test_that(paste("create adds files specified by fileNames",
                 "to local tree structure and remote REST service"), {
 
-    collectionContent <- c("animal", "animal/fish", "ball")
-    fakeREST <- FakeRESTService$new(collectionContent)
-
+    fakeREST <- FakeRESTService$new()
     api <- Arvados$new("myToken", "myHostName")
     api$setRESTService(fakeREST)
     collection <- Collection$new(api, "myUUID")
 
-    files <- c("dog", "cat")
-    collection$create(files, "animal")
+    collection$create(c("animal/dog", "animal/cat"))
 
     dog <- collection$get("animal/dog")
     cat <- collection$get("animal/cat")
@@ -262,3 +240,58 @@ test_that("get returns arvados file or subcollection from internal tree structur
     expect_that(fishIsNotNull, is_true())
     expect_that(fish$getName(), equals("fish"))
 })
+
+test_that(paste("copy copies content to a new location inside file tree",
+                "and on REST service"), {
+
+    collectionContent <- c("animal", "animal/dog", "ball")
+    fakeREST <- FakeRESTService$new(collectionContent)
+
+    api <- Arvados$new("myToken", "myHostName")
+    api$setRESTService(fakeREST)
+    collection <- Collection$new(api, "myUUID")
+
+    collection$copy("animal/dog", "dog")
+
+    dogExistsOnOldLocation <- !is.null(collection$get("animal/dog"))
+    dogExistsOnNewLocation <- !is.null(collection$get("dog"))
+
+    expect_that(dogExistsOnOldLocation, is_true())
+    expect_that(dogExistsOnNewLocation, is_true())
+    expect_that(fakeREST$copyCallCount, equals(1))
+})
+
+test_that("copy raises exception if new location is not valid", {
+
+    collectionContent <- c("animal", "animal/fish", "ball")
+    fakeREST <- FakeRESTService$new(collectionContent)
+
+    api <- Arvados$new("myToken", "myHostName")
+    api$setRESTService(fakeREST)
+    collection <- Collection$new(api, "myUUID")
+
+    expect_that(collection$copy("fish", "object"),
+                throws_error("Content you want to copy doesn't exist in the collection.",
+                             fixed = TRUE))
+})
+
+test_that("refresh invalidates current tree structure", {
+
+    collectionContent <- c("animal", "animal/fish", "ball")
+    fakeREST <- FakeRESTService$new(collectionContent)
+
+    api <- Arvados$new("myToken", "myHostName")
+    api$setRESTService(fakeREST)
+    collection <- Collection$new(api, "aaaaa-j7d0g-ccccccccccccccc")
+
+    # Before refresh
+    fish <- collection$get("animal/fish")
+    expect_that(fish$getName(), equals("fish"))
+    expect_that(fish$getCollection()$uuid, equals("aaaaa-j7d0g-ccccccccccccccc"))
+
+    collection$refresh()
+
+    # After refresh
+    expect_that(fish$getName(), equals("fish"))
+    expect_true(is.null(fish$getCollection()))
+})
index 26f459b17355903640676b7d4a717bd2c9052890..64988e33db2c3c4614112d2eb993687d6e169199 100644 (file)
@@ -135,6 +135,40 @@ test_that("move raises exception if server response code is not between 200 and
                 throws_error("Server code: 404"))
 })
 
+test_that("copy calls REST service properly", {
+
+    uuid <- "aaaaa-j7d0g-ccccccccccccccc"
+    expectedURL <- "https://webDavHost/c=aaaaa-j7d0g-ccccccccccccccc/file"
+    fakeHttp <- FakeHttpRequest$new(expectedURL)
+    fakeHttpParser <- FakeHttpParser$new()
+
+    REST <- RESTService$new("token", "https://host/",
+                            fakeHttp, fakeHttpParser,
+                            0, "https://webDavHost/")
+
+    REST$copy("file", "newDestination/file", uuid)
+
+    expect_that(fakeHttp$URLIsProperlyConfigured, is_true())
+    expect_that(fakeHttp$requestHeaderContainsAuthorizationField, is_true())
+    expect_that(fakeHttp$requestHeaderContainsDestinationField, is_true())
+    expect_that(fakeHttp$numberOfCOPYRequests, equals(1))
+})
+
+test_that("copy raises exception if server response code is not between 200 and 300", {
+
+    uuid <- "aaaaa-j7d0g-ccccccccccccccc"
+    response <- list()
+    response$status_code <- 404
+    fakeHttp <- FakeHttpRequest$new(serverResponse = response)
+
+    REST <- RESTService$new("token", "https://host/",
+                            fakeHttp, HttpParser$new(),
+                            0, "https://webDavHost/")
+
+    expect_that(REST$copy("file", "newDestination/file", uuid),
+                throws_error("Server code: 404"))
+})
+
 test_that("getCollectionContent retreives correct content from WebDAV server", {
 
