Improve Collections create and move methods and update documentation
authorFuad Muhic <fmuhic@capeannenterprises.com>
Thu, 26 Jul 2018 14:09:14 +0000 (16:09 +0200)
committerFuad Muhic <fmuhic@capeannenterprises.com>
Thu, 26 Jul 2018 14:09:14 +0000 (16:09 +0200)
Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

60 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/Subcollection.R
sdk/R/R/zzz.R
sdk/R/README.Rmd
sdk/R/man/Collection.Rd
sdk/R/man/api_client_authorizations.create_system_auth.Rd
sdk/R/man/api_client_authorizations.list.Rd
sdk/R/man/api_clients.list.Rd
sdk/R/man/authorized_keys.list.Rd
sdk/R/man/collections.list.Rd
sdk/R/man/collections.provenance.Rd
sdk/R/man/collections.trash.Rd
sdk/R/man/collections.untrash.Rd
sdk/R/man/collections.used_by.Rd
sdk/R/man/container_requests.list.Rd
sdk/R/man/containers.auth.Rd
sdk/R/man/containers.list.Rd
sdk/R/man/containers.lock.Rd
sdk/R/man/containers.secret_mounts.Rd
sdk/R/man/containers.unlock.Rd
sdk/R/man/groups.contents.Rd
sdk/R/man/groups.list.Rd
sdk/R/man/groups.trash.Rd
sdk/R/man/groups.untrash.Rd
sdk/R/man/humans.list.Rd
sdk/R/man/job_tasks.list.Rd
sdk/R/man/jobs.cancel.Rd
sdk/R/man/jobs.create.Rd
sdk/R/man/jobs.list.Rd
sdk/R/man/jobs.lock.Rd
sdk/R/man/jobs.queue.Rd
sdk/R/man/keep_disks.list.Rd
sdk/R/man/keep_disks.ping.Rd
sdk/R/man/keep_services.list.Rd
sdk/R/man/links.get_permissions.Rd
sdk/R/man/links.list.Rd
sdk/R/man/logs.list.Rd
sdk/R/man/nodes.list.Rd
sdk/R/man/nodes.ping.Rd
sdk/R/man/pipeline_instances.cancel.Rd
sdk/R/man/pipeline_instances.list.Rd
sdk/R/man/pipeline_templates.list.Rd
sdk/R/man/projects.list.Rd
sdk/R/man/repositories.list.Rd
sdk/R/man/specimens.list.Rd
sdk/R/man/traits.list.Rd
sdk/R/man/user_agreements.list.Rd
sdk/R/man/users.activate.Rd
sdk/R/man/users.list.Rd
sdk/R/man/users.merge.Rd
sdk/R/man/users.setup.Rd
sdk/R/man/users.unsetup.Rd
sdk/R/man/users.update_uuid.Rd
sdk/R/man/virtual_machines.list.Rd
sdk/R/man/virtual_machines.logins.Rd
sdk/R/man/workflows.list.Rd
sdk/R/tests/testthat/test-Collection.R

index de2aade4adf77c2f6e088c2ca5cb85fa2ec33e2e..744cb3c296163906be8be5858e0713e8d43aa44e 100644 (file)
@@ -1,7 +1,7 @@
 #' 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.
@@ -9,9 +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.
@@ -20,9 +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.
@@ -31,9 +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.
@@ -41,106 +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
+#' @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.
@@ -148,9 +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.
@@ -160,9 +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.
@@ -172,9 +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.
@@ -182,50 +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.
@@ -233,9 +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.
@@ -245,9 +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.
@@ -257,9 +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.
@@ -267,78 +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.
@@ -346,9 +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.
@@ -358,9 +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.
@@ -370,9 +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.
@@ -380,29 +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
 
 #' 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.
@@ -410,9 +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.
@@ -422,9 +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.
@@ -434,9 +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.
@@ -444,29 +444,29 @@ 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.
@@ -474,9 +474,9 @@ NULL
 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.
@@ -486,9 +486,9 @@ NULL
 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.
@@ -498,9 +498,9 @@ NULL
 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.
@@ -508,29 +508,29 @@ NULL
 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
+#' @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.
@@ -538,9 +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.
@@ -550,9 +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.
@@ -562,9 +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.
@@ -572,70 +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.
@@ -643,9 +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.
@@ -654,9 +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.
@@ -665,9 +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.
@@ -675,29 +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.
@@ -705,9 +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.
@@ -716,9 +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.
@@ -727,9 +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.
@@ -737,29 +737,29 @@ 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
 
 #' 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.
@@ -767,26 +767,26 @@ NULL
 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
+#' @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.
@@ -795,9 +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.
@@ -805,77 +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.
@@ -883,9 +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.
@@ -895,9 +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.
@@ -907,9 +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.
@@ -917,47 +917,47 @@ 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.
@@ -965,9 +965,9 @@ NULL
 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.
@@ -978,9 +978,9 @@ NULL
 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.
@@ -990,9 +990,9 @@ NULL
 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.
@@ -1000,40 +1000,40 @@ NULL
 NULL
 
