[arvados] created: 2.6.0-301-g0c90bc265
git repository hosting
git at public.arvados.org
Wed Jun 21 20:39:30 UTC 2023
at 0c90bc2654862c7ba079fb552b303aaf26de1403 (commit)
commit 0c90bc2654862c7ba079fb552b303aaf26de1403
Author: Peter Amstutz <peter.amstutz at curii.com>
Date: Wed Jun 21 16:34:26 2023 -0400
20660: Add devtools::check to run_test.R
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>
diff --git a/sdk/R/DESCRIPTION b/sdk/R/DESCRIPTION
index b20675d66..c6c01adeb 100644
--- a/sdk/R/DESCRIPTION
+++ b/sdk/R/DESCRIPTION
@@ -11,7 +11,7 @@ URL: http://doc.arvados.org
License: Apache-2.0
Encoding: UTF-8
LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
Imports:
R6,
httr,
diff --git a/sdk/R/man/Arvados.Rd b/sdk/R/man/Arvados.Rd
index d028d0a07..924bfeae9 100644
--- a/sdk/R/man/Arvados.Rd
+++ b/sdk/R/man/Arvados.Rd
@@ -18,260 +18,316 @@ arv <- Arvados$new(authToken = "ARVADOS_API_TOKEN", hostName = "ARVADOS_API_HOST
## Method `Arvados$project_exist`
## ------------------------------------------------
-arv$project_exist(uuid = projectUUID)
+\dontrun{
+arv$project_exist(uuid = "projectUUID")
+}
## ------------------------------------------------
## Method `Arvados$project_get`
## ------------------------------------------------
-project <- arv$project_get(uuid = projectUUID)
+\dontrun{
+project <- arv$project_get(uuid = 'projectUUID')
+}
## ------------------------------------------------
## Method `Arvados$project_create`
## ------------------------------------------------
+\dontrun{
Properties <- list() # should contain a list of new properties to be added
new_project <- arv$project_create(name = "project name", description = "project description", owner_uuid = "project UUID", properties = NULL, ensureUniqueName = "false")
+}
## ------------------------------------------------
## Method `Arvados$project_properties_set`
## ------------------------------------------------
+\dontrun{
Properties <- list() # should contain a list of new properties to be added
arv$project_properties_set(Properties, uuid)
+}
## ------------------------------------------------
## Method `Arvados$project_properties_append`
## ------------------------------------------------
+\dontrun{
newProperties <- list() # should contain a list of new properties to be added
arv$project_properties_append(properties = newProperties, uuid)
+}
## ------------------------------------------------
## Method `Arvados$project_properties_get`
## ------------------------------------------------
+\dontrun{
arv$project_properties_get(projectUUID)
+}
## ------------------------------------------------
## Method `Arvados$project_properties_delete`
## ------------------------------------------------
+\dontrun{
Properties <- list() # should contain a list of new properties to be added
arv$project_properties_delete(Properties, projectUUID)
+}
## ------------------------------------------------
## Method `Arvados$project_update`
## ------------------------------------------------
+\dontrun{
newProperties <- list() # should contain a list of new properties to be added
arv$project_update(name = "new project name", properties = newProperties, uuid = projectUUID)
+}
## ------------------------------------------------
## Method `Arvados$project_list`
## ------------------------------------------------
+\dontrun{
listOfprojects <- arv$project_list(list(list("owner_uuid", "=", projectUUID))) # Sample query which show projects within the project of a given UUID
+}
+
+## ------------------------------------------------
+## Method `Arvados$project_delete`
+## ------------------------------------------------
+
+\dontrun{
+arv$project_delete(uuid = 'projectUUID')
+}
+
+## ------------------------------------------------
+## Method `Arvados$collections_get`
+## ------------------------------------------------
+
+\dontrun{
+collection <- arv$collections_get(uuid = collectionUUID)
+}
## ------------------------------------------------
## Method `Arvados$collections_create`
## ------------------------------------------------
+\dontrun{
Properties <- list() # should contain a list of new properties to be added
arv$collections_create(name = "collectionTitle", description = "collectionDescription", ownerUUID = "collectionOwner", properties = Properties)
+}
## ------------------------------------------------
## Method `Arvados$collections_update`
## ------------------------------------------------
-collection <- arv$collections_create(name = "newCollectionTitle", description = "newCollectionDescription", ownerUUID = "collectionOwner", properties = NULL)
+\dontrun{
+collection <- arv$collections_update(name = "newCollectionTitle", description = "newCollectionDescription", ownerUUID = "collectionOwner", properties = NULL, uuid = "collectionUUID")
+}
## ------------------------------------------------
## Method `Arvados$collections_delete`
## ------------------------------------------------
+\dontrun{
arv$collection_delete(collectionUUID)
+}
## ------------------------------------------------
## Method `Arvados$collections_provenance`
## ------------------------------------------------
+\dontrun{
collection <- arv$collections_provenance(collectionUUID)
+}
## ------------------------------------------------
## Method `Arvados$collections_trash`
## ------------------------------------------------
+\dontrun{
arv$collections_trash(collectionUUID)
+}
## ------------------------------------------------
## Method `Arvados$collections_untrash`
## ------------------------------------------------
+\dontrun{
arv$collections_untrash(collectionUUID)
+}
## ------------------------------------------------
## Method `Arvados$collections_list`
## ------------------------------------------------
-collectionList <- arv$collections.list(list(list("name", "=", "Example")))
+\dontrun{
+collectionList <- arv$collections_list(list(list("name", "=", "Example")))
+}
## ------------------------------------------------
## Method `Arvados$project_permission_give`
## ------------------------------------------------
+\dontrun{
arv$project_permission_give(type = "can_read", uuid = objectUUID, user = userUUID)
+}
## ------------------------------------------------
## Method `Arvados$project_permission_refuse`
## ------------------------------------------------
+\dontrun{
arv$project_permission_refuse(type = "can_read", uuid = objectUUID, user = userUUID)
+}
## ------------------------------------------------
## Method `Arvados$project_permission_update`
## ------------------------------------------------
+\dontrun{
arv$project_permission_update(typeOld = "can_read", typeNew = "can_write", uuid = objectUUID, user = userUUID)
+}
## ------------------------------------------------
## Method `Arvados$project_permission_check`
## ------------------------------------------------
+\dontrun{
arv$project_permission_check(type = "can_read", uuid = objectUUID, user = userUUID)
}
+}
\section{Methods}{
\subsection{Public methods}{
\itemize{
-\item \href{#method-new}{\code{Arvados$new()}}
-\item \href{#method-project_exist}{\code{Arvados$project_exist()}}
-\item \href{#method-project_get}{\code{Arvados$project_get()}}
-\item \href{#method-project_create}{\code{Arvados$project_create()}}
-\item \href{#method-project_properties_set}{\code{Arvados$project_properties_set()}}
-\item \href{#method-project_properties_append}{\code{Arvados$project_properties_append()}}
-\item \href{#method-project_properties_get}{\code{Arvados$project_properties_get()}}
-\item \href{#method-project_properties_delete}{\code{Arvados$project_properties_delete()}}
-\item \href{#method-project_update}{\code{Arvados$project_update()}}
-\item \href{#method-project_list}{\code{Arvados$project_list()}}
-\item \href{#method-project_delete}{\code{Arvados$project_delete()}}
-\item \href{#method-api_clients_get}{\code{Arvados$api_clients_get()}}
-\item \href{#method-api_clients_create}{\code{Arvados$api_clients_create()}}
-\item \href{#method-api_clients_update}{\code{Arvados$api_clients_update()}}
-\item \href{#method-api_clients_delete}{\code{Arvados$api_clients_delete()}}
-\item \href{#method-api_clients_list}{\code{Arvados$api_clients_list()}}
-\item \href{#method-api_client_authorizations_get}{\code{Arvados$api_client_authorizations_get()}}
-\item \href{#method-api_client_authorizations_create}{\code{Arvados$api_client_authorizations_create()}}
-\item \href{#method-api_client_authorizations_update}{\code{Arvados$api_client_authorizations_update()}}
-\item \href{#method-api_client_authorizations_delete}{\code{Arvados$api_client_authorizations_delete()}}
-\item \href{#method-api_client_authorizations_create_system_auth}{\code{Arvados$api_client_authorizations_create_system_auth()}}
-\item \href{#method-api_client_authorizations_current}{\code{Arvados$api_client_authorizations_current()}}
-\item \href{#method-api_client_authorizations_list}{\code{Arvados$api_client_authorizations_list()}}
-\item \href{#method-authorized_keys_get}{\code{Arvados$authorized_keys_get()}}
-\item \href{#method-authorized_keys_create}{\code{Arvados$authorized_keys_create()}}
-\item \href{#method-authorized_keys_update}{\code{Arvados$authorized_keys_update()}}
-\item \href{#method-authorized_keys_delete}{\code{Arvados$authorized_keys_delete()}}
-\item \href{#method-authorized_keys_list}{\code{Arvados$authorized_keys_list()}}
-\item \href{#method-collections_get}{\code{Arvados$collections_get()}}
-\item \href{#method-collections_create}{\code{Arvados$collections_create()}}
-\item \href{#method-collections_update}{\code{Arvados$collections_update()}}
-\item \href{#method-collections_delete}{\code{Arvados$collections_delete()}}
-\item \href{#method-collections_provenance}{\code{Arvados$collections_provenance()}}
-\item \href{#method-collections_used_by}{\code{Arvados$collections_used_by()}}
-\item \href{#method-collections_trash}{\code{Arvados$collections_trash()}}
-\item \href{#method-collections_untrash}{\code{Arvados$collections_untrash()}}
-\item \href{#method-collections_list}{\code{Arvados$collections_list()}}
-\item \href{#method-containers_get}{\code{Arvados$containers_get()}}
-\item \href{#method-containers_create}{\code{Arvados$containers_create()}}
-\item \href{#method-containers_update}{\code{Arvados$containers_update()}}
-\item \href{#method-containers_delete}{\code{Arvados$containers_delete()}}
-\item \href{#method-containers_auth}{\code{Arvados$containers_auth()}}
-\item \href{#method-containers_lock}{\code{Arvados$containers_lock()}}
-\item \href{#method-containers_unlock}{\code{Arvados$containers_unlock()}}
-\item \href{#method-containers_secret_mounts}{\code{Arvados$containers_secret_mounts()}}
-\item \href{#method-containers_current}{\code{Arvados$containers_current()}}
-\item \href{#method-containers_list}{\code{Arvados$containers_list()}}
-\item \href{#method-container_requests_get}{\code{Arvados$container_requests_get()}}
-\item \href{#method-container_requests_create}{\code{Arvados$container_requests_create()}}
-\item \href{#method-container_requests_update}{\code{Arvados$container_requests_update()}}
-\item \href{#method-container_requests_delete}{\code{Arvados$container_requests_delete()}}
-\item \href{#method-container_requests_list}{\code{Arvados$container_requests_list()}}
-\item \href{#method-groups_get}{\code{Arvados$groups_get()}}
-\item \href{#method-groups_create}{\code{Arvados$groups_create()}}
-\item \href{#method-groups_update}{\code{Arvados$groups_update()}}
-\item \href{#method-groups_delete}{\code{Arvados$groups_delete()}}
-\item \href{#method-groups_contents}{\code{Arvados$groups_contents()}}
-\item \href{#method-groups_shared}{\code{Arvados$groups_shared()}}
-\item \href{#method-groups_trash}{\code{Arvados$groups_trash()}}
-\item \href{#method-groups_untrash}{\code{Arvados$groups_untrash()}}
-\item \href{#method-groups_list}{\code{Arvados$groups_list()}}
-\item \href{#method-keep_services_get}{\code{Arvados$keep_services_get()}}
-\item \href{#method-keep_services_create}{\code{Arvados$keep_services_create()}}
-\item \href{#method-keep_services_update}{\code{Arvados$keep_services_update()}}
-\item \href{#method-keep_services_delete}{\code{Arvados$keep_services_delete()}}
-\item \href{#method-keep_services_accessible}{\code{Arvados$keep_services_accessible()}}
-\item \href{#method-keep_services_list}{\code{Arvados$keep_services_list()}}
-\item \href{#method-project_permission_give}{\code{Arvados$project_permission_give()}}
-\item \href{#method-project_permission_refuse}{\code{Arvados$project_permission_refuse()}}
-\item \href{#method-project_permission_update}{\code{Arvados$project_permission_update()}}
-\item \href{#method-project_permission_check}{\code{Arvados$project_permission_check()}}
-\item \href{#method-links_get}{\code{Arvados$links_get()}}
-\item \href{#method-links_create}{\code{Arvados$links_create()}}
-\item \href{#method-links_update}{\code{Arvados$links_update()}}
-\item \href{#method-links_delete}{\code{Arvados$links_delete()}}
-\item \href{#method-links_list}{\code{Arvados$links_list()}}
-\item \href{#method-links_get_permissions}{\code{Arvados$links_get_permissions()}}
-\item \href{#method-logs_get}{\code{Arvados$logs_get()}}
-\item \href{#method-logs_create}{\code{Arvados$logs_create()}}
-\item \href{#method-logs_update}{\code{Arvados$logs_update()}}
-\item \href{#method-logs_delete}{\code{Arvados$logs_delete()}}
-\item \href{#method-logs_list}{\code{Arvados$logs_list()}}
-\item \href{#method-users_get}{\code{Arvados$users_get()}}
-\item \href{#method-users_create}{\code{Arvados$users_create()}}
-\item \href{#method-users_update}{\code{Arvados$users_update()}}
-\item \href{#method-users_delete}{\code{Arvados$users_delete()}}
-\item \href{#method-users_current}{\code{Arvados$users_current()}}
-\item \href{#method-users_system}{\code{Arvados$users_system()}}