     uuid <- "aaaaa-j7d0g-ccccccccccccccc"
index 6845801e59abb8155736fddcf4d92595ef67f018..a6e420962bce9777d56d69c4ded58c015986b288 100644 (file)
@@ -309,7 +309,7 @@ test_that(paste("move raises exception if newLocationInCollection",
     fish <- collection$get("animal/fish")
 
     expect_that(fish$move("objects/dog"),
-                throws_error("Unable to get destination subcollection"))
+                throws_error("Unable to get destination subcollection."))
 })
 
 test_that("move moves subcollection inside collection tree", {
@@ -358,3 +358,87 @@ test_that(paste("getSizeInBytes delegates size calculation",
 
     expect_that(resourceSize, equals(100))
 })
+
+#########################
+test_that(paste("copy raises exception if subcollection",
+                "doesn't belong to any collection"), {
+
+    animal <- Subcollection$new("animal")
+
+    expect_that(animal$copy("new/location"),
+                throws_error("Subcollection doesn't belong to any collection."))
+})
+
+test_that("copy raises exception if new location contains content with the same name", {
+
+    collectionContent <- c("animal",
+                           "animal/fish",
+                           "animal/dog",
+                           "animal/fish/shark",
+                           "fish")
+    fakeREST <- FakeRESTService$new(collectionContent)
+
+    api <- Arvados$new("myToken", "myHostName")
+    api$setRESTService(fakeREST)
+    collection <- Collection$new(api, "myUUID")
+    fish <- collection$get("animal/fish")
+
+    expect_that(fish$copy("fish"),
+                throws_error("Destination already contains content with same name."))
+
+})
+
+test_that(paste("copy raises exception if location parameter is invalid"), {
+
+    collectionContent <- c("animal",
+                           "animal/fish",
+                           "animal/dog",
+                           "animal/fish/shark",
+                           "ball")
+    fakeREST <- FakeRESTService$new(collectionContent)
+
+    api <- Arvados$new("myToken", "myHostName")
+    api$setRESTService(fakeREST)
+
+    collection <- Collection$new(api, "myUUID")
+    fish <- collection$get("animal/fish")
+
+    expect_that(fish$copy("objects/dog"),
+                throws_error("Unable to get destination subcollection."))
+})
+
+test_that("copy copies subcollection inside collection tree", {
+
+    collectionContent <- c("animal",
+                           "animal/fish",
+                           "animal/dog",
+                           "animal/fish/shark",
+                           "ball")
+    fakeREST <- FakeRESTService$new(collectionContent)
+
+    api <- Arvados$new("myToken", "myHostName")
+    api$setRESTService(fakeREST)
+    collection <- Collection$new(api, "myUUID")
+    fish <- collection$get("animal/fish")
+
+    fish$copy("fish")
+    fishExistsOnOldLocation <- !is.null(collection$get("animal/fish"))
+    fishExistsOnNewLocation <- !is.null(collection$get("fish"))
+
+    expect_that(fishExistsOnOldLocation, is_true())
+    expect_that(fishExistsOnNewLocation, is_true())
+})
+
+test_that("duplicate performs deep cloning of Subcollection", {
+    foo <- ArvadosFile$new("foo")
+    bar <- ArvadosFile$new("bar")
+    sub <- Subcollection$new("qux")
+    sub$add(foo)
+    sub$add(bar)
+
+    newSub1 <- sub$duplicate()
+    newSub2 <- sub$duplicate("quux")
+
+    expect_that(newSub1$getFileListing(), equals(sub$getFileListing()))
+    expect_that(sort(newSub2$getFileListing()), equals(c("quux/bar", "quux/foo")))
+})