 #' nodes.ping
-#'
+#' 
 #' nodes.ping is a method defined in Arvados class.
-#'
+#' 
 #' @usage arv$nodes.ping(uuid, ping_secret)
-#' @param uuid
-#' @param 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
+#' @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.
@@ -1041,9 +1041,9 @@ NULL
 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.
@@ -1052,9 +1052,9 @@ NULL
 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.
@@ -1063,9 +1063,9 @@ NULL
 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.
@@ -1073,39 +1073,39 @@ NULL
 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
+#' @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
+#' @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.
@@ -1113,9 +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.
@@ -1125,9 +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.
@@ -1137,9 +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.
@@ -1147,38 +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.
@@ -1186,9 +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.
@@ -1198,9 +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.
@@ -1210,9 +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.
@@ -1220,29 +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.
@@ -1250,9 +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.
@@ -1262,9 +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.
@@ -1274,9 +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.
@@ -1284,39 +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
 
 #' 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.
@@ -1324,9 +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.
@@ -1336,9 +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.
@@ -1348,9 +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.
@@ -1358,38 +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.
@@ -1397,9 +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.
@@ -1409,9 +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.
@@ -1421,9 +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.
@@ -1431,29 +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.
@@ -1461,9 +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.
@@ -1472,9 +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.
@@ -1483,9 +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.
@@ -1493,28 +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.
@@ -1522,9 +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.
@@ -1533,9 +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.
@@ -1544,9 +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.
@@ -1554,29 +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.
@@ -1584,9 +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.
@@ -1596,9 +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.
@@ -1608,9 +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.
@@ -1618,48 +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.
@@ -1667,9 +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.
@@ -1679,9 +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.
@@ -1691,9 +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.
@@ -1701,29 +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.
@@ -1731,9 +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.
@@ -1742,9 +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.
@@ -1753,9 +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.
@@ -1763,72 +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.
@@ -1836,9 +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.
@@ -1848,9 +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.
@@ -1860,9 +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.
@@ -1870,56 +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.
@@ -1927,9 +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.
@@ -1938,9 +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.
@@ -1949,9 +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.
@@ -1959,22 +1959,22 @@ NULL
 NULL
 
 #' project.list
-#'
+#' 
 #' projects.list wrapps groups.list method by setting group_class attribute to "project".
-#'
+#' 
 #' @usage arv$projects.list(filters = NULL,
 #'     where = NULL, order = NULL, distinct = NULL,
 #'     limit = "100", offset = "0", count = "exact",
 #'     include_trash = NULL, uuid = NULL, recursive = NULL)
-#' @param filters
-#' @param where
-#' @param order
-#' @param distinct
-#' @param limit
-#' @param offset
-#' @param count
+#' @param filters 
+#' @param where 
+#' @param order 
+#' @param distinct 
+#' @param limit 
+#' @param offset 
+#' @param count 
 #' @param include_trash Include items whose is_trashed attribute is true.
-#' @param uuid
+#' @param uuid 
 #' @param recursive Include contents from child groups recursively.
 #' @return Group object.
 #' @name projects.list
@@ -2247,19 +2247,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("users/${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
                },
 
@@ -2267,23 +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
                },
 
@@ -2291,23 +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
                },
 
@@ -2315,19 +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
                },
 
@@ -2335,19 +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
                },
 
@@ -2355,19 +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
                },
 
@@ -2375,19 +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
                },
 
@@ -2396,21 +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
                },
 
@@ -2418,19 +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
                },
 
@@ -2438,19 +2438,19 @@ 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
                },
 
@@ -2459,20 +2459,20 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("users/merge")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(new_owner_uuid = new_owner_uuid,
                                                          new_user_token = new_user_token, redirect_to_new_user = redirect_to_new_user)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -2482,21 +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
                },
 
@@ -2504,19 +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
                },
 
@@ -2525,23 +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
                },
 
@@ -2549,23 +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
                },
 
@@ -2573,19 +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
                },
 
@@ -2593,20 +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
                },
 
@@ -2614,19 +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
                },
 
@@ -2637,21 +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
                },
 
@@ -2659,19 +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
                },
 
@@ -2679,23 +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
                },
 
@@ -2703,23 +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
                },
 
@@ -2727,19 +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
                },
 
@@ -2747,19 +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
                },
 
@@ -2767,19 +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
                },
 
@@ -2787,19 +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
                },
 
@@ -2807,19 +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
                },
 
@@ -2827,19 +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
                },
 
@@ -2850,21 +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
                },
 
@@ -2872,19 +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
                },
 
@@ -2892,23 +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
                },
 
@@ -2916,23 +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
                },
 
@@ -2940,19 +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
                },
 
@@ -2963,21 +2963,21 @@ 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
                },
 
@@ -2985,19 +2985,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -3006,23 +3006,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("container_requests")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(containerrequest) > 0)
-                               body <- jsonlite::toJSON(list(containerrequest = containerrequest),
+                               body <- jsonlite::toJSON(list(containerrequest = containerrequest), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -3030,23 +3030,23 @@ Arvados <- R6::R6Class(
                {
                        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(containerrequest) > 0)
-                               body <- jsonlite::toJSON(list(containerrequest = containerrequest),
+                               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
                },
 