-\item \href{#method-users_activate}{\code{Arvados$users_activate()}}
-\item \href{#method-users_setup}{\code{Arvados$users_setup()}}
-\item \href{#method-users_unsetup}{\code{Arvados$users_unsetup()}}
-\item \href{#method-users_merge}{\code{Arvados$users_merge()}}
-\item \href{#method-users_list}{\code{Arvados$users_list()}}
-\item \href{#method-repositories_get}{\code{Arvados$repositories_get()}}
-\item \href{#method-repositories_create}{\code{Arvados$repositories_create()}}
-\item \href{#method-repositories_update}{\code{Arvados$repositories_update()}}
-\item \href{#method-repositories_delete}{\code{Arvados$repositories_delete()}}
-\item \href{#method-repositories_get_all_permissions}{\code{Arvados$repositories_get_all_permissions()}}
-\item \href{#method-repositories_list}{\code{Arvados$repositories_list()}}
-\item \href{#method-virtual_machines_get}{\code{Arvados$virtual_machines_get()}}
-\item \href{#method-virtual_machines_create}{\code{Arvados$virtual_machines_create()}}
-\item \href{#method-virtual_machines_update}{\code{Arvados$virtual_machines_update()}}
-\item \href{#method-virtual_machines_delete}{\code{Arvados$virtual_machines_delete()}}
-\item \href{#method-virtual_machines_logins}{\code{Arvados$virtual_machines_logins()}}
-\item \href{#method-virtual_machines_get_all_logins}{\code{Arvados$virtual_machines_get_all_logins()}}
-\item \href{#method-virtual_machines_list}{\code{Arvados$virtual_machines_list()}}
-\item \href{#method-workflows_get}{\code{Arvados$workflows_get()}}
-\item \href{#method-workflows_create}{\code{Arvados$workflows_create()}}
-\item \href{#method-workflows_update}{\code{Arvados$workflows_update()}}
-\item \href{#method-workflows_delete}{\code{Arvados$workflows_delete()}}
-\item \href{#method-workflows_list}{\code{Arvados$workflows_list()}}
-\item \href{#method-user_agreements_get}{\code{Arvados$user_agreements_get()}}
-\item \href{#method-user_agreements_create}{\code{Arvados$user_agreements_create()}}
-\item \href{#method-user_agreements_update}{\code{Arvados$user_agreements_update()}}
-\item \href{#method-user_agreements_delete}{\code{Arvados$user_agreements_delete()}}
-\item \href{#method-user_agreements_signatures}{\code{Arvados$user_agreements_signatures()}}
-\item \href{#method-user_agreements_sign}{\code{Arvados$user_agreements_sign()}}
-\item \href{#method-user_agreements_list}{\code{Arvados$user_agreements_list()}}
-\item \href{#method-user_agreements_new}{\code{Arvados$user_agreements_new()}}
-\item \href{#method-configs_get}{\code{Arvados$configs_get()}}
-\item \href{#method-getHostName}{\code{Arvados$getHostName()}}
-\item \href{#method-getToken}{\code{Arvados$getToken()}}
-\item \href{#method-setRESTService}{\code{Arvados$setRESTService()}}
-\item \href{#method-getRESTService}{\code{Arvados$getRESTService()}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-new"></a>}}
-\if{latex}{\out{\hypertarget{method-new}{}}}
+\item \href{#method-Arvados-new}{\code{Arvados$new()}}
+\item \href{#method-Arvados-project_exist}{\code{Arvados$project_exist()}}
+\item \href{#method-Arvados-project_get}{\code{Arvados$project_get()}}
+\item \href{#method-Arvados-project_create}{\code{Arvados$project_create()}}
+\item \href{#method-Arvados-project_properties_set}{\code{Arvados$project_properties_set()}}
+\item \href{#method-Arvados-project_properties_append}{\code{Arvados$project_properties_append()}}
+\item \href{#method-Arvados-project_properties_get}{\code{Arvados$project_properties_get()}}
+\item \href{#method-Arvados-project_properties_delete}{\code{Arvados$project_properties_delete()}}
+\item \href{#method-Arvados-project_update}{\code{Arvados$project_update()}}
+\item \href{#method-Arvados-project_list}{\code{Arvados$project_list()}}
+\item \href{#method-Arvados-project_delete}{\code{Arvados$project_delete()}}
+\item \href{#method-Arvados-api_clients_get}{\code{Arvados$api_clients_get()}}
+\item \href{#method-Arvados-api_clients_create}{\code{Arvados$api_clients_create()}}
+\item \href{#method-Arvados-api_clients_update}{\code{Arvados$api_clients_update()}}
+\item \href{#method-Arvados-api_clients_delete}{\code{Arvados$api_clients_delete()}}
+\item \href{#method-Arvados-api_clients_list}{\code{Arvados$api_clients_list()}}
+\item \href{#method-Arvados-api_client_authorizations_get}{\code{Arvados$api_client_authorizations_get()}}
+\item \href{#method-Arvados-api_client_authorizations_create}{\code{Arvados$api_client_authorizations_create()}}
+\item \href{#method-Arvados-api_client_authorizations_update}{\code{Arvados$api_client_authorizations_update()}}
+\item \href{#method-Arvados-api_client_authorizations_delete}{\code{Arvados$api_client_authorizations_delete()}}
+\item \href{#method-Arvados-api_client_authorizations_create_system_auth}{\code{Arvados$api_client_authorizations_create_system_auth()}}
+\item \href{#method-Arvados-api_client_authorizations_current}{\code{Arvados$api_client_authorizations_current()}}
+\item \href{#method-Arvados-api_client_authorizations_list}{\code{Arvados$api_client_authorizations_list()}}
+\item \href{#method-Arvados-authorized_keys_get}{\code{Arvados$authorized_keys_get()}}
+\item \href{#method-Arvados-authorized_keys_create}{\code{Arvados$authorized_keys_create()}}
+\item \href{#method-Arvados-authorized_keys_update}{\code{Arvados$authorized_keys_update()}}
+\item \href{#method-Arvados-authorized_keys_delete}{\code{Arvados$authorized_keys_delete()}}
+\item \href{#method-Arvados-authorized_keys_list}{\code{Arvados$authorized_keys_list()}}
+\item \href{#method-Arvados-collections_get}{\code{Arvados$collections_get()}}
+\item \href{#method-Arvados-collections_create}{\code{Arvados$collections_create()}}
+\item \href{#method-Arvados-collections_update}{\code{Arvados$collections_update()}}
+\item \href{#method-Arvados-collections_delete}{\code{Arvados$collections_delete()}}
+\item \href{#method-Arvados-collections_provenance}{\code{Arvados$collections_provenance()}}
+\item \href{#method-Arvados-collections_used_by}{\code{Arvados$collections_used_by()}}
+\item \href{#method-Arvados-collections_trash}{\code{Arvados$collections_trash()}}
+\item \href{#method-Arvados-collections_untrash}{\code{Arvados$collections_untrash()}}
+\item \href{#method-Arvados-collections_list}{\code{Arvados$collections_list()}}
+\item \href{#method-Arvados-containers_get}{\code{Arvados$containers_get()}}
+\item \href{#method-Arvados-containers_create}{\code{Arvados$containers_create()}}
+\item \href{#method-Arvados-containers_update}{\code{Arvados$containers_update()}}
+\item \href{#method-Arvados-containers_delete}{\code{Arvados$containers_delete()}}
+\item \href{#method-Arvados-containers_auth}{\code{Arvados$containers_auth()}}
+\item \href{#method-Arvados-containers_lock}{\code{Arvados$containers_lock()}}
+\item \href{#method-Arvados-containers_unlock}{\code{Arvados$containers_unlock()}}
+\item \href{#method-Arvados-containers_secret_mounts}{\code{Arvados$containers_secret_mounts()}}
+\item \href{#method-Arvados-containers_current}{\code{Arvados$containers_current()}}
+\item \href{#method-Arvados-containers_list}{\code{Arvados$containers_list()}}
+\item \href{#method-Arvados-container_requests_get}{\code{Arvados$container_requests_get()}}
+\item \href{#method-Arvados-container_requests_create}{\code{Arvados$container_requests_create()}}
+\item \href{#method-Arvados-container_requests_update}{\code{Arvados$container_requests_update()}}
+\item \href{#method-Arvados-container_requests_delete}{\code{Arvados$container_requests_delete()}}
+\item \href{#method-Arvados-container_requests_list}{\code{Arvados$container_requests_list()}}
+\item \href{#method-Arvados-groups_get}{\code{Arvados$groups_get()}}
+\item \href{#method-Arvados-groups_create}{\code{Arvados$groups_create()}}
+\item \href{#method-Arvados-groups_update}{\code{Arvados$groups_update()}}
+\item \href{#method-Arvados-groups_delete}{\code{Arvados$groups_delete()}}
+\item \href{#method-Arvados-groups_contents}{\code{Arvados$groups_contents()}}
+\item \href{#method-Arvados-groups_shared}{\code{Arvados$groups_shared()}}
+\item \href{#method-Arvados-groups_trash}{\code{Arvados$groups_trash()}}
+\item \href{#method-Arvados-groups_untrash}{\code{Arvados$groups_untrash()}}
+\item \href{#method-Arvados-groups_list}{\code{Arvados$groups_list()}}
+\item \href{#method-Arvados-keep_services_get}{\code{Arvados$keep_services_get()}}
+\item \href{#method-Arvados-keep_services_create}{\code{Arvados$keep_services_create()}}
+\item \href{#method-Arvados-keep_services_update}{\code{Arvados$keep_services_update()}}
+\item \href{#method-Arvados-keep_services_delete}{\code{Arvados$keep_services_delete()}}
+\item \href{#method-Arvados-keep_services_accessible}{\code{Arvados$keep_services_accessible()}}
+\item \href{#method-Arvados-keep_services_list}{\code{Arvados$keep_services_list()}}
+\item \href{#method-Arvados-project_permission_give}{\code{Arvados$project_permission_give()}}
+\item \href{#method-Arvados-project_permission_refuse}{\code{Arvados$project_permission_refuse()}}
+\item \href{#method-Arvados-project_permission_update}{\code{Arvados$project_permission_update()}}
+\item \href{#method-Arvados-project_permission_check}{\code{Arvados$project_permission_check()}}
+\item \href{#method-Arvados-links_get}{\code{Arvados$links_get()}}
+\item \href{#method-Arvados-links_create}{\code{Arvados$links_create()}}
+\item \href{#method-Arvados-links_update}{\code{Arvados$links_update()}}
+\item \href{#method-Arvados-links_delete}{\code{Arvados$links_delete()}}
+\item \href{#method-Arvados-links_list}{\code{Arvados$links_list()}}
+\item \href{#method-Arvados-links_get_permissions}{\code{Arvados$links_get_permissions()}}
+\item \href{#method-Arvados-logs_get}{\code{Arvados$logs_get()}}
+\item \href{#method-Arvados-logs_create}{\code{Arvados$logs_create()}}
+\item \href{#method-Arvados-logs_update}{\code{Arvados$logs_update()}}
+\item \href{#method-Arvados-logs_delete}{\code{Arvados$logs_delete()}}
+\item \href{#method-Arvados-logs_list}{\code{Arvados$logs_list()}}
+\item \href{#method-Arvados-users_get}{\code{Arvados$users_get()}}
+\item \href{#method-Arvados-users_create}{\code{Arvados$users_create()}}
+\item \href{#method-Arvados-users_update}{\code{Arvados$users_update()}}
+\item \href{#method-Arvados-users_delete}{\code{Arvados$users_delete()}}
+\item \href{#method-Arvados-users_current}{\code{Arvados$users_current()}}
+\item \href{#method-Arvados-users_system}{\code{Arvados$users_system()}}
+\item \href{#method-Arvados-users_activate}{\code{Arvados$users_activate()}}
+\item \href{#method-Arvados-users_setup}{\code{Arvados$users_setup()}}
+\item \href{#method-Arvados-users_unsetup}{\code{Arvados$users_unsetup()}}
+\item \href{#method-Arvados-users_merge}{\code{Arvados$users_merge()}}
+\item \href{#method-Arvados-users_list}{\code{Arvados$users_list()}}
+\item \href{#method-Arvados-repositories_get}{\code{Arvados$repositories_get()}}
+\item \href{#method-Arvados-repositories_create}{\code{Arvados$repositories_create()}}
+\item \href{#method-Arvados-repositories_update}{\code{Arvados$repositories_update()}}
+\item \href{#method-Arvados-repositories_delete}{\code{Arvados$repositories_delete()}}
+\item \href{#method-Arvados-repositories_get_all_permissions}{\code{Arvados$repositories_get_all_permissions()}}
+\item \href{#method-Arvados-repositories_list}{\code{Arvados$repositories_list()}}
+\item \href{#method-Arvados-virtual_machines_get}{\code{Arvados$virtual_machines_get()}}
+\item \href{#method-Arvados-virtual_machines_create}{\code{Arvados$virtual_machines_create()}}
+\item \href{#method-Arvados-virtual_machines_update}{\code{Arvados$virtual_machines_update()}}
+\item \href{#method-Arvados-virtual_machines_delete}{\code{Arvados$virtual_machines_delete()}}
+\item \href{#method-Arvados-virtual_machines_logins}{\code{Arvados$virtual_machines_logins()}}
+\item \href{#method-Arvados-virtual_machines_get_all_logins}{\code{Arvados$virtual_machines_get_all_logins()}}
+\item \href{#method-Arvados-virtual_machines_list}{\code{Arvados$virtual_machines_list()}}
+\item \href{#method-Arvados-workflows_get}{\code{Arvados$workflows_get()}}
+\item \href{#method-Arvados-workflows_create}{\code{Arvados$workflows_create()}}
+\item \href{#method-Arvados-workflows_update}{\code{Arvados$workflows_update()}}
+\item \href{#method-Arvados-workflows_delete}{\code{Arvados$workflows_delete()}}
+\item \href{#method-Arvados-workflows_list}{\code{Arvados$workflows_list()}}
+\item \href{#method-Arvados-user_agreements_get}{\code{Arvados$user_agreements_get()}}
+\item \href{#method-Arvados-user_agreements_create}{\code{Arvados$user_agreements_create()}}
+\item \href{#method-Arvados-user_agreements_update}{\code{Arvados$user_agreements_update()}}
+\item \href{#method-Arvados-user_agreements_delete}{\code{Arvados$user_agreements_delete()}}
+\item \href{#method-Arvados-user_agreements_signatures}{\code{Arvados$user_agreements_signatures()}}
+\item \href{#method-Arvados-user_agreements_sign}{\code{Arvados$user_agreements_sign()}}
+\item \href{#method-Arvados-user_agreements_list}{\code{Arvados$user_agreements_list()}}
+\item \href{#method-Arvados-user_agreements_new}{\code{Arvados$user_agreements_new()}}
+\item \href{#method-Arvados-configs_get}{\code{Arvados$configs_get()}}
+\item \href{#method-Arvados-getHostName}{\code{Arvados$getHostName()}}
+\item \href{#method-Arvados-getToken}{\code{Arvados$getToken()}}
+\item \href{#method-Arvados-setRESTService}{\code{Arvados$setRESTService()}}
+\item \href{#method-Arvados-getRESTService}{\code{Arvados$getRESTService()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Arvados-new"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-new}{}}}
\subsection{Method \code{new()}}{
Initialize new enviroment.
\subsection{Usage}{
@@ -302,8 +358,8 @@ A new `Arvados` object.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-project_exist"></a>}}
-\if{latex}{\out{\hypertarget{method-project_exist}{}}}
+\if{html}{\out{<a id="method-Arvados-project_exist"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-project_exist}{}}}
\subsection{Method \code{project_exist()}}{
project_exist enables checking if the project with such a UUID exist.
\subsection{Usage}{
@@ -319,7 +375,9 @@ project_exist enables checking if the project with such a UUID exist.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arv$project_exist(uuid = projectUUID)
+\preformatted{\dontrun{
+arv$project_exist(uuid = "projectUUID")
+}
}
\if{html}{\out{</div>}}
@@ -327,8 +385,8 @@ project_exist enables checking if the project with such a UUID exist.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-project_get"></a>}}
-\if{latex}{\out{\hypertarget{method-project_get}{}}}
+\if{html}{\out{<a id="method-Arvados-project_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-project_get}{}}}
\subsection{Method \code{project_get()}}{
project_get returns the demanded project.
\subsection{Usage}{
@@ -344,7 +402,9 @@ project_get returns the demanded project.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{project <- arv$project_get(uuid = projectUUID)
+\preformatted{\dontrun{
+project <- arv$project_get(uuid = 'projectUUID')
+}
}
\if{html}{\out{</div>}}
@@ -352,8 +412,8 @@ project_get returns the demanded project.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-project_create"></a>}}
-\if{latex}{\out{\hypertarget{method-project_create}{}}}
+\if{html}{\out{<a id="method-Arvados-project_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-project_create}{}}}
\subsection{Method \code{project_create()}}{
project_create creates a new project of a given name and description.
\subsection{Usage}{
@@ -383,17 +443,19 @@ project_create creates a new project of a given name and description.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{Properties <- list() # should contain a list of new properties to be added
+\preformatted{\dontrun{
+Properties <- list() # should contain a list of new properties to be added
new_project <- arv$project_create(name = "project name", description = "project description", owner_uuid = "project UUID", properties = NULL, ensureUniqueName = "false")
}
+}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-project_properties_set"></a>}}
-\if{latex}{\out{\hypertarget{method-project_properties_set}{}}}
+\if{html}{\out{<a id="method-Arvados-project_properties_set"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-project_properties_set}{}}}
\subsection{Method \code{project_properties_set()}}{
project_properties_set is a method defined in Arvados class that enables setting properties. Allows to set or overwrite the properties. In case there are set already it overwrites them.
\subsection{Usage}{
@@ -411,17 +473,19 @@ project_properties_set is a method defined in Arvados class that enables setting
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{Properties <- list() # should contain a list of new properties to be added
+\preformatted{\dontrun{
+Properties <- list() # should contain a list of new properties to be added
arv$project_properties_set(Properties, uuid)
}
+}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-project_properties_append"></a>}}
-\if{latex}{\out{\hypertarget{method-project_properties_append}{}}}
+\if{html}{\out{<a id="method-Arvados-project_properties_append"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-project_properties_append}{}}}
\subsection{Method \code{project_properties_append()}}{
project_properties_append is a method defined in Arvados class that enables appending properties. Allows to add new properties.
\subsection{Usage}{
@@ -431,25 +495,27 @@ project_properties_append is a method defined in Arvados class that enables appe
\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
-\item{\code{uuid}}{The UUID of a project or a file.}
+\item{\code{properties}}{List of new properties.}
-\item{\code{listOfNewProperties}}{List of new properties.}
+\item{\code{uuid}}{The UUID of a project or a file.}
}
\if{html}{\out{</div>}}
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{newProperties <- list() # should contain a list of new properties to be added
+\preformatted{\dontrun{
+newProperties <- list() # should contain a list of new properties to be added
arv$project_properties_append(properties = newProperties, uuid)
}
+}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-project_properties_get"></a>}}
-\if{latex}{\out{\hypertarget{method-project_properties_get}{}}}
+\if{html}{\out{<a id="method-Arvados-project_properties_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-project_properties_get}{}}}
\subsection{Method \code{project_properties_get()}}{
project_properties_get is a method defined in Arvados class that returns properties.
\subsection{Usage}{
@@ -465,7 +531,9 @@ project_properties_get is a method defined in Arvados class that returns propert
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arv$project_properties_get(projectUUID)
+\preformatted{\dontrun{
+arv$project_properties_get(projectUUID)
+}
}
\if{html}{\out{</div>}}
@@ -473,8 +541,8 @@ project_properties_get is a method defined in Arvados class that returns propert
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-project_properties_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-project_properties_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-project_properties_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-project_properties_delete}{}}}
\subsection{Method \code{project_properties_delete()}}{
project_properties_delete is a method defined in Arvados class that deletes list of properties.
\subsection{Usage}{
@@ -492,17 +560,19 @@ project_properties_delete is a method defined in Arvados class that deletes list
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{Properties <- list() # should contain a list of new properties to be added
+\preformatted{\dontrun{
+Properties <- list() # should contain a list of new properties to be added
arv$project_properties_delete(Properties, projectUUID)
}
+}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-project_update"></a>}}
-\if{latex}{\out{\hypertarget{method-project_update}{}}}
+\if{html}{\out{<a id="method-Arvados-project_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-project_update}{}}}
\subsection{Method \code{project_update()}}{
project_update enables updating project. New name, description and properties may be given.
\subsection{Usage}{
@@ -520,17 +590,19 @@ project_update enables updating project. New name, description and properties ma
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{newProperties <- list() # should contain a list of new properties to be added
+\preformatted{\dontrun{
+newProperties <- list() # should contain a list of new properties to be added
arv$project_update(name = "new project name", properties = newProperties, uuid = projectUUID)
}
+}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-project_list"></a>}}
-\if{latex}{\out{\hypertarget{method-project_list}{}}}
+\if{html}{\out{<a id="method-Arvados-project_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-project_list}{}}}
\subsection{Method \code{project_list()}}{
project_list enables listing project by its name, uuid, properties, permissions.
\subsection{Usage}{
@@ -560,7 +632,9 @@ project_list enables listing project by its name, uuid, properties, permissions.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{listOfprojects <- arv$project_list(list(list("owner_uuid", "=", projectUUID))) # Sample query which show projects within the project of a given UUID
+\preformatted{\dontrun{
+listOfprojects <- arv$project_list(list(list("owner_uuid", "=", projectUUID))) # Sample query which show projects within the project of a given UUID
+}
}
\if{html}{\out{</div>}}
@@ -568,8 +642,8 @@ project_list enables listing project by its name, uuid, properties, permissions.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-project_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-project_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-project_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-project_delete}{}}}
\subsection{Method \code{project_delete()}}{
project_delete trashes project of a given uuid. It can be restored from trash or deleted permanently.
\subsection{Usage}{
@@ -583,10 +657,20 @@ project_delete trashes project of a given uuid. It can be restored from trash or
}
\if{html}{\out{</div>}}
}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{\dontrun{
+arv$project_delete(uuid = 'projectUUID')
+}
+}
+\if{html}{\out{</div>}}
+
+}
+
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-api_clients_get"></a>}}
-\if{latex}{\out{\hypertarget{method-api_clients_get}{}}}
+\if{html}{\out{<a id="method-Arvados-api_clients_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-api_clients_get}{}}}
\subsection{Method \code{api_clients_get()}}{
api_clients_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -602,8 +686,8 @@ api_clients_get is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-api_clients_create"></a>}}
-\if{latex}{\out{\hypertarget{method-api_clients_create}{}}}
+\if{html}{\out{<a id="method-Arvados-api_clients_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-api_clients_create}{}}}
\subsection{Method \code{api_clients_create()}}{
api_clients_create is a method defined in Arvados class.
\subsection{Usage}{
@@ -627,8 +711,8 @@ api_clients_create is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-api_clients_update"></a>}}
-\if{latex}{\out{\hypertarget{method-api_clients_update}{}}}
+\if{html}{\out{<a id="method-Arvados-api_clients_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-api_clients_update}{}}}
\subsection{Method \code{api_clients_update()}}{
api_clients_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -646,8 +730,8 @@ api_clients_update is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-api_clients_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-api_clients_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-api_clients_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-api_clients_delete}{}}}
\subsection{Method \code{api_clients_delete()}}{
api_clients_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -663,8 +747,8 @@ api_clients_delete is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-api_clients_list"></a>}}
-\if{latex}{\out{\hypertarget{method-api_clients_list}{}}}
+\if{html}{\out{<a id="method-Arvados-api_clients_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-api_clients_list}{}}}
\subsection{Method \code{api_clients_list()}}{
api_clients_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -693,8 +777,8 @@ api_clients_list is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-api_client_authorizations_get"></a>}}
-\if{latex}{\out{\hypertarget{method-api_client_authorizations_get}{}}}
+\if{html}{\out{<a id="method-Arvados-api_client_authorizations_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-api_client_authorizations_get}{}}}
\subsection{Method \code{api_client_authorizations_get()}}{
api_client_authorizations_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -710,8 +794,8 @@ api_client_authorizations_get is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-api_client_authorizations_create"></a>}}
-\if{latex}{\out{\hypertarget{method-api_client_authorizations_create}{}}}
+\if{html}{\out{<a id="method-Arvados-api_client_authorizations_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-api_client_authorizations_create}{}}}
\subsection{Method \code{api_client_authorizations_create()}}{
api_client_authorizations_create is a method defined in Arvados class.
\subsection{Usage}{
@@ -735,8 +819,8 @@ api_client_authorizations_create is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-api_client_authorizations_update"></a>}}
-\if{latex}{\out{\hypertarget{method-api_client_authorizations_update}{}}}
+\if{html}{\out{<a id="method-Arvados-api_client_authorizations_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-api_client_authorizations_update}{}}}
\subsection{Method \code{api_client_authorizations_update()}}{
api_client_authorizations_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -754,8 +838,8 @@ api_client_authorizations_update is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-api_client_authorizations_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-api_client_authorizations_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-api_client_authorizations_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-api_client_authorizations_delete}{}}}
\subsection{Method \code{api_client_authorizations_delete()}}{
api_client_authorizations_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -771,8 +855,8 @@ api_client_authorizations_delete is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-api_client_authorizations_create_system_auth"></a>}}
-\if{latex}{\out{\hypertarget{method-api_client_authorizations_create_system_auth}{}}}
+\if{html}{\out{<a id="method-Arvados-api_client_authorizations_create_system_auth"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-api_client_authorizations_create_system_auth}{}}}
\subsection{Method \code{api_client_authorizations_create_system_auth()}}{
api_client_authorizations_create_system_auth is a method defined in Arvados class.
\subsection{Usage}{
@@ -784,8 +868,8 @@ api_client_authorizations_create_system_auth is a method defined in Arvados clas
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-api_client_authorizations_current"></a>}}
-\if{latex}{\out{\hypertarget{method-api_client_authorizations_current}{}}}
+\if{html}{\out{<a id="method-Arvados-api_client_authorizations_current"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-api_client_authorizations_current}{}}}
\subsection{Method \code{api_client_authorizations_current()}}{
api_client_authorizations_current is a method defined in Arvados class.
\subsection{Usage}{
@@ -794,8 +878,8 @@ api_client_authorizations_current is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-api_client_authorizations_list"></a>}}
-\if{latex}{\out{\hypertarget{method-api_client_authorizations_list}{}}}
+\if{html}{\out{<a id="method-Arvados-api_client_authorizations_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-api_client_authorizations_list}{}}}
\subsection{Method \code{api_client_authorizations_list()}}{
api_client_authorizations_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -824,8 +908,8 @@ api_client_authorizations_list is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-authorized_keys_get"></a>}}
-\if{latex}{\out{\hypertarget{method-authorized_keys_get}{}}}
+\if{html}{\out{<a id="method-Arvados-authorized_keys_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-authorized_keys_get}{}}}
\subsection{Method \code{authorized_keys_get()}}{
authorized_keys_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -841,8 +925,8 @@ authorized_keys_get is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-authorized_keys_create"></a>}}
-\if{latex}{\out{\hypertarget{method-authorized_keys_create}{}}}
+\if{html}{\out{<a id="method-Arvados-authorized_keys_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-authorized_keys_create}{}}}
\subsection{Method \code{authorized_keys_create()}}{
authorized_keys_create is a method defined in Arvados class.