@@ -3054,19 +3054,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -3077,21 +3077,21 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -3099,19 +3099,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -3120,23 +3120,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("authorized_keys")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(authorizedkey) > 0)
-                               body <- jsonlite::toJSON(list(authorizedkey = authorizedkey),
+                               body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -3144,23 +3144,23 @@ Arvados <- R6::R6Class(
                {
                        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(authorizedkey) > 0)
-                               body <- jsonlite::toJSON(list(authorizedkey = authorizedkey),
+                               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
                },
 
@@ -3168,19 +3168,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -3191,21 +3191,21 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -3213,19 +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
                },
 
@@ -3233,23 +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
                },
 
@@ -3257,23 +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
                },
 
@@ -3281,19 +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
                },
 
@@ -3301,19 +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
                },
 
@@ -3321,19 +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
                },
 
@@ -3341,19 +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
                },
 
@@ -3361,19 +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
                },
 
@@ -3384,22 +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
                },
 
@@ -3407,19 +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
                },
 
@@ -3427,23 +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
                },
 
@@ -3451,23 +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
                },
 
@@ -3475,19 +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
                },
 
@@ -3497,21 +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
                },
 
@@ -3519,19 +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
                },
 
@@ -3539,23 +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
                },
 
@@ -3563,23 +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
                },
 
@@ -3587,19 +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
                },
 
@@ -3610,21 +3610,21 @@ 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
                },
 
@@ -3632,19 +3632,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -3654,26 +3654,26 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("jobs")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name,
                                                          find_or_create = find_or_create, filters = filters,
                                                          minimum_script_version = minimum_script_version,
                                                          exclude_script_versions = exclude_script_versions)
-
+                       
                        if(length(job) > 0)
-                               body <- jsonlite::toJSON(list(job = job),
+                               body <- jsonlite::toJSON(list(job = job), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -3681,23 +3681,23 @@ Arvados <- R6::R6Class(
                {
                        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(job) > 0)
-                               body <- jsonlite::toJSON(list(job = job),
+                               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
                },
 
@@ -3705,19 +3705,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -3727,21 +3727,21 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -3749,19 +3749,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -3769,19 +3769,19 @@ Arvados <- R6::R6Class(
                {
                        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$exec("POST", url, headers, body,
                                                           queryArgs, private$numRetries)
                        resource <- private$REST$httpParser$parseJSONResponse(response)
-
+                       
                        if(!is.null(resource$errors))
                                stop(resource$errors)
-
+                       
                        resource
                },
 
@@ -3789,19 +3789,19 @@ Arvados <- R6::R6Class(
                {
                        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 <- 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
                },
 
@@ -3811,21 +3811,21 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("jobs")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -3833,19 +3833,19 @@ Arvados <- R6::R6Class(
                {
                        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$exec("GET", url, headers, body,
                                                           queryArgs, private$numRetries)
                        resource <- private$REST$httpParser$parseJSONResponse(response)
-
+                       
                        if(!is.null(resource$errors))
                                stop(resource$errors)
-
+                       
                        resource
                },
 
@@ -3853,23 +3853,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("keep_disks")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(keepdisk) > 0)
-                               body <- jsonlite::toJSON(list(keepdisk = keepdisk),
+                               body <- jsonlite::toJSON(list(keepdisk = keepdisk), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -3877,23 +3877,23 @@ Arvados <- R6::R6Class(
                {
                        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
-
+                       
                        if(length(keepdisk) > 0)
-                               body <- jsonlite::toJSON(list(keepdisk = keepdisk),
+                               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
                },
 
@@ -3901,19 +3901,19 @@ Arvados <- R6::R6Class(
                {
                        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$exec("DELETE", url, headers, body,
                                                           queryArgs, private$numRetries)
                        resource <- private$REST$httpParser$parseJSONResponse(response)
-
+                       
                        if(!is.null(resource$errors))
                                stop(resource$errors)
-
+                       
                        resource
                },
 
@@ -3923,22 +3923,22 @@ Arvados <- R6::R6Class(
                {
                        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$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(uuid = uuid, ping_secret = ping_secret,
                                                          node_uuid = node_uuid, filesystem_uuid = filesystem_uuid,
                                                          service_host = service_host, service_port = service_port,
                                                          service_ssl_flag = service_ssl_flag)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -3949,21 +3949,21 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -3971,19 +3971,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -3992,24 +3992,24 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("nodes")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name,
                                                          assign_slot = assign_slot)
-
+                       
                        if(length(node) > 0)
-                               body <- jsonlite::toJSON(list(node = node),
+                               body <- jsonlite::toJSON(list(node = node), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -4017,23 +4017,23 @@ Arvados <- R6::R6Class(
                {
                        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 <- list(assign_slot = assign_slot)
-
+                       
                        if(length(node) > 0)
-                               body <- jsonlite::toJSON(list(node = node),
+                               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
                },
 
@@ -4041,19 +4041,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -4061,19 +4061,19 @@ Arvados <- R6::R6Class(
                {
                        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(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
                },
 
@@ -4083,21 +4083,21 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -4105,19 +4105,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -4125,23 +4125,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("links")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(link) > 0)
-                               body <- jsonlite::toJSON(list(link = link),
+                               body <- jsonlite::toJSON(list(link = link), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -4149,23 +4149,23 @@ Arvados <- R6::R6Class(
                {
                        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(link) > 0)
-                               body <- jsonlite::toJSON(list(link = link),
+                               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
                },
 