\subsection{Usage}{
@@ -866,8 +950,8 @@ authorized_keys_create is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-authorized_keys_update"></a>}}
-\if{latex}{\out{\hypertarget{method-authorized_keys_update}{}}}
+\if{html}{\out{<a id="method-Arvados-authorized_keys_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-authorized_keys_update}{}}}
\subsection{Method \code{authorized_keys_update()}}{
authorized_keys_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -885,8 +969,8 @@ authorized_keys_update is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-authorized_keys_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-authorized_keys_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-authorized_keys_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-authorized_keys_delete}{}}}
\subsection{Method \code{authorized_keys_delete()}}{
authorized_keys_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -902,8 +986,8 @@ authorized_keys_delete is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-authorized_keys_list"></a>}}
-\if{latex}{\out{\hypertarget{method-authorized_keys_list}{}}}
+\if{html}{\out{<a id="method-Arvados-authorized_keys_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-authorized_keys_list}{}}}
\subsection{Method \code{authorized_keys_list()}}{
authorized_keys_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -932,8 +1016,8 @@ authorized_keys_list is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-collections_get"></a>}}
-\if{latex}{\out{\hypertarget{method-collections_get}{}}}
+\if{html}{\out{<a id="method-Arvados-collections_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-collections_get}{}}}
\subsection{Method \code{collections_get()}}{
collections_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -943,15 +1027,24 @@ collections_get is a method defined in Arvados class.
\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
-\item{\code{uuid}}{The UUID of the Collection in question.
-collection <- arv$collections_get(uuid = collectionUUID)}
+\item{\code{uuid}}{The UUID of the Collection in question.}
+}
+\if{html}{\out{</div>}}
+}
+\subsection{Examples}{
+\if{html}{\out{<div class="r example copy">}}
+\preformatted{\dontrun{
+collection <- arv$collections_get(uuid = collectionUUID)
+}
}
\if{html}{\out{</div>}}
+
}
+
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-collections_create"></a>}}
-\if{latex}{\out{\hypertarget{method-collections_create}{}}}
+\if{html}{\out{<a id="method-Arvados-collections_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-collections_create}{}}}
\subsection{Method \code{collections_create()}}{
collections_create is a method defined in Arvados class that enables collections creation.
\subsection{Usage}{
@@ -984,17 +1077,19 @@ collections_create is a method defined in Arvados class that enables collections
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{Properties <- list() # should contain a list of new properties to be added
+\preformatted{\dontrun{
+Properties <- list() # should contain a list of new properties to be added
arv$collections_create(name = "collectionTitle", description = "collectionDescription", ownerUUID = "collectionOwner", properties = Properties)
}
+}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-collections_update"></a>}}
-\if{latex}{\out{\hypertarget{method-collections_update}{}}}
+\if{html}{\out{<a id="method-Arvados-collections_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-collections_update}{}}}
\subsection{Method \code{collections_update()}}{
collections_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -1024,7 +1119,9 @@ collections_update is a method defined in Arvados class.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{collection <- arv$collections_create(name = "newCollectionTitle", description = "newCollectionDescription", ownerUUID = "collectionOwner", properties = NULL)
+\preformatted{\dontrun{
+collection <- arv$collections_update(name = "newCollectionTitle", description = "newCollectionDescription", ownerUUID = "collectionOwner", properties = NULL, uuid = "collectionUUID")
+}
}
\if{html}{\out{</div>}}
@@ -1032,8 +1129,8 @@ collections_update is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-collections_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-collections_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-collections_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-collections_delete}{}}}
\subsection{Method \code{collections_delete()}}{
collections_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -1049,7 +1146,9 @@ collections_delete is a method defined in Arvados class.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arv$collection_delete(collectionUUID)
+\preformatted{\dontrun{
+arv$collection_delete(collectionUUID)
+}
}
\if{html}{\out{</div>}}
@@ -1057,8 +1156,8 @@ collections_delete is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-collections_provenance"></a>}}
-\if{latex}{\out{\hypertarget{method-collections_provenance}{}}}
+\if{html}{\out{<a id="method-Arvados-collections_provenance"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-collections_provenance}{}}}
\subsection{Method \code{collections_provenance()}}{
collections_provenance is a method defined in Arvados class, it returns the collection by uuid.
\subsection{Usage}{
@@ -1074,7 +1173,9 @@ collections_provenance is a method defined in Arvados class, it returns the coll
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{collection <- arv$collections_provenance(collectionUUID)
+\preformatted{\dontrun{
+collection <- arv$collections_provenance(collectionUUID)
+}
}
\if{html}{\out{</div>}}
@@ -1082,8 +1183,8 @@ collections_provenance is a method defined in Arvados class, it returns the coll
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-collections_used_by"></a>}}
-\if{latex}{\out{\hypertarget{method-collections_used_by}{}}}
+\if{html}{\out{<a id="method-Arvados-collections_used_by"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-collections_used_by}{}}}
\subsection{Method \code{collections_used_by()}}{
collections_used_by is a method defined in Arvados class, it returns collection by portable_data_hash.
\subsection{Usage}{
@@ -1099,8 +1200,8 @@ collections_used_by is a method defined in Arvados class, it returns collection
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-collections_trash"></a>}}
-\if{latex}{\out{\hypertarget{method-collections_trash}{}}}
+\if{html}{\out{<a id="method-Arvados-collections_trash"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-collections_trash}{}}}
\subsection{Method \code{collections_trash()}}{
collections_trash is a method defined in Arvados class, it moves collection to trash.
\subsection{Usage}{
@@ -1116,7 +1217,9 @@ collections_trash is a method defined in Arvados class, it moves collection to t
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arv$collections_trash(collectionUUID)
+\preformatted{\dontrun{
+arv$collections_trash(collectionUUID)
+}
}
\if{html}{\out{</div>}}
@@ -1124,8 +1227,8 @@ collections_trash is a method defined in Arvados class, it moves collection to t
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-collections_untrash"></a>}}
-\if{latex}{\out{\hypertarget{method-collections_untrash}{}}}
+\if{html}{\out{<a id="method-Arvados-collections_untrash"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-collections_untrash}{}}}
\subsection{Method \code{collections_untrash()}}{
collections_untrash is a method defined in Arvados class, it moves collection from trash to project.
\subsection{Usage}{
@@ -1141,7 +1244,9 @@ collections_untrash is a method defined in Arvados class, it moves collection fr
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arv$collections_untrash(collectionUUID)
+\preformatted{\dontrun{
+arv$collections_untrash(collectionUUID)
+}
}
\if{html}{\out{</div>}}
@@ -1149,8 +1254,8 @@ collections_untrash is a method defined in Arvados class, it moves collection fr
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-collections_list"></a>}}
-\if{latex}{\out{\hypertarget{method-collections_list}{}}}
+\if{html}{\out{<a id="method-Arvados-collections_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-collections_list}{}}}
\subsection{Method \code{collections_list()}}{
collections_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -1185,7 +1290,9 @@ collections_list is a method defined in Arvados class.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{collectionList <- arv$collections.list(list(list("name", "=", "Example")))
+\preformatted{\dontrun{
+collectionList <- arv$collections_list(list(list("name", "=", "Example")))
+}
}
\if{html}{\out{</div>}}
@@ -1193,8 +1300,8 @@ collections_list is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-containers_get"></a>}}
-\if{latex}{\out{\hypertarget{method-containers_get}{}}}
+\if{html}{\out{<a id="method-Arvados-containers_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-containers_get}{}}}
\subsection{Method \code{containers_get()}}{
containers_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -1210,8 +1317,8 @@ containers_get is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-containers_create"></a>}}
-\if{latex}{\out{\hypertarget{method-containers_create}{}}}
+\if{html}{\out{<a id="method-Arvados-containers_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-containers_create}{}}}
\subsection{Method \code{containers_create()}}{
containers_create is a method defined in Arvados class.
\subsection{Usage}{
@@ -1235,8 +1342,8 @@ containers_create is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-containers_update"></a>}}
-\if{latex}{\out{\hypertarget{method-containers_update}{}}}
+\if{html}{\out{<a id="method-Arvados-containers_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-containers_update}{}}}
\subsection{Method \code{containers_update()}}{
containers_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -1254,8 +1361,8 @@ containers_update is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-containers_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-containers_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-containers_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-containers_delete}{}}}
\subsection{Method \code{containers_delete()}}{
containers_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -1271,8 +1378,8 @@ containers_delete is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-containers_auth"></a>}}
-\if{latex}{\out{\hypertarget{method-containers_auth}{}}}
+\if{html}{\out{<a id="method-Arvados-containers_auth"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-containers_auth}{}}}
\subsection{Method \code{containers_auth()}}{
containers_auth is a method defined in Arvados class.
\subsection{Usage}{
@@ -1288,8 +1395,8 @@ containers_auth is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-containers_lock"></a>}}
-\if{latex}{\out{\hypertarget{method-containers_lock}{}}}
+\if{html}{\out{<a id="method-Arvados-containers_lock"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-containers_lock}{}}}
\subsection{Method \code{containers_lock()}}{
containers_lock is a method defined in Arvados class.
\subsection{Usage}{
@@ -1305,8 +1412,8 @@ containers_lock is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-containers_unlock"></a>}}
-\if{latex}{\out{\hypertarget{method-containers_unlock}{}}}
+\if{html}{\out{<a id="method-Arvados-containers_unlock"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-containers_unlock}{}}}
\subsection{Method \code{containers_unlock()}}{
containers_unlock is a method defined in Arvados class.
\subsection{Usage}{
@@ -1322,8 +1429,8 @@ containers_unlock is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-containers_secret_mounts"></a>}}
-\if{latex}{\out{\hypertarget{method-containers_secret_mounts}{}}}
+\if{html}{\out{<a id="method-Arvados-containers_secret_mounts"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-containers_secret_mounts}{}}}
\subsection{Method \code{containers_secret_mounts()}}{
containers_secret_mounts is a method defined in Arvados class.
\subsection{Usage}{
@@ -1339,8 +1446,8 @@ containers_secret_mounts is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-containers_current"></a>}}
-\if{latex}{\out{\hypertarget{method-containers_current}{}}}
+\if{html}{\out{<a id="method-Arvados-containers_current"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-containers_current}{}}}
\subsection{Method \code{containers_current()}}{
containers_current is a method defined in Arvados class.
\subsection{Usage}{
@@ -1349,8 +1456,8 @@ containers_current is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-containers_list"></a>}}
-\if{latex}{\out{\hypertarget{method-containers_list}{}}}
+\if{html}{\out{<a id="method-Arvados-containers_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-containers_list}{}}}
\subsection{Method \code{containers_list()}}{
containers_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -1379,8 +1486,8 @@ containers_list is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-container_requests_get"></a>}}
-\if{latex}{\out{\hypertarget{method-container_requests_get}{}}}
+\if{html}{\out{<a id="method-Arvados-container_requests_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-container_requests_get}{}}}
\subsection{Method \code{container_requests_get()}}{
container_requests_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -1396,8 +1503,8 @@ container_requests_get is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-container_requests_create"></a>}}
-\if{latex}{\out{\hypertarget{method-container_requests_create}{}}}
+\if{html}{\out{<a id="method-Arvados-container_requests_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-container_requests_create}{}}}
\subsection{Method \code{container_requests_create()}}{
container_requests_create is a method defined in Arvados class.
\subsection{Usage}{
@@ -1421,8 +1528,8 @@ container_requests_create is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-container_requests_update"></a>}}
-\if{latex}{\out{\hypertarget{method-container_requests_update}{}}}
+\if{html}{\out{<a id="method-Arvados-container_requests_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-container_requests_update}{}}}
\subsection{Method \code{container_requests_update()}}{
container_requests_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -1440,8 +1547,8 @@ container_requests_update is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-container_requests_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-container_requests_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-container_requests_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-container_requests_delete}{}}}
\subsection{Method \code{container_requests_delete()}}{
container_requests_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -1457,8 +1564,8 @@ container_requests_delete is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-container_requests_list"></a>}}
-\if{latex}{\out{\hypertarget{method-container_requests_list}{}}}
+\if{html}{\out{<a id="method-Arvados-container_requests_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-container_requests_list}{}}}
\subsection{Method \code{container_requests_list()}}{
container_requests_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -1490,8 +1597,8 @@ container_requests_list is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-groups_get"></a>}}
-\if{latex}{\out{\hypertarget{method-groups_get}{}}}
+\if{html}{\out{<a id="method-Arvados-groups_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-groups_get}{}}}
\subsection{Method \code{groups_get()}}{
groups_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -1507,8 +1614,8 @@ groups_get is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-groups_create"></a>}}
-\if{latex}{\out{\hypertarget{method-groups_create}{}}}
+\if{html}{\out{<a id="method-Arvados-groups_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-groups_create}{}}}
\subsection{Method \code{groups_create()}}{
groups_create is a method defined in Arvados class that supports project creation.
\subsection{Usage}{
@@ -1535,8 +1642,8 @@ groups_create is a method defined in Arvados class that supports project creatio
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-groups_update"></a>}}
-\if{latex}{\out{\hypertarget{method-groups_update}{}}}
+\if{html}{\out{<a id="method-Arvados-groups_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-groups_update}{}}}
\subsection{Method \code{groups_update()}}{
groups_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -1556,8 +1663,8 @@ groups_update is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-groups_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-groups_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-groups_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-groups_delete}{}}}
\subsection{Method \code{groups_delete()}}{
groups_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -1573,8 +1680,8 @@ groups_delete is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-groups_contents"></a>}}
-\if{latex}{\out{\hypertarget{method-groups_contents}{}}}
+\if{html}{\out{<a id="method-Arvados-groups_contents"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-groups_contents}{}}}
\subsection{Method \code{groups_contents()}}{
groups_contents is a method defined in Arvados class.
\subsection{Usage}{
@@ -1612,8 +1719,8 @@ groups_contents is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-groups_shared"></a>}}
-\if{latex}{\out{\hypertarget{method-groups_shared}{}}}
+\if{html}{\out{<a id="method-Arvados-groups_shared"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-groups_shared}{}}}
\subsection{Method \code{groups_shared()}}{
groups_shared is a method defined in Arvados class.
\subsection{Usage}{
@@ -1646,8 +1753,8 @@ groups_shared is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-groups_trash"></a>}}
-\if{latex}{\out{\hypertarget{method-groups_trash}{}}}
+\if{html}{\out{<a id="method-Arvados-groups_trash"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-groups_trash}{}}}
\subsection{Method \code{groups_trash()}}{
groups_trash is a method defined in Arvados class.