@@ -4173,19 +4173,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -4195,21 +4195,21 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("links")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
                                                          limit = limit, offset = offset, count = count)
-
+                       
                        body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -4217,19 +4217,19 @@ Arvados <- R6::R6Class(
                {
                        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 <- 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
                },
 
@@ -4237,19 +4237,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -4258,23 +4258,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("keep_services")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(keepservice) > 0)
-                               body <- jsonlite::toJSON(list(keepservice = keepservice),
+                               body <- jsonlite::toJSON(list(keepservice = keepservice), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -4282,23 +4282,23 @@ Arvados <- R6::R6Class(
                {
                        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(keepservice) > 0)
-                               body <- jsonlite::toJSON(list(keepservice = keepservice),
+                               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
                },
 
@@ -4306,19 +4306,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -4326,19 +4326,19 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("keep_services/accessible")
                        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
                },
 
@@ -4349,21 +4349,21 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -4371,19 +4371,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -4392,23 +4392,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("pipeline_templates")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(pipelinetemplate) > 0)
-                               body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate),
+                               body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -4416,23 +4416,23 @@ Arvados <- R6::R6Class(
                {
                        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(pipelinetemplate) > 0)
-                               body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate),
+                               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
                },
 
@@ -4440,19 +4440,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -4463,21 +4463,21 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -4485,19 +4485,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -4506,23 +4506,23 @@ Arvados <- R6::R6Class(
                {
                        endPoint <- stringr::str_interp("pipeline_instances")
                        url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token),
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
-
+                       
                        if(length(pipelineinstance) > 0)
-                               body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance),
+                               body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
-
+                       
                        response <- private$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
                },
 
@@ -4530,23 +4530,23 @@ Arvados <- R6::R6Class(
                {
                        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
-
+                       
                        if(length(pipelineinstance) > 0)
-                               body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance),
+                               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
                },
 
@@ -4554,19 +4554,19 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -4574,19 +4574,19 @@ Arvados <- R6::R6Class(
                {
                        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 <- 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
                },
 
@@ -4597,21 +4597,21 @@ Arvados <- R6::R6Class(
                {
                        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
                },
 
@@ -4619,19 +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
                },
 
@@ -4639,23 +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
                },
 
@@ -4663,23 +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
                },
 
@@ -4687,19 +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
                },
 
@@ -4707,19 +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
                },
 
@@ -4730,21 +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
                },
 
@@ -4752,19 +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
                },
 
@@ -4772,23 +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
                },
 
@@ -4796,23 +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
                },
 
@@ -4820,19 +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
                },
 
@@ -4843,21 +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
                },
 
@@ -4865,19 +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
                },
 
@@ -4885,23 +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
                },
 
@@ -4909,23 +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
                },
 
@@ -4933,19 +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
                },
 
@@ -4955,21 +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
                },
 
@@ -4977,19 +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
                },
 
@@ -4997,23 +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
                },
 
@@ -5021,23 +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
                },
 
@@ -5045,19 +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
                },
 
@@ -5067,21 +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
                },
 
@@ -5089,19 +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
                },
 
@@ -5110,23 +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
                },
 
@@ -5134,23 +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
                },
 
@@ -5158,19 +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
                },
 
@@ -5178,19 +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
                },
 
@@ -5198,19 +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
                },
 
@@ -5221,21 +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
                },
 
@@ -5243,19 +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
                },
 
@@ -5263,23 +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
                },
 
@@ -5287,23 +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
                },
 
@@ -5311,19 +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
                },
 
@@ -5334,21 +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
                },
 
@@ -5356,19 +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
                },
 
@@ -5376,23 +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
                },
 
@@ -5400,23 +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
                },
 
@@ -5424,19 +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
                },
 
@@ -5447,22 +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
                },
 
@@ -5470,19 +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
                },
 
@@ -5490,19 +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
                },
 
@@ -5513,22 +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
                },
 
@@ -5536,19 +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
                },
 
@@ -5557,23 +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
                },
 
@@ -5581,23 +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
                },
 
@@ -5605,19 +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
                },
 
@@ -5625,19 +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
                },
 
@@ -5645,19 +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
                },
 
@@ -5668,21 +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
                },
 
@@ -5690,19 +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 2257d99bfe9a8ed9d42d18a026fe6974eb20a76c..70bb4450eccca6efd453002dc7a0962c904fb0d0 100644 (file)
@@ -258,18 +258,23 @@ ArvadosFile <- R6::R6Class(
 
         attachToNewParent = function(content, newParent)
         {
-            #Note: We temporary set parents collection to NULL. This will ensure that
-            #      add method doesn't post this 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(content)
+            content$setCollection(parentsCollection, setRecursively = FALSE)
             newParent$setCollection(parentsCollection, setRecursively = FALSE)
         },
 