\subsection{Usage}{
@@ -1663,8 +1770,8 @@ groups_trash is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-groups_untrash"></a>}}
-\if{latex}{\out{\hypertarget{method-groups_untrash}{}}}
+\if{html}{\out{<a id="method-Arvados-groups_untrash"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-groups_untrash}{}}}
\subsection{Method \code{groups_untrash()}}{
groups_untrash is a method defined in Arvados class.
\subsection{Usage}{
@@ -1680,8 +1787,8 @@ groups_untrash is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-groups_list"></a>}}
-\if{latex}{\out{\hypertarget{method-groups_list}{}}}
+\if{html}{\out{<a id="method-Arvados-groups_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-groups_list}{}}}
\subsection{Method \code{groups_list()}}{
groups_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -1713,8 +1820,8 @@ groups_list is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-keep_services_get"></a>}}
-\if{latex}{\out{\hypertarget{method-keep_services_get}{}}}
+\if{html}{\out{<a id="method-Arvados-keep_services_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-keep_services_get}{}}}
\subsection{Method \code{keep_services_get()}}{
keep_services_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -1730,8 +1837,8 @@ keep_services_get is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-keep_services_create"></a>}}
-\if{latex}{\out{\hypertarget{method-keep_services_create}{}}}
+\if{html}{\out{<a id="method-Arvados-keep_services_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-keep_services_create}{}}}
\subsection{Method \code{keep_services_create()}}{
keep_services_create is a method defined in Arvados class.
\subsection{Usage}{
@@ -1755,8 +1862,8 @@ keep_services_create is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-keep_services_update"></a>}}
-\if{latex}{\out{\hypertarget{method-keep_services_update}{}}}
+\if{html}{\out{<a id="method-Arvados-keep_services_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-keep_services_update}{}}}
\subsection{Method \code{keep_services_update()}}{
keep_services_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -1774,8 +1881,8 @@ keep_services_update is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-keep_services_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-keep_services_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-keep_services_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-keep_services_delete}{}}}
\subsection{Method \code{keep_services_delete()}}{
keep_services_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -1791,8 +1898,8 @@ keep_services_delete is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-keep_services_accessible"></a>}}
-\if{latex}{\out{\hypertarget{method-keep_services_accessible}{}}}
+\if{html}{\out{<a id="method-Arvados-keep_services_accessible"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-keep_services_accessible}{}}}
\subsection{Method \code{keep_services_accessible()}}{
keep_services_accessible is a method defined in Arvados class.
\subsection{Usage}{
@@ -1801,8 +1908,8 @@ keep_services_accessible is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-keep_services_list"></a>}}
-\if{latex}{\out{\hypertarget{method-keep_services_list}{}}}
+\if{html}{\out{<a id="method-Arvados-keep_services_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-keep_services_list}{}}}
\subsection{Method \code{keep_services_list()}}{
keep_services_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -1831,8 +1938,8 @@ keep_services_list is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-project_permission_give"></a>}}
-\if{latex}{\out{\hypertarget{method-project_permission_give}{}}}
+\if{html}{\out{<a id="method-Arvados-project_permission_give"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-project_permission_give}{}}}
\subsection{Method \code{project_permission_give()}}{
project_permission_give is a method defined in Arvados class that enables sharing files with another users.
\subsection{Usage}{
@@ -1852,7 +1959,9 @@ project_permission_give is a method defined in Arvados class that enables sharin
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arv$project_permission_give(type = "can_read", uuid = objectUUID, user = userUUID)
+\preformatted{\dontrun{
+arv$project_permission_give(type = "can_read", uuid = objectUUID, user = userUUID)
+}
}
\if{html}{\out{</div>}}
@@ -1860,8 +1969,8 @@ project_permission_give is a method defined in Arvados class that enables sharin
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-project_permission_refuse"></a>}}
-\if{latex}{\out{\hypertarget{method-project_permission_refuse}{}}}
+\if{html}{\out{<a id="method-Arvados-project_permission_refuse"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-project_permission_refuse}{}}}
\subsection{Method \code{project_permission_refuse()}}{
project_permission_refuse is a method defined in Arvados class that unables sharing files with another users.
\subsection{Usage}{
@@ -1881,7 +1990,9 @@ project_permission_refuse is a method defined in Arvados class that unables shar
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arv$project_permission_refuse(type = "can_read", uuid = objectUUID, user = userUUID)
+\preformatted{\dontrun{
+arv$project_permission_refuse(type = "can_read", uuid = objectUUID, user = userUUID)
+}
}
\if{html}{\out{</div>}}
@@ -1889,8 +2000,8 @@ project_permission_refuse is a method defined in Arvados class that unables shar
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-project_permission_update"></a>}}
-\if{latex}{\out{\hypertarget{method-project_permission_update}{}}}
+\if{html}{\out{<a id="method-Arvados-project_permission_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-project_permission_update}{}}}
\subsection{Method \code{project_permission_update()}}{
project_permission_update is a method defined in Arvados class that enables updating permissions.
\subsection{Usage}{
@@ -1912,7 +2023,9 @@ project_permission_update is a method defined in Arvados class that enables upda
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arv$project_permission_update(typeOld = "can_read", typeNew = "can_write", uuid = objectUUID, user = userUUID)
+\preformatted{\dontrun{
+arv$project_permission_update(typeOld = "can_read", typeNew = "can_write", uuid = objectUUID, user = userUUID)
+}
}
\if{html}{\out{</div>}}
@@ -1920,8 +2033,8 @@ project_permission_update is a method defined in Arvados class that enables upda
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-project_permission_check"></a>}}
-\if{latex}{\out{\hypertarget{method-project_permission_check}{}}}
+\if{html}{\out{<a id="method-Arvados-project_permission_check"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-project_permission_check}{}}}
\subsection{Method \code{project_permission_check()}}{
project_permission_check is a method defined in Arvados class that enables checking file permissions.
\subsection{Usage}{
@@ -1941,7 +2054,9 @@ project_permission_check is a method defined in Arvados class that enables check
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arv$project_permission_check(type = "can_read", uuid = objectUUID, user = userUUID)
+\preformatted{\dontrun{
+arv$project_permission_check(type = "can_read", uuid = objectUUID, user = userUUID)
+}
}
\if{html}{\out{</div>}}
@@ -1949,8 +2064,8 @@ project_permission_check is a method defined in Arvados class that enables check
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-links_get"></a>}}
-\if{latex}{\out{\hypertarget{method-links_get}{}}}
+\if{html}{\out{<a id="method-Arvados-links_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-links_get}{}}}
\subsection{Method \code{links_get()}}{
links_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -1966,8 +2081,8 @@ links_get is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-links_create"></a>}}
-\if{latex}{\out{\hypertarget{method-links_create}{}}}
+\if{html}{\out{<a id="method-Arvados-links_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-links_create}{}}}
\subsection{Method \code{links_create()}}{
links_create is a method defined in Arvados class.
\subsection{Usage}{
@@ -1987,8 +2102,8 @@ links_create is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-links_update"></a>}}
-\if{latex}{\out{\hypertarget{method-links_update}{}}}
+\if{html}{\out{<a id="method-Arvados-links_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-links_update}{}}}
\subsection{Method \code{links_update()}}{
links_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -2006,8 +2121,8 @@ links_update is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-links_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-links_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-links_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-links_delete}{}}}
\subsection{Method \code{links_delete()}}{
links_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -2023,8 +2138,8 @@ links_delete is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-links_list"></a>}}
-\if{latex}{\out{\hypertarget{method-links_list}{}}}
+\if{html}{\out{<a id="method-Arvados-links_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-links_list}{}}}
\subsection{Method \code{links_list()}}{
links_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -2053,8 +2168,8 @@ links_list is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-links_get_permissions"></a>}}
-\if{latex}{\out{\hypertarget{method-links_get_permissions}{}}}
+\if{html}{\out{<a id="method-Arvados-links_get_permissions"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-links_get_permissions}{}}}
\subsection{Method \code{links_get_permissions()}}{
links_get_permissions is a method defined in Arvados class.
\subsection{Usage}{
@@ -2070,8 +2185,8 @@ links_get_permissions is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-logs_get"></a>}}
-\if{latex}{\out{\hypertarget{method-logs_get}{}}}
+\if{html}{\out{<a id="method-Arvados-logs_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-logs_get}{}}}
\subsection{Method \code{logs_get()}}{
logs_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -2087,8 +2202,8 @@ logs_get is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-logs_create"></a>}}
-\if{latex}{\out{\hypertarget{method-logs_create}{}}}
+\if{html}{\out{<a id="method-Arvados-logs_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-logs_create}{}}}
\subsection{Method \code{logs_create()}}{
logs_create is a method defined in Arvados class.
\subsection{Usage}{
@@ -2108,8 +2223,8 @@ logs_create is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-logs_update"></a>}}
-\if{latex}{\out{\hypertarget{method-logs_update}{}}}
+\if{html}{\out{<a id="method-Arvados-logs_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-logs_update}{}}}
\subsection{Method \code{logs_update()}}{
logs_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -2127,8 +2242,8 @@ logs_update is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-logs_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-logs_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-logs_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-logs_delete}{}}}
\subsection{Method \code{logs_delete()}}{
logs_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -2144,8 +2259,8 @@ logs_delete is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-logs_list"></a>}}
-\if{latex}{\out{\hypertarget{method-logs_list}{}}}
+\if{html}{\out{<a id="method-Arvados-logs_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-logs_list}{}}}
\subsection{Method \code{logs_list()}}{
logs_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -2174,8 +2289,8 @@ logs_list is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-users_get"></a>}}
-\if{latex}{\out{\hypertarget{method-users_get}{}}}
+\if{html}{\out{<a id="method-Arvados-users_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-users_get}{}}}
\subsection{Method \code{users_get()}}{
users_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -2191,8 +2306,8 @@ users_get is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-users_create"></a>}}
-\if{latex}{\out{\hypertarget{method-users_create}{}}}
+\if{html}{\out{<a id="method-Arvados-users_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-users_create}{}}}
\subsection{Method \code{users_create()}}{
users_create is a method defined in Arvados class.
\subsection{Usage}{
@@ -2212,8 +2327,8 @@ users_create is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-users_update"></a>}}
-\if{latex}{\out{\hypertarget{method-users_update}{}}}
+\if{html}{\out{<a id="method-Arvados-users_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-users_update}{}}}
\subsection{Method \code{users_update()}}{
users_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -2231,8 +2346,8 @@ users_update is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-users_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-users_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-users_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-users_delete}{}}}
\subsection{Method \code{users_delete()}}{
users_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -2248,8 +2363,8 @@ users_delete is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-users_current"></a>}}
-\if{latex}{\out{\hypertarget{method-users_current}{}}}
+\if{html}{\out{<a id="method-Arvados-users_current"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-users_current}{}}}
\subsection{Method \code{users_current()}}{
users_current is a method defined in Arvados class.
\subsection{Usage}{
@@ -2258,8 +2373,8 @@ users_current is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-users_system"></a>}}
-\if{latex}{\out{\hypertarget{method-users_system}{}}}
+\if{html}{\out{<a id="method-Arvados-users_system"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-users_system}{}}}
\subsection{Method \code{users_system()}}{
users_system is a method defined in Arvados class.
\subsection{Usage}{
@@ -2268,8 +2383,8 @@ users_system is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-users_activate"></a>}}
-\if{latex}{\out{\hypertarget{method-users_activate}{}}}
+\if{html}{\out{<a id="method-Arvados-users_activate"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-users_activate}{}}}
\subsection{Method \code{users_activate()}}{
users_activate is a method defined in Arvados class.
\subsection{Usage}{
@@ -2285,8 +2400,8 @@ users_activate is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-users_setup"></a>}}
-\if{latex}{\out{\hypertarget{method-users_setup}{}}}
+\if{html}{\out{<a id="method-Arvados-users_setup"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-users_setup}{}}}
\subsection{Method \code{users_setup()}}{
users_setup is a method defined in Arvados class.
\subsection{Usage}{
@@ -2301,8 +2416,8 @@ users_setup is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-users_unsetup"></a>}}
-\if{latex}{\out{\hypertarget{method-users_unsetup}{}}}
+\if{html}{\out{<a id="method-Arvados-users_unsetup"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-users_unsetup}{}}}
\subsection{Method \code{users_unsetup()}}{
users_unsetup is a method defined in Arvados class.
\subsection{Usage}{
@@ -2318,8 +2433,8 @@ users_unsetup is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-users_merge"></a>}}
-\if{latex}{\out{\hypertarget{method-users_merge}{}}}
+\if{html}{\out{<a id="method-Arvados-users_merge"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-users_merge}{}}}
\subsection{Method \code{users_merge()}}{
users_merge is a method defined in Arvados class.
\subsection{Usage}{
@@ -2334,8 +2449,8 @@ users_merge is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-users_list"></a>}}
-\if{latex}{\out{\hypertarget{method-users_list}{}}}
+\if{html}{\out{<a id="method-Arvados-users_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-users_list}{}}}
\subsection{Method \code{users_list()}}{
users_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -2364,8 +2479,8 @@ users_list is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-repositories_get"></a>}}
-\if{latex}{\out{\hypertarget{method-repositories_get}{}}}
+\if{html}{\out{<a id="method-Arvados-repositories_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-repositories_get}{}}}
\subsection{Method \code{repositories_get()}}{
repositories_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -2381,8 +2496,8 @@ repositories_get is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-repositories_create"></a>}}
-\if{latex}{\out{\hypertarget{method-repositories_create}{}}}
+\if{html}{\out{<a id="method-Arvados-repositories_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-repositories_create}{}}}
\subsection{Method \code{repositories_create()}}{
repositories_create is a method defined in Arvados class.