         dettachFromCurrentParent = function()
         {
-            #Note: We temporary set parents collection to NULL. This will ensure that
-            #      remove method doesn't remove this file 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$setCollection(NULL, setRecursively = FALSE)
index f88eb0e7cdfd36a097cf79494a4d298b5d199d35..8869d7be67846b449200fe2c675936dd1c4133db 100644 (file)
@@ -23,9 +23,10 @@ source("./R/util.R")
 #' @section Methods:
 #' \describe{
 #'   \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.}
-#'   \item{create(fileNames, relativePath = "")}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
+#'   \item{create(files)}{Creates one or more ArvadosFiles and adds them to the collection at specified path.}
 #'   \item{remove(fileNames)}{Remove one or more files from the collection.}
-#'   \item{move(content, newLocation)}{Moves ArvadosFile or Subcollection to another location in the collection.}
+#'   \item{move(content, destination)}{Moves ArvadosFile or Subcollection to another location in the collection.}
+#'   \item{copy(content, destination)}{Copies ArvadosFile or Subcollection to another location in the collection.}
 #'   \item{getFileListing()}{Returns collections file content as character vector.}
 #'   \item{get(relativePath)}{If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.}
 #' }
@@ -36,9 +37,6 @@ source("./R/util.R")
 #' arv <- Arvados$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$remove("location/to/my/file.cpp")
@@ -88,6 +86,9 @@ Collection <- R6::R6Class(
             if("ArvadosFile"   %in% class(content) ||
                "Subcollection" %in% class(content))
             {
+                if(!is.null(content$getCollection()))
+                    stop("Content already belongs to a collection.")
+
                 if(content$getName() == "")
                     stop("Content has invalid name.")
 
@@ -102,50 +103,32 @@ Collection <- R6::R6Class(
             }
         },
 
-        create = function(fileNames, relativePath = "")
+        create = function(files)
         {
             if(is.null(private$tree))
                 private$generateCollectionTreeStructure()
 
-            if(relativePath == ""  ||
-               relativePath == "." ||
-               relativePath == "./")
-            {
-                subcollection <- private$tree$getTree()
-            }
-            else
-            {
-                relativePath  <- trimFromEnd(relativePath, "/")
-                subcollection <- self$get(relativePath)
-            }
-
-            if(is.null(subcollection))
-                stop(paste("Subcollection", relativePath, "doesn't exist."))
-
-            if(is.character(fileNames))
+            if(is.character(files))
             {
-                arvadosFiles <- NULL
-                sapply(fileNames, function(fileName)
+                sapply(files, function(file)
                 {
-                    childWithSameName <- subcollection$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 = ", "), ")"),
                             "."))
             }
         },
@@ -215,8 +198,11 @@ Collection <- R6::R6Class(
 
         refresh = function()
         {
-            private$tree$getTree()$setCollection(NULL, setRecursively = TRUE)
-            private$tree <- NULL
+            if(!is.null(private$tree))
+            {
+                private$tree$getTree()$setCollection(NULL, setRecursively = TRUE)
+                private$tree <- NULL
+            }
         },
 
         getFileListing = function()
index 2d4af094aa1c96b98b585cba059085c95b537f8c..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$getName())
@@ -121,24 +113,3 @@ CollectionTree <- R6::R6Class(
         }
     )
 )
-
-# deepCopyArvadosComposite = function(composite) 
-# {
-    # if("ArvadosFile" %in% class(content))
-    # {
-        # newFile <- ArvadosFile$new(content$name)
-        # newFile$setCollection(content$getCollection())
-
-        # return(newFile)
-    # }
-    # else if("Subcollection" %in% class(content))
-    # {
-        # root <- Subcollection$new(content$name)
-        # root$setCollection(content$getCollection())
-    # }
-    # else
-        # stop("Arvados composite is corrupted. It can contain only ArvadosFile or Subcollection.")
-    
-    
-
-# }
index 5fd21c192ac9928fce674d1ba3c17bbe258e9513..17a9ef3ee3ba6180546763da637a8824905d66dc 100644 (file)
@@ -79,6 +79,9 @@ Subcollection <- R6::R6Class(
             if("ArvadosFile"   %in% class(content) ||
                "Subcollection" %in% class(content))
             {
+                if(!is.null(content$getCollection()))
+                    stop("Content already belongs to a collection.")
+
                 if(content$getName() == "")
                     stop("Content has invalid name.")
 
@@ -298,18 +301,23 @@ Subcollection <- R6::R6Class(
 
         attachToNewParent = function(content, newParent)
         {
-            #Note: We temporary set parents collection to NULL. This will ensure that
-            #      add method doesn't post this 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(content)
+            content$setCollection(parentsCollection, setRecursively = FALSE)
             newParent$setCollection(parentsCollection, setRecursively = FALSE)
         },
 