\subsection{Usage}{
@@ -2406,8 +2521,8 @@ repositories_create is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-repositories_update"></a>}}
-\if{latex}{\out{\hypertarget{method-repositories_update}{}}}
+\if{html}{\out{<a id="method-Arvados-repositories_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-repositories_update}{}}}
\subsection{Method \code{repositories_update()}}{
repositories_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -2425,8 +2540,8 @@ repositories_update is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-repositories_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-repositories_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-repositories_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-repositories_delete}{}}}
\subsection{Method \code{repositories_delete()}}{
repositories_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -2442,8 +2557,8 @@ repositories_delete is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-repositories_get_all_permissions"></a>}}
-\if{latex}{\out{\hypertarget{method-repositories_get_all_permissions}{}}}
+\if{html}{\out{<a id="method-Arvados-repositories_get_all_permissions"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-repositories_get_all_permissions}{}}}
\subsection{Method \code{repositories_get_all_permissions()}}{
repositories_get_all_permissions is a method defined in Arvados class.
\subsection{Usage}{
@@ -2452,8 +2567,8 @@ repositories_get_all_permissions is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-repositories_list"></a>}}
-\if{latex}{\out{\hypertarget{method-repositories_list}{}}}
+\if{html}{\out{<a id="method-Arvados-repositories_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-repositories_list}{}}}
\subsection{Method \code{repositories_list()}}{
repositories_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -2482,8 +2597,8 @@ repositories_list is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-virtual_machines_get"></a>}}
-\if{latex}{\out{\hypertarget{method-virtual_machines_get}{}}}
+\if{html}{\out{<a id="method-Arvados-virtual_machines_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-virtual_machines_get}{}}}
\subsection{Method \code{virtual_machines_get()}}{
virtual_machines_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -2499,8 +2614,8 @@ virtual_machines_get is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-virtual_machines_create"></a>}}
-\if{latex}{\out{\hypertarget{method-virtual_machines_create}{}}}
+\if{html}{\out{<a id="method-Arvados-virtual_machines_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-virtual_machines_create}{}}}
\subsection{Method \code{virtual_machines_create()}}{
virtual_machines_create is a method defined in Arvados class.
\subsection{Usage}{
@@ -2524,8 +2639,8 @@ virtual_machines_create is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-virtual_machines_update"></a>}}
-\if{latex}{\out{\hypertarget{method-virtual_machines_update}{}}}
+\if{html}{\out{<a id="method-Arvados-virtual_machines_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-virtual_machines_update}{}}}
\subsection{Method \code{virtual_machines_update()}}{
virtual_machines_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -2543,8 +2658,8 @@ virtual_machines_update is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-virtual_machines_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-virtual_machines_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-virtual_machines_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-virtual_machines_delete}{}}}
\subsection{Method \code{virtual_machines_delete()}}{
virtual_machines_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -2560,8 +2675,8 @@ virtual_machines_delete is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-virtual_machines_logins"></a>}}
-\if{latex}{\out{\hypertarget{method-virtual_machines_logins}{}}}
+\if{html}{\out{<a id="method-Arvados-virtual_machines_logins"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-virtual_machines_logins}{}}}
\subsection{Method \code{virtual_machines_logins()}}{
virtual_machines_logins is a method defined in Arvados class.
\subsection{Usage}{
@@ -2577,8 +2692,8 @@ virtual_machines_logins is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-virtual_machines_get_all_logins"></a>}}
-\if{latex}{\out{\hypertarget{method-virtual_machines_get_all_logins}{}}}
+\if{html}{\out{<a id="method-Arvados-virtual_machines_get_all_logins"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-virtual_machines_get_all_logins}{}}}
\subsection{Method \code{virtual_machines_get_all_logins()}}{
virtual_machines_get_all_logins is a method defined in Arvados class.
\subsection{Usage}{
@@ -2587,8 +2702,8 @@ virtual_machines_get_all_logins is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-virtual_machines_list"></a>}}
-\if{latex}{\out{\hypertarget{method-virtual_machines_list}{}}}
+\if{html}{\out{<a id="method-Arvados-virtual_machines_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-virtual_machines_list}{}}}
\subsection{Method \code{virtual_machines_list()}}{
virtual_machines_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -2617,8 +2732,8 @@ virtual_machines_list is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-workflows_get"></a>}}
-\if{latex}{\out{\hypertarget{method-workflows_get}{}}}
+\if{html}{\out{<a id="method-Arvados-workflows_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-workflows_get}{}}}
\subsection{Method \code{workflows_get()}}{
workflows_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -2634,8 +2749,8 @@ workflows_get is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-workflows_create"></a>}}
-\if{latex}{\out{\hypertarget{method-workflows_create}{}}}
+\if{html}{\out{<a id="method-Arvados-workflows_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-workflows_create}{}}}
\subsection{Method \code{workflows_create()}}{
workflows_create is a method defined in Arvados class.
\subsection{Usage}{
@@ -2659,8 +2774,8 @@ workflows_create is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-workflows_update"></a>}}
-\if{latex}{\out{\hypertarget{method-workflows_update}{}}}
+\if{html}{\out{<a id="method-Arvados-workflows_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-workflows_update}{}}}
\subsection{Method \code{workflows_update()}}{
workflows_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -2678,8 +2793,8 @@ workflows_update is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-workflows_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-workflows_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-workflows_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-workflows_delete}{}}}
\subsection{Method \code{workflows_delete()}}{
workflows_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -2695,8 +2810,8 @@ workflows_delete is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-workflows_list"></a>}}
-\if{latex}{\out{\hypertarget{method-workflows_list}{}}}
+\if{html}{\out{<a id="method-Arvados-workflows_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-workflows_list}{}}}
\subsection{Method \code{workflows_list()}}{
workflows_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -2725,8 +2840,8 @@ workflows_list is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-user_agreements_get"></a>}}
-\if{latex}{\out{\hypertarget{method-user_agreements_get}{}}}
+\if{html}{\out{<a id="method-Arvados-user_agreements_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-user_agreements_get}{}}}
\subsection{Method \code{user_agreements_get()}}{
user_agreements_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -2742,8 +2857,8 @@ user_agreements_get is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-user_agreements_create"></a>}}
-\if{latex}{\out{\hypertarget{method-user_agreements_create}{}}}
+\if{html}{\out{<a id="method-Arvados-user_agreements_create"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-user_agreements_create}{}}}
\subsection{Method \code{user_agreements_create()}}{
user_agreements_create is a method defined in Arvados class.
\subsection{Usage}{
@@ -2767,8 +2882,8 @@ user_agreements_create is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-user_agreements_update"></a>}}
-\if{latex}{\out{\hypertarget{method-user_agreements_update}{}}}
+\if{html}{\out{<a id="method-Arvados-user_agreements_update"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-user_agreements_update}{}}}
\subsection{Method \code{user_agreements_update()}}{
user_agreements_update is a method defined in Arvados class.
\subsection{Usage}{
@@ -2786,8 +2901,8 @@ user_agreements_update is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-user_agreements_delete"></a>}}
-\if{latex}{\out{\hypertarget{method-user_agreements_delete}{}}}
+\if{html}{\out{<a id="method-Arvados-user_agreements_delete"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-user_agreements_delete}{}}}
\subsection{Method \code{user_agreements_delete()}}{
user_agreements_delete is a method defined in Arvados class.
\subsection{Usage}{
@@ -2803,8 +2918,8 @@ user_agreements_delete is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-user_agreements_signatures"></a>}}
-\if{latex}{\out{\hypertarget{method-user_agreements_signatures}{}}}
+\if{html}{\out{<a id="method-Arvados-user_agreements_signatures"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-user_agreements_signatures}{}}}
\subsection{Method \code{user_agreements_signatures()}}{
user_agreements_signatures is a method defined in Arvados class.
\subsection{Usage}{
@@ -2813,8 +2928,8 @@ user_agreements_signatures is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-user_agreements_sign"></a>}}
-\if{latex}{\out{\hypertarget{method-user_agreements_sign}{}}}
+\if{html}{\out{<a id="method-Arvados-user_agreements_sign"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-user_agreements_sign}{}}}
\subsection{Method \code{user_agreements_sign()}}{
user_agreements_sign is a method defined in Arvados class.
\subsection{Usage}{
@@ -2823,8 +2938,8 @@ user_agreements_sign is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-user_agreements_list"></a>}}
-\if{latex}{\out{\hypertarget{method-user_agreements_list}{}}}
+\if{html}{\out{<a id="method-Arvados-user_agreements_list"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-user_agreements_list}{}}}
\subsection{Method \code{user_agreements_list()}}{
user_agreements_list is a method defined in Arvados class.
\subsection{Usage}{
@@ -2853,8 +2968,8 @@ user_agreements_list is a method defined in Arvados class.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-user_agreements_new"></a>}}
-\if{latex}{\out{\hypertarget{method-user_agreements_new}{}}}
+\if{html}{\out{<a id="method-Arvados-user_agreements_new"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-user_agreements_new}{}}}
\subsection{Method \code{user_agreements_new()}}{
user_agreements_new is a method defined in Arvados class.
\subsection{Usage}{
@@ -2863,8 +2978,8 @@ user_agreements_new is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-configs_get"></a>}}
-\if{latex}{\out{\hypertarget{method-configs_get}{}}}
+\if{html}{\out{<a id="method-Arvados-configs_get"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-configs_get}{}}}
\subsection{Method \code{configs_get()}}{
configs_get is a method defined in Arvados class.
\subsection{Usage}{
@@ -2873,8 +2988,8 @@ configs_get is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getHostName"></a>}}
-\if{latex}{\out{\hypertarget{method-getHostName}{}}}
+\if{html}{\out{<a id="method-Arvados-getHostName"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-getHostName}{}}}
\subsection{Method \code{getHostName()}}{
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{Arvados$getHostName()}\if{html}{\out{</div>}}
@@ -2882,8 +2997,8 @@ configs_get is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getToken"></a>}}
-\if{latex}{\out{\hypertarget{method-getToken}{}}}
+\if{html}{\out{<a id="method-Arvados-getToken"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-getToken}{}}}
\subsection{Method \code{getToken()}}{
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{Arvados$getToken()}\if{html}{\out{</div>}}
@@ -2891,8 +3006,8 @@ configs_get is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-setRESTService"></a>}}
-\if{latex}{\out{\hypertarget{method-setRESTService}{}}}
+\if{html}{\out{<a id="method-Arvados-setRESTService"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-setRESTService}{}}}
\subsection{Method \code{setRESTService()}}{
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{Arvados$setRESTService(newREST)}\if{html}{\out{</div>}}
@@ -2900,8 +3015,8 @@ configs_get is a method defined in Arvados class.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getRESTService"></a>}}
-\if{latex}{\out{\hypertarget{method-getRESTService}{}}}
+\if{html}{\out{<a id="method-Arvados-getRESTService"></a>}}
+\if{latex}{\out{\hypertarget{method-Arvados-getRESTService}{}}}
\subsection{Method \code{getRESTService()}}{
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{Arvados$getRESTService()}\if{html}{\out{</div>}}
diff --git a/sdk/R/man/ArvadosFile.Rd b/sdk/R/man/ArvadosFile.Rd
index 8275b7b60..81c25af5f 100644
--- a/sdk/R/man/ArvadosFile.Rd
+++ b/sdk/R/man/ArvadosFile.Rd
@@ -12,97 +12,117 @@ ArvadosFile class represents a file inside Arvados collection.
## Method `ArvadosFile$new`
## ------------------------------------------------
+\dontrun{
myFile <- ArvadosFile$new("myFile")
+}
## ------------------------------------------------
## Method `ArvadosFile$getName`
## ------------------------------------------------
+\dontrun{
arvadosFile$getName()
+}
## ------------------------------------------------
## Method `ArvadosFile$getFileListing`
## ------------------------------------------------
+\dontrun{
arvadosFile$getFileListing()
+}
## ------------------------------------------------
## Method `ArvadosFile$getSizeInBytes`
## ------------------------------------------------
+\dontrun{
arvadosFile$getSizeInBytes()
+}
## ------------------------------------------------
## Method `ArvadosFile$read`
## ------------------------------------------------
+\dontrun{
collection <- Collection$new(arv, collectionUUID)
arvadosFile <- collection$get(fileName)
fileContent <- arvadosFile$read("text")
+}
## ------------------------------------------------
## Method `ArvadosFile$connection`
## ------------------------------------------------
+\dontrun{
collection <- Collection$new(arv, collectionUUID)
arvadosFile <- collection$get(fileName)
arvConnection <- arvadosFile$connection("w")
+}
## ------------------------------------------------
## Method `ArvadosFile$flush`
## ------------------------------------------------
+\dontrun{
collection <- Collection$new(arv, collectionUUID)
arvadosFile <- collection$get(fileName)
myFile$write("This is new file content")
arvadosFile$flush()
+}
## ------------------------------------------------
## Method `ArvadosFile$write`
## ------------------------------------------------
+\dontrun{
collection <- Collection$new(arv, collectionUUID)
arvadosFile <- collection$get(fileName)
myFile$write("This is new file content")
+}
## ------------------------------------------------
## Method `ArvadosFile$move`
## ------------------------------------------------
+\dontrun{
arvadosFile$move(newPath)
+}
## ------------------------------------------------
## Method `ArvadosFile$copy`
## ------------------------------------------------
+\dontrun{
arvadosFile$copy("NewName.format")
}
+}
\section{Methods}{
\subsection{Public methods}{
\itemize{
-\item \href{#method-new}{\code{ArvadosFile$new()}}
-\item \href{#method-getName}{\code{ArvadosFile$getName()}}
-\item \href{#method-getFileListing}{\code{ArvadosFile$getFileListing()}}
-\item \href{#method-getSizeInBytes}{\code{ArvadosFile$getSizeInBytes()}}
-\item \href{#method-get}{\code{ArvadosFile$get()}}
-\item \href{#method-getFirst}{\code{ArvadosFile$getFirst()}}
-\item \href{#method-getCollection}{\code{ArvadosFile$getCollection()}}
-\item \href{#method-setCollection}{\code{ArvadosFile$setCollection()}}
-\item \href{#method-getRelativePath}{\code{ArvadosFile$getRelativePath()}}
-\item \href{#method-getParent}{\code{ArvadosFile$getParent()}}
-\item \href{#method-setParent}{\code{ArvadosFile$setParent()}}
-\item \href{#method-read}{\code{ArvadosFile$read()}}
-\item \href{#method-connection}{\code{ArvadosFile$connection()}}
-\item \href{#method-flush}{\code{ArvadosFile$flush()}}
-\item \href{#method-write}{\code{ArvadosFile$write()}}
-\item \href{#method-move}{\code{ArvadosFile$move()}}
-\item \href{#method-copy}{\code{ArvadosFile$copy()}}
-\item \href{#method-duplicate}{\code{ArvadosFile$duplicate()}}
+\item \href{#method-ArvadosFile-new}{\code{ArvadosFile$new()}}
+\item \href{#method-ArvadosFile-getName}{\code{ArvadosFile$getName()}}
+\item \href{#method-ArvadosFile-getFileListing}{\code{ArvadosFile$getFileListing()}}
+\item \href{#method-ArvadosFile-getSizeInBytes}{\code{ArvadosFile$getSizeInBytes()}}
+\item \href{#method-ArvadosFile-get}{\code{ArvadosFile$get()}}
+\item \href{#method-ArvadosFile-getFirst}{\code{ArvadosFile$getFirst()}}
+\item \href{#method-ArvadosFile-getCollection}{\code{ArvadosFile$getCollection()}}
+\item \href{#method-ArvadosFile-setCollection}{\code{ArvadosFile$setCollection()}}
+\item \href{#method-ArvadosFile-getRelativePath}{\code{ArvadosFile$getRelativePath()}}
+\item \href{#method-ArvadosFile-getParent}{\code{ArvadosFile$getParent()}}
+\item \href{#method-ArvadosFile-setParent}{\code{ArvadosFile$setParent()}}
+\item \href{#method-ArvadosFile-read}{\code{ArvadosFile$read()}}
+\item \href{#method-ArvadosFile-connection}{\code{ArvadosFile$connection()}}
+\item \href{#method-ArvadosFile-flush}{\code{ArvadosFile$flush()}}
+\item \href{#method-ArvadosFile-write}{\code{ArvadosFile$write()}}
+\item \href{#method-ArvadosFile-move}{\code{ArvadosFile$move()}}
+\item \href{#method-ArvadosFile-copy}{\code{ArvadosFile$copy()}}
+\item \href{#method-ArvadosFile-duplicate}{\code{ArvadosFile$duplicate()}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-new"></a>}}
-\if{latex}{\out{\hypertarget{method-new}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-new"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-new}{}}}
\subsection{Method \code{new()}}{
Initialize new enviroment.