         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$setCollection(NULL, setRecursively = FALSE)
index c98f803e5ea8e123b4e058b8256850668b5ae068..fa0cda45bfc65dfefb2c681eabee5c3668e822d9 100644 (file)
@@ -1,3 +1,7 @@
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
 .onLoad <- function(libName, pkgName)
 {
     minAllowedRVersion <- "3.3.0"
index 001a3efc13b8cf9afcd01ffb6e28fa4b5e19d1ce..7ea226fd0931d61a2c8c2e92f8d892f3406918b3 100644 (file)
@@ -186,31 +186,16 @@ size <- arvadosSubcollection$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}
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$remove("location/to/my/file.cpp")
index 5bef96f9c5e9f53d5d01d53a7a84b4a490eecd1b..3eb172aabf0741f0b81dd228dd2878cc505bc526 100644 (file)
@@ -7,6 +7,11 @@
 arv$api_client_authorizations.create_system_auth(api_client_id = NULL,
        scopes = NULL)
 }
+\arguments{
+\item{api_client_id}{}
+
+\item{scopes}{}
+}
 \value{
 ApiClientAuthorization object.
 }
index 983bf4478d18cda7dae733167997ed9eb4c50ea7..7c8ae69cd5073ab47d0a942c99381a03dcaf614c 100644 (file)
@@ -9,6 +9,23 @@ arv$api_client_authorizations.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 ApiClientAuthorizationList object.
 }
index 21523096d0a7ca6d8e31cc0578b5a2af9f4f4f5d..0679c9c12ef826e7b3628e0ed239ad007f836cc9 100644 (file)
@@ -9,6 +9,23 @@ arv$api_clients.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 ApiClientList object.
 }
index c477b54a9281e56e89ade13a654ba473b272a249..cd19bc60c011254b37077e61d5caa77641bd9020 100644 (file)
@@ -9,6 +9,23 @@ arv$authorized_keys.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 AuthorizedKeyList object.
 }
index cc5badebe40a64f187acbf240f5330591ceb2cdb..87f6f78e3393555cf236fb4f7c51a5ecc20cffa1 100644 (file)
@@ -10,6 +10,22 @@ arv$collections.list(filters = NULL,
        count = "exact", include_trash = NULL)
 }
 \arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+
 \item{include_trash}{Include collections whose is_trashed attribute is true.}
 }
 \value{
index 72b164e50ed9d54dfc9353a4dd5b8855a6443fcd..001a7b47c7e997a48d572d260bfedeefcabd542e 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$collections.provenance(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 Collection object.
 }
index f01c191db0c0ab00da92d6214e6ab985a8781e8a..4862109b9f6a7c13031893c3715639ac7e092d02 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$collections.trash(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 Collection object.
 }
index 6e63fd4f378817078585435dfedd60734172d86f..c41bc3d9046ec0383a1838b93fbdc8de44859356 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$collections.untrash(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 Collection object.
 }
index 0ea0dc3240036407ffc3bc40eb3f75d8261250ce..53b8e493f7218534638b09a7bcbf870d75c5e44e 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$collections.used_by(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 Collection object.
 }
index b0ce4de0d961cc2da262f42d3c1c89b09462abec..9c2412beedcf62c3c4f4304896967bce9d4f7008 100644 (file)
@@ -9,6 +9,23 @@ arv$container_requests.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 ContainerRequestList object.
 }
index 2aa51caccef8c17c5a3f3458852057431bf3a2e3..a594d2f19606843577647a66755260b283fa518c 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$containers.auth(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 Container object.
 }
index 7b3d2fccc5cf2cef47238b6a667058da59ee4495..d4457961352f0f14abb6d38266fd2f6683a35295 100644 (file)
@@ -9,6 +9,23 @@ arv$containers.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 ContainerList object.
 }
index b8d7c08650f0d759bf209a56885ee75e5be43ff6..72bcdf0f81f4b14a5433688f54c1042095da145a 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$containers.lock(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 Container object.
 }
index 2cccba3aaa463cedc394ff126d08529f939662ec..d0f8444fa4db39f89b7bbf57bb338e2e81048660 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$containers.secret_mounts(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 Container object.
 }
index 2bba7ee5a92218ab4e4f75c0dad0415d431e013c..5c41f2059a9ba5ec033fbb4fd6d27dbe7a8318f9 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$containers.unlock(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 Container object.
 }
index 1273f445d50837895e3febcb7d498b2b56442c47..26647df4f7f85e0315b4ee1f58e5fa7194e4d9b9 100644 (file)
@@ -10,8 +10,24 @@ arv$groups.contents(filters = NULL,
        include_trash = NULL, uuid = NULL, recursive = NULL)
 }
 \arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+
 \item{include_trash}{Include items whose is_trashed attribute is true.}
 
+\item{uuid}{}
+
 \item{recursive}{Include contents from child groups recursively.}
 }
 \value{
index c76a27ad9e74288a2105dc4b93aec2eec000626b..7699f3ef4bacdcd00df214dfe9909ddc43089c66 100644 (file)
@@ -10,6 +10,22 @@ arv$groups.list(filters = NULL,
        count = "exact", include_trash = NULL)
 }
 \arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+
 \item{include_trash}{Include items whose is_trashed attribute is true.}
 }
 \value{
index ecd2b10c86c8c01b554f46ca9f170097c6b5e881..c529618f71d9e585159149dd8b623a03e85116d3 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$groups.trash(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 Group object.
 }
index ef1f19a1067ae774b77d19c66ecbc1906ce2b8e5..014190c8feacdfce7666bb94f7ebef03e9a7da86 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$groups.untrash(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 Group object.
 }
index c9fad5fd324538e85ed0d82e3e8052f8247b792c..a8db4c7f69696c0eb015676161ea5f198be036a7 100644 (file)
@@ -9,6 +9,23 @@ arv$humans.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 HumanList object.
 }
index 2184d9655ee8a5051f7b9fffd98e1c79baf3c0cf..51c4b4942c8dd29ad44105fe626cd9dfdf251d2b 100644 (file)
@@ -9,6 +9,23 @@ arv$job_tasks.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 JobTaskList object.
 }
index 16cda4aa6ad0cffb1002d8549724c027cdaf2f6d..7399d28a8de8b648232e4d167d135af410b6152f 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$jobs.cancel(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 Job object.
 }
index d8e52d4f940423b6180456458e02518b59687142..4c4d61ae765bd2dc69a393fa6c1ca0117b42bd4c 100644 (file)
@@ -12,6 +12,14 @@ arv$jobs.create(job, ensure_unique_name = "false",
 \item{job}{Job object.}
 