\subsection{Usage}{
@@ -121,7 +141,9 @@ A new `ArvadosFile` object.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{myFile <- ArvadosFile$new("myFile")
+\preformatted{\dontrun{
+myFile <- ArvadosFile$new("myFile")
+}
}
\if{html}{\out{</div>}}
@@ -129,8 +151,8 @@ A new `ArvadosFile` object.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getName"></a>}}
-\if{latex}{\out{\hypertarget{method-getName}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-getName"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-getName}{}}}
\subsection{Method \code{getName()}}{
Returns name of the file.
\subsection{Usage}{
@@ -139,7 +161,9 @@ Returns name of the file.
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arvadosFile$getName()
+\preformatted{\dontrun{
+arvadosFile$getName()
+}
}
\if{html}{\out{</div>}}
@@ -147,8 +171,8 @@ Returns name of the file.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getFileListing"></a>}}
-\if{latex}{\out{\hypertarget{method-getFileListing}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-getFileListing"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-getFileListing}{}}}
\subsection{Method \code{getFileListing()}}{
Returns collections file content as character vector.
\subsection{Usage}{
@@ -164,7 +188,9 @@ Returns collections file content as character vector.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arvadosFile$getFileListing()
+\preformatted{\dontrun{
+arvadosFile$getFileListing()
+}
}
\if{html}{\out{</div>}}
@@ -172,8 +198,8 @@ Returns collections file content as character vector.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getSizeInBytes"></a>}}
-\if{latex}{\out{\hypertarget{method-getSizeInBytes}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-getSizeInBytes"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-getSizeInBytes}{}}}
\subsection{Method \code{getSizeInBytes()}}{
Returns collections content size in bytes.
\subsection{Usage}{
@@ -182,7 +208,9 @@ Returns collections content size in bytes.
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arvadosFile$getSizeInBytes()
+\preformatted{\dontrun{
+arvadosFile$getSizeInBytes()
+}
}
\if{html}{\out{</div>}}
@@ -190,8 +218,8 @@ Returns collections content size in bytes.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-get"></a>}}
-\if{latex}{\out{\hypertarget{method-get}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-get"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-get}{}}}
\subsection{Method \code{get()}}{
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$get(fileLikeObjectName)}\if{html}{\out{</div>}}
@@ -199,8 +227,8 @@ Returns collections content size in bytes.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getFirst"></a>}}
-\if{latex}{\out{\hypertarget{method-getFirst}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-getFirst"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-getFirst}{}}}
\subsection{Method \code{getFirst()}}{
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{ArvadosFile$getFirst()}\if{html}{\out{</div>}}
@@ -208,8 +236,8 @@ Returns collections content size in bytes.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getCollection"></a>}}
-\if{latex}{\out{\hypertarget{method-getCollection}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-getCollection"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-getCollection}{}}}
\subsection{Method \code{getCollection()}}{
Returns collection UUID.
\subsection{Usage}{
@@ -218,8 +246,8 @@ Returns collection UUID.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-setCollection"></a>}}
-\if{latex}{\out{\hypertarget{method-setCollection}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-setCollection"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-setCollection}{}}}
\subsection{Method \code{setCollection()}}{
Sets new collection.
\subsection{Usage}{
@@ -228,8 +256,8 @@ Sets new collection.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getRelativePath"></a>}}
-\if{latex}{\out{\hypertarget{method-getRelativePath}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-getRelativePath"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-getRelativePath}{}}}
\subsection{Method \code{getRelativePath()}}{
Returns file path relative to the root.
\subsection{Usage}{
@@ -238,8 +266,8 @@ Returns file path relative to the root.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getParent"></a>}}
-\if{latex}{\out{\hypertarget{method-getParent}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-getParent"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-getParent}{}}}
\subsection{Method \code{getParent()}}{
Returns project UUID.
\subsection{Usage}{
@@ -248,8 +276,8 @@ Returns project UUID.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-setParent"></a>}}
-\if{latex}{\out{\hypertarget{method-setParent}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-setParent"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-setParent}{}}}
\subsection{Method \code{setParent()}}{
Sets project collection.
\subsection{Usage}{
@@ -258,8 +286,8 @@ Sets project collection.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-read"></a>}}
-\if{latex}{\out{\hypertarget{method-read}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-read"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-read}{}}}
\subsection{Method \code{read()}}{
Read file content.
\subsection{Usage}{
@@ -279,18 +307,20 @@ Read file content.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{collection <- Collection$new(arv, collectionUUID)
+\preformatted{\dontrun{
+collection <- Collection$new(arv, collectionUUID)
arvadosFile <- collection$get(fileName)
fileContent <- arvadosFile$read("text")
}
+}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-connection"></a>}}
-\if{latex}{\out{\hypertarget{method-connection}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-connection"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-connection}{}}}
\subsection{Method \code{connection()}}{
Get connection opened in "read" or "write" mode.
\subsection{Usage}{
@@ -306,18 +336,20 @@ Get connection opened in "read" or "write" mode.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{collection <- Collection$new(arv, collectionUUID)
+\preformatted{\dontrun{
+collection <- Collection$new(arv, collectionUUID)
arvadosFile <- collection$get(fileName)
arvConnection <- arvadosFile$connection("w")
}
+}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-flush"></a>}}
-\if{latex}{\out{\hypertarget{method-flush}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-flush"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-flush}{}}}
\subsection{Method \code{flush()}}{
Write connections content to a file or override current content of the file.
\subsection{Usage}{
@@ -326,19 +358,21 @@ Write connections content to a file or override current content of the file.
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{collection <- Collection$new(arv, collectionUUID)
+\preformatted{\dontrun{
+collection <- Collection$new(arv, collectionUUID)
arvadosFile <- collection$get(fileName)
myFile$write("This is new file content")
arvadosFile$flush()
}
+}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-write"></a>}}
-\if{latex}{\out{\hypertarget{method-write}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-write"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-write}{}}}
\subsection{Method \code{write()}}{
Write to file or override current content of the file.
\subsection{Usage}{
@@ -356,18 +390,20 @@ Write to file or override current content of the file.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{collection <- Collection$new(arv, collectionUUID)
+\preformatted{\dontrun{
+collection <- Collection$new(arv, collectionUUID)
arvadosFile <- collection$get(fileName)
myFile$write("This is new file content")
}
+}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-move"></a>}}
-\if{latex}{\out{\hypertarget{method-move}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-move"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-move}{}}}
\subsection{Method \code{move()}}{
Moves file to a new location inside collection.
\subsection{Usage}{
@@ -383,7 +419,9 @@ Moves file to a new location inside collection.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arvadosFile$move(newPath)
+\preformatted{\dontrun{
+arvadosFile$move(newPath)
+}
}
\if{html}{\out{</div>}}
@@ -391,8 +429,8 @@ Moves file to a new location inside collection.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-copy"></a>}}
-\if{latex}{\out{\hypertarget{method-copy}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-copy"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-copy}{}}}
\subsection{Method \code{copy()}}{
Copies file to a new location inside collection.
\subsection{Usage}{
@@ -408,7 +446,9 @@ Copies file to a new location inside collection.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arvadosFile$copy("NewName.format")
+\preformatted{\dontrun{
+arvadosFile$copy("NewName.format")
+}
}
\if{html}{\out{</div>}}
@@ -416,8 +456,8 @@ Copies file to a new location inside collection.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-duplicate"></a>}}
-\if{latex}{\out{\hypertarget{method-duplicate}{}}}
+\if{html}{\out{<a id="method-ArvadosFile-duplicate"></a>}}
+\if{latex}{\out{\hypertarget{method-ArvadosFile-duplicate}{}}}
\subsection{Method \code{duplicate()}}{
Duplicate file and gives it a new name.
\subsection{Usage}{
diff --git a/sdk/R/man/ArvadosR.Rd b/sdk/R/man/ArvadosR.Rd
index 1432491f6..fe6297a27 100644
--- a/sdk/R/man/ArvadosR.Rd
+++ b/sdk/R/man/ArvadosR.Rd
@@ -4,7 +4,6 @@
\alias{ArvadosR}
\title{ArvadosR}
\description{
-
Arvados is an open source platform for managing, processing, and sharing genomic and other large scientific and biomedical data. With Arvados, bioinformaticians run and scale compute-intensive workflows, developers create biomedical applications, and IT administrators manage large compute and storage resources.
}
\seealso{
@@ -16,6 +15,8 @@ Arvados is an open source platform for managing, processing, and sharing genomic
\itemize{
\item Lucas Di Pentima
\item Ward Vandewege
+\item Fuad Muhic
\item Peter Amstutz
-\item Fuad Muhic}
+\item Aneta Stanczyk
+\item Piotr Nowosielski}
}
diff --git a/sdk/R/man/Collection.Rd b/sdk/R/man/Collection.Rd
index bb72cc1b3..8ac6fcce1 100644
--- a/sdk/R/man/Collection.Rd
+++ b/sdk/R/man/Collection.Rd
@@ -13,24 +13,29 @@ for exaplme actions like creating, updating, moving or removing are possible.