 \item{ensure_unique_name}{Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.}
+
+\item{find_or_create}{}
+
+\item{filters}{}
+
+\item{minimum_script_version}{}
+
+\item{exclude_script_versions}{}
 }
 \value{
 Job object.
index 33840b0a498df7211a3ff93f6524c51d3b0d0ae0..53055f5878b4fb73a0bcb598f645872b7dd4f84d 100644 (file)
@@ -8,6 +8,23 @@ arv$jobs.list(filters = NULL, where = NULL,
        order = NULL, select = NULL, distinct = NULL,
        limit = "100", offset = "0", count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 JobList object.
 }
index 51500fc44d90f724d30ae28685b22f1655df0f4b..3c2e2328096d8ca74cbf62940d1774a4fb898fb6 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$jobs.lock(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 Job object.
 }
index e92d01063f6a9a4394cad7abf83e5e8e541c8e8f..a9deaa971cb989e6f35df00bc8564b39ef4a28c6 100644 (file)
@@ -9,6 +9,23 @@ arv$jobs.queue(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 Job object.
 }
index 79d7b0a636efc89cd9de1f3c719eef89d2c6015c..fdb599f70fed149c16a42e24ec62e72a6e1589eb 100644 (file)
@@ -9,6 +9,23 @@ arv$keep_disks.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 KeepDiskList object.
 }
index 2952c31e129fab1d6dec4f96b5d8441d8b76f45e..6ae55955f6c8b57a08a12ede405a76bc78f3a335 100644 (file)
@@ -8,6 +8,21 @@ arv$keep_disks.ping(uuid = NULL,
        ping_secret, node_uuid = NULL, filesystem_uuid = NULL,
        service_host = NULL, service_port, service_ssl_flag)
 }
+\arguments{
+\item{uuid}{}
+
+\item{ping_secret}{}
+
+\item{node_uuid}{}
+
+\item{filesystem_uuid}{}
+
+\item{service_host}{}
+
+\item{service_port}{}
+
+\item{service_ssl_flag}{}
+}
 \value{
 KeepDisk object.
 }
index 73f5fb854af5a0527f9d8152ea0913e44f1646e6..22aa3aa1073b691c382a43459e9fd7e491725bfa 100644 (file)
@@ -9,6 +9,23 @@ arv$keep_services.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 KeepServiceList object.
 }
index 457c38e149898ddc9415530b1c912ad3320c278e..982dbb9691cad266f8eba807475d2e35cd49b280 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$links.get_permissions(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 Link object.
 }
index a3fc988a3809b188c464578fb7812937d8860dba..540fdc1683454df4582daff74b39b98aaf69599f 100644 (file)
@@ -9,6 +9,23 @@ arv$links.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 LinkList object.
 }
index 88c8bbdc7c54d3e117d59b81c667da01d131b4db..58dbdb71ea02c4d9703a504e09acd04d7fdca86e 100644 (file)
@@ -8,6 +8,23 @@ arv$logs.list(filters = NULL, where = NULL,
        order = NULL, select = NULL, distinct = NULL,
        limit = "100", offset = "0", count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 LogList object.
 }
index 6074a38a65f8058d02f9f4d1137c3c8735f74ae6..7ccfad6d934f4b03cd3cf467b6a30189681fad90 100644 (file)
@@ -9,6 +9,23 @@ arv$nodes.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 NodeList object.
 }
index b8775a2e0d1722131fa94e51d98fb395f0d00217..e77d2b5b89b4e11237f5efab680c050a088fb996 100644 (file)
@@ -6,6 +6,11 @@
 \usage{
 arv$nodes.ping(uuid, ping_secret)
 }
+\arguments{
+\item{uuid}{}
+
+\item{ping_secret}{}
+}
 \value{
 Node object.
 }
index 6de31340549b23b6a7914e16daec02e784277d4f..026de816fbc9cebc347427ba33575045a5d71a67 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$pipeline_instances.cancel(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 PipelineInstance object.
 }
index 74b5db2bb9f7e4cad6448a926d953877c2151d65..407f94446d2bac06dd915b52b0797551c495b8d5 100644 (file)
@@ -9,6 +9,23 @@ arv$pipeline_instances.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 PipelineInstanceList object.
 }
index 846008e4d164a2d190dcafe98a106c9ce3bea16f..c6c7413d5e7c407f7281d22058143224d152dcfa 100644 (file)
@@ -9,6 +9,23 @@ arv$pipeline_templates.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 PipelineTemplateList object.
 }
index 22b5175ceb4e97bbb91e01d6cba194f4d891d243..ff4c1c9edb8dcc21dc0b7b30061cd15711a2c0d3 100644 (file)
@@ -10,8 +10,24 @@ arv$projects.list(filters = NULL,
        include_trash = NULL, uuid = NULL, recursive = NULL)
 }
 \arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+
 \item{include_trash}{Include items whose is_trashed attribute is true.}
 
+\item{uuid}{}
+
 \item{recursive}{Include contents from child groups recursively.}
 }
 \value{
index e19c87c6caf707dea65766180ec2b6eb243af2c7..d1f4772e74305823a729378b7f6518da06c338f1 100644 (file)
@@ -9,6 +9,23 @@ arv$repositories.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 RepositoryList object.
 }
index c05ce5f26ceba4b3e61894d237db0f55d629ded5..4e07f4ab28214b61122881c632f93b7e05dd6188 100644 (file)
@@ -9,6 +9,23 @@ arv$specimens.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 SpecimenList object.
 }
index 77a13cae38e51b8d7e4edcaf2bf188fca85f9a00..e91b9299491b887d1833efe8d3323f219941298a 100644 (file)
@@ -9,6 +9,23 @@ arv$traits.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 TraitList object.
 }
index c9914d5f16f822557c3cab6b26353d1fda9db296..5e6986189d8c8027007f3ed007a68a430dff8c2f 100644 (file)
@@ -9,6 +9,23 @@ arv$user_agreements.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 UserAgreementList object.
 }
index bba8162322e42dfdf87832e8778d6d4ae3063da4..201caf4c89283fff9fed78537f5f1176556d178e 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$users.activate(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 User object.
 }
index 98fa2141a3a32145799084b35b1f1060ecd0d088..71319433b8e16e14fc6aa648bde5f3b9cc530933 100644 (file)
@@ -9,6 +9,23 @@ arv$users.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 UserList object.
 }
index ee97244f30b856adbe2f37bafca804cbe045ca36..a539591a6ad72e4eb5c4b98a08a6cec9ee59b095 100644 (file)
@@ -7,6 +7,13 @@
 arv$users.merge(new_owner_uuid,
        new_user_token, redirect_to_new_user = NULL)
 }
+\arguments{
+\item{new_owner_uuid}{}
+
+\item{new_user_token}{}
+
+\item{redirect_to_new_user}{}
+}
 \value{
 User object.
 }
index 764bc525969661bcea8253f5a8a5125f10fe1bd5..869403d3ed965832e2dbb3484d7412b15794ba90 100644 (file)
@@ -7,6 +7,17 @@
 arv$users.setup(user = NULL, openid_prefix = NULL,
        repo_name = NULL, vm_uuid = NULL, send_notification_email = "false")
 }
+\arguments{
+\item{user}{}
+
+\item{openid_prefix}{}
+
+\item{repo_name}{}
+
+\item{vm_uuid}{}
+
+\item{send_notification_email}{}
+}
 \value{
 User object.
 }
index 0753a34d2330c9c1316387ccba706c29a2d093ed..85de6f9782d0852eed394e8e2be92df2239199cd 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$users.unsetup(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 User object.
 }
index 591599dfe8f5ae7300213819bbd018ce35e0d71f..af62c2c825d3da2efa26a555d78d7fc480e30d9e 100644 (file)
@@ -6,6 +6,11 @@
 \usage{
 arv$users.update_uuid(uuid, new_uuid)
 }
+\arguments{
+\item{uuid}{}
+
+\item{new_uuid}{}
+}
 \value{
 User object.
 }
index 0f3b440b821d7109c208f51b97465cdbb2592b23..42ed58b0e1e09264896e764d2073e8524c992560 100644 (file)
@@ -9,6 +9,23 @@ arv$virtual_machines.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 VirtualMachineList object.
 }
index bb6d21ed914c150d33f96e5e241410f67083a298..7e25110aa4dc1bcb336c7b0aa78c339b9c21cad1 100644 (file)
@@ -6,6 +6,9 @@
 \usage{
 arv$virtual_machines.logins(uuid)
 }
+\arguments{
+\item{uuid}{}
+}
 \value{
 VirtualMachine object.
 }
index b8a6a03ec7799912a3cf148c8bd31c1e09c0626c..e24b74d0307e146a72d696479a08e693235acc97 100644 (file)
@@ -9,6 +9,23 @@ arv$workflows.list(filters = NULL,
        distinct = NULL, limit = "100", offset = "0",
        count = "exact")
 }
+\arguments{
+\item{filters}{}
+
+\item{where}{}
+
+\item{order}{}
+
+\item{select}{}
+
+\item{distinct}{}
+
+\item{limit}{}
+
+\item{offset}{}
+
+\item{count}{}
+}
 \value{
 WorkflowList object.
 }
index 76668c2eb05eaef2c8e2f977e1d62bc858a7bbf3..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")
@@ -296,3 +274,24 @@ test_that("copy raises exception if new location is not valid", {
                 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()))
+})