## Method `Collection$new`
## ------------------------------------------------
+\dontrun{
collection <- Collection$new(arv, CollectionUUID)
+}
## ------------------------------------------------
## Method `Collection$readArvFile`
## ------------------------------------------------
+\dontrun{
collection <- Collection$new(arv, collectionUUID)
readFile <- collection$readArvFile(arvadosFile, istable = 'yes') # table
readFile <- collection$readArvFile(arvadosFile, istable = 'no') # text
readFile <- collection$readArvFile(arvadosFile) # xlsx, csv, tsv, rds, rdata
-readFile <- collection$readArvFile(arvadosFile, fileclass = 'lala') # fasta
+readFile <- collection$readArvFile(arvadosFile, fileclass = 'fasta') # fasta
readFile <- collection$readArvFile(arvadosFile, Ncol= 4, Nrow = 32) # binary, only numbers
readFile <- collection$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text
+}
## ------------------------------------------------
## Method `Collection$writeFile`
## ------------------------------------------------
+\dontrun{
collection <- Collection$new(arv, collectionUUID)
writeFile <- collection$writeFile(name = "myoutput.csv", file = file, fileFormat = "csv", istable = NULL, collectionUUID = collectionUUID) # csv
writeFile <- collection$writeFile(name = "myoutput.tsv", file = file, fileFormat = "tsv", istable = NULL, collectionUUID = collectionUUID) # tsv
@@ -39,49 +44,64 @@ writeFile <- collection$writeFile(name = "myoutputtable.txt", file = file, fileF
writeFile <- collection$writeFile(name = "myoutputtext.txt", file = file, fileFormat = "txt", istable = "no", collectionUUID = collectionUUID) # txt text
writeFile <- collection$writeFile(name = "myoutputbinary.dat", file = file, fileFormat = "dat", collectionUUID = collectionUUID) # binary
writeFile <- collection$writeFile(name = "myoutputxlsx.xlsx", file = file, fileFormat = "xlsx", collectionUUID = collectionUUID) # xlsx
+}
## ------------------------------------------------
## Method `Collection$create`
## ------------------------------------------------
+\dontrun{
collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))
+}
## ------------------------------------------------
## Method `Collection$remove`
## ------------------------------------------------
+\dontrun{
collection$remove(fileName.format)
+}
## ------------------------------------------------
## Method `Collection$move`
## ------------------------------------------------
+\dontrun{
collection$move("fileName.format", path)
+}
## ------------------------------------------------
## Method `Collection$copy`
## ------------------------------------------------
+\dontrun{
copied <- collection$copy("oldName.format", "newName.format")
+}
## ------------------------------------------------
## Method `Collection$refresh`
## ------------------------------------------------
+\dontrun{
collection$refresh()
+}
## ------------------------------------------------
## Method `Collection$getFileListing`
## ------------------------------------------------
+\dontrun{
list <- collection$getFileListing()
+}
## ------------------------------------------------
## Method `Collection$get`
## ------------------------------------------------
+\dontrun{
arvadosFile <- collection$get(fileName)
}
+}
\seealso{
\code{\link{https://github.com/arvados/arvados/tree/main/sdk/R}}
}
@@ -95,24 +115,24 @@ arvadosFile <- collection$get(fileName)
\section{Methods}{
\subsection{Public methods}{
\itemize{
-\item \href{#method-new}{\code{Collection$new()}}
-\item \href{#method-add}{\code{Collection$add()}}
-\item \href{#method-readArvFile}{\code{Collection$readArvFile()}}
-\item \href{#method-writeFile}{\code{Collection$writeFile()}}
-\item \href{#method-create}{\code{Collection$create()}}
-\item \href{#method-remove}{\code{Collection$remove()}}
-\item \href{#method-move}{\code{Collection$move()}}
-\item \href{#method-copy}{\code{Collection$copy()}}
-\item \href{#method-refresh}{\code{Collection$refresh()}}
-\item \href{#method-getFileListing}{\code{Collection$getFileListing()}}
-\item \href{#method-get}{\code{Collection$get()}}
-\item \href{#method-getRESTService}{\code{Collection$getRESTService()}}
-\item \href{#method-setRESTService}{\code{Collection$setRESTService()}}
+\item \href{#method-Collection-new}{\code{Collection$new()}}
+\item \href{#method-Collection-add}{\code{Collection$add()}}
+\item \href{#method-Collection-readArvFile}{\code{Collection$readArvFile()}}
+\item \href{#method-Collection-writeFile}{\code{Collection$writeFile()}}
+\item \href{#method-Collection-create}{\code{Collection$create()}}
+\item \href{#method-Collection-remove}{\code{Collection$remove()}}
+\item \href{#method-Collection-move}{\code{Collection$move()}}
+\item \href{#method-Collection-copy}{\code{Collection$copy()}}
+\item \href{#method-Collection-refresh}{\code{Collection$refresh()}}
+\item \href{#method-Collection-getFileListing}{\code{Collection$getFileListing()}}
+\item \href{#method-Collection-get}{\code{Collection$get()}}
+\item \href{#method-Collection-getRESTService}{\code{Collection$getRESTService()}}
+\item \href{#method-Collection-setRESTService}{\code{Collection$setRESTService()}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-new"></a>}}
-\if{latex}{\out{\hypertarget{method-new}{}}}
+\if{html}{\out{<a id="method-Collection-new"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-new}{}}}
\subsection{Method \code{new()}}{
Initialize new enviroment.
\subsection{Usage}{
@@ -133,7 +153,9 @@ A new `Collection` object.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{collection <- Collection$new(arv, CollectionUUID)
+\preformatted{\dontrun{
+collection <- Collection$new(arv, CollectionUUID)
+}
}
\if{html}{\out{</div>}}
@@ -141,8 +163,8 @@ A new `Collection` object.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add"></a>}}
-\if{latex}{\out{\hypertarget{method-add}{}}}
+\if{html}{\out{<a id="method-Collection-add"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-add}{}}}
\subsection{Method \code{add()}}{
Adds ArvadosFile or Subcollection specified by content to the collection. Used only with ArvadosFile or Subcollection.
\subsection{Usage}{
@@ -160,8 +182,8 @@ Adds ArvadosFile or Subcollection specified by content to the collection. Used o
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-readArvFile"></a>}}
-\if{latex}{\out{\hypertarget{method-readArvFile}{}}}
+\if{html}{\out{<a id="method-Collection-readArvFile"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-readArvFile}{}}}
\subsection{Method \code{readArvFile()}}{
Read file content.
\subsection{Usage}{
@@ -198,22 +220,24 @@ Read file content.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{collection <- Collection$new(arv, collectionUUID)
+\preformatted{\dontrun{
+collection <- Collection$new(arv, collectionUUID)
readFile <- collection$readArvFile(arvadosFile, istable = 'yes') # table
readFile <- collection$readArvFile(arvadosFile, istable = 'no') # text
readFile <- collection$readArvFile(arvadosFile) # xlsx, csv, tsv, rds, rdata
-readFile <- collection$readArvFile(arvadosFile, fileclass = 'lala') # fasta
+readFile <- collection$readArvFile(arvadosFile, fileclass = 'fasta') # fasta
readFile <- collection$readArvFile(arvadosFile, Ncol= 4, Nrow = 32) # binary, only numbers
readFile <- collection$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text
}
+}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-writeFile"></a>}}
-\if{latex}{\out{\hypertarget{method-writeFile}{}}}
+\if{html}{\out{<a id="method-Collection-writeFile"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-writeFile}{}}}
\subsection{Method \code{writeFile()}}{
Write file content
\subsection{Usage}{
@@ -240,7 +264,8 @@ Write file content
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{collection <- Collection$new(arv, collectionUUID)
+\preformatted{\dontrun{
+collection <- Collection$new(arv, collectionUUID)
writeFile <- collection$writeFile(name = "myoutput.csv", file = file, fileFormat = "csv", istable = NULL, collectionUUID = collectionUUID) # csv
writeFile <- collection$writeFile(name = "myoutput.tsv", file = file, fileFormat = "tsv", istable = NULL, collectionUUID = collectionUUID) # tsv
writeFile <- collection$writeFile(name = "myoutput.fasta", file = file, fileFormat = "fasta", istable = NULL, collectionUUID = collectionUUID) # fasta
@@ -249,14 +274,15 @@ writeFile <- collection$writeFile(name = "myoutputtext.txt", file = file, fileFo
writeFile <- collection$writeFile(name = "myoutputbinary.dat", file = file, fileFormat = "dat", collectionUUID = collectionUUID) # binary
writeFile <- collection$writeFile(name = "myoutputxlsx.xlsx", file = file, fileFormat = "xlsx", collectionUUID = collectionUUID) # xlsx
}
+}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-create"></a>}}
-\if{latex}{\out{\hypertarget{method-create}{}}}
+\if{html}{\out{<a id="method-Collection-create"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-create}{}}}
\subsection{Method \code{create()}}{
Creates one or more ArvadosFiles and adds them to the collection at specified path.
\subsection{Usage}{
@@ -272,7 +298,9 @@ Creates one or more ArvadosFiles and adds them to the collection at specified pa
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))
+\preformatted{\dontrun{
+collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))
+}
}
\if{html}{\out{</div>}}
@@ -280,8 +308,8 @@ Creates one or more ArvadosFiles and adds them to the collection at specified pa
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-remove"></a>}}
-\if{latex}{\out{\hypertarget{method-remove}{}}}
+\if{html}{\out{<a id="method-Collection-remove"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-remove}{}}}
\subsection{Method \code{remove()}}{
Remove one or more files from the collection.
\subsection{Usage}{
@@ -297,7 +325,9 @@ Remove one or more files from the collection.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{collection$remove(fileName.format)
+\preformatted{\dontrun{
+collection$remove(fileName.format)
+}
}
\if{html}{\out{</div>}}
@@ -305,8 +335,8 @@ Remove one or more files from the collection.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-move"></a>}}
-\if{latex}{\out{\hypertarget{method-move}{}}}
+\if{html}{\out{<a id="method-Collection-move"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-move}{}}}
\subsection{Method \code{move()}}{
Moves ArvadosFile or Subcollection to another location in the collection.
\subsection{Usage}{
@@ -324,7 +354,9 @@ Moves ArvadosFile or Subcollection to another location in the collection.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{collection$move("fileName.format", path)
+\preformatted{\dontrun{
+collection$move("fileName.format", path)
+}
}
\if{html}{\out{</div>}}
@@ -332,8 +364,8 @@ Moves ArvadosFile or Subcollection to another location in the collection.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-copy"></a>}}
-\if{latex}{\out{\hypertarget{method-copy}{}}}
+\if{html}{\out{<a id="method-Collection-copy"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-copy}{}}}
\subsection{Method \code{copy()}}{
Copies ArvadosFile or Subcollection to another location in the collection.
\subsection{Usage}{
@@ -351,7 +383,9 @@ Copies ArvadosFile or Subcollection to another location in the collection.
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{copied <- collection$copy("oldName.format", "newName.format")
+\preformatted{\dontrun{
+copied <- collection$copy("oldName.format", "newName.format")
+}
}
\if{html}{\out{</div>}}
@@ -359,8 +393,8 @@ Copies ArvadosFile or Subcollection to another location in the collection.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-refresh"></a>}}
-\if{latex}{\out{\hypertarget{method-refresh}{}}}
+\if{html}{\out{<a id="method-Collection-refresh"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-refresh}{}}}
\subsection{Method \code{refresh()}}{
Refreshes the environment.
\subsection{Usage}{
@@ -369,7 +403,9 @@ Refreshes the environment.
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{collection$refresh()
+\preformatted{\dontrun{
+collection$refresh()
+}
}
\if{html}{\out{</div>}}
@@ -377,8 +413,8 @@ Refreshes the environment.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getFileListing"></a>}}
-\if{latex}{\out{\hypertarget{method-getFileListing}{}}}
+\if{html}{\out{<a id="method-Collection-getFileListing"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-getFileListing}{}}}
\subsection{Method \code{getFileListing()}}{
Returns collections file content as character vector.
\subsection{Usage}{
@@ -387,7 +423,9 @@ Returns collections file content as character vector.
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{list <- collection$getFileListing()
+\preformatted{\dontrun{
+list <- collection$getFileListing()
+}
}
\if{html}{\out{</div>}}
@@ -395,8 +433,8 @@ Returns collections file content as character vector.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-get"></a>}}
-\if{latex}{\out{\hypertarget{method-get}{}}}
+\if{html}{\out{<a id="method-Collection-get"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-get}{}}}
\subsection{Method \code{get()}}{
If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.
\subsection{Usage}{
@@ -412,7 +450,9 @@ If relativePath is valid, returns ArvadosFile or Subcollection specified by rela
}
\subsection{Examples}{
\if{html}{\out{<div class="r example copy">}}
-\preformatted{arvadosFile <- collection$get(fileName)
+\preformatted{\dontrun{
+arvadosFile <- collection$get(fileName)
+}
}
\if{html}{\out{</div>}}
@@ -420,8 +460,8 @@ If relativePath is valid, returns ArvadosFile or Subcollection specified by rela
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getRESTService"></a>}}
-\if{latex}{\out{\hypertarget{method-getRESTService}{}}}
+\if{html}{\out{<a id="method-Collection-getRESTService"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-getRESTService}{}}}
\subsection{Method \code{getRESTService()}}{
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{Collection$getRESTService()}\if{html}{\out{</div>}}
@@ -429,8 +469,8 @@ If relativePath is valid, returns ArvadosFile or Subcollection specified by rela
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-setRESTService"></a>}}
-\if{latex}{\out{\hypertarget{method-setRESTService}{}}}
+\if{html}{\out{<a id="method-Collection-setRESTService"></a>}}
+\if{latex}{\out{\hypertarget{method-Collection-setRESTService}{}}}
\subsection{Method \code{setRESTService()}}{
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{Collection$setRESTService(newRESTService)}\if{html}{\out{</div>}}
diff --git a/sdk/R/man/Subcollection.Rd b/sdk/R/man/Subcollection.Rd
index 1c9ec96e1..9faf0c279 100644
--- a/sdk/R/man/Subcollection.Rd
+++ b/sdk/R/man/Subcollection.Rd
@@ -10,27 +10,27 @@ It is essentially a composite of arvadosFiles and other subcollections.
\section{Methods}{
\subsection{Public methods}{
\itemize{
-\item \href{#method-new}{\code{Subcollection$new()}}
-\item \href{#method-getName}{\code{Subcollection$getName()}}
-\item \href{#method-getRelativePath}{\code{Subcollection$getRelativePath()}}
-\item \href{#method-add}{\code{Subcollection$add()}}
-\item \href{#method-remove}{\code{Subcollection$remove()}}
-\item \href{#method-getFileListing}{\code{Subcollection$getFileListing()}}
-\item \href{#method-getSizeInBytes}{\code{Subcollection$getSizeInBytes()}}
-\item \href{#method-move}{\code{Subcollection$move()}}
-\item \href{#method-copy}{\code{Subcollection$copy()}}
-\item \href{#method-duplicate}{\code{Subcollection$duplicate()}}
-\item \href{#method-get}{\code{Subcollection$get()}}
-\item \href{#method-getFirst}{\code{Subcollection$getFirst()}}
-\item \href{#method-setCollection}{\code{Subcollection$setCollection()}}
-\item \href{#method-getCollection}{\code{Subcollection$getCollection()}}
-\item \href{#method-getParent}{\code{Subcollection$getParent()}}
-\item \href{#method-setParent}{\code{Subcollection$setParent()}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-new"></a>}}
-\if{latex}{\out{\hypertarget{method-new}{}}}
+\item \href{#method-Subcollection-new}{\code{Subcollection$new()}}
+\item \href{#method-Subcollection-getName}{\code{Subcollection$getName()}}
+\item \href{#method-Subcollection-getRelativePath}{\code{Subcollection$getRelativePath()}}
+\item \href{#method-Subcollection-add}{\code{Subcollection$add()}}
+\item \href{#method-Subcollection-remove}{\code{Subcollection$remove()}}
+\item \href{#method-Subcollection-getFileListing}{\code{Subcollection$getFileListing()}}
+\item \href{#method-Subcollection-getSizeInBytes}{\code{Subcollection$getSizeInBytes()}}
+\item \href{#method-Subcollection-move}{\code{Subcollection$move()}}
+\item \href{#method-Subcollection-copy}{\code{Subcollection$copy()}}
+\item \href{#method-Subcollection-duplicate}{\code{Subcollection$duplicate()}}
+\item \href{#method-Subcollection-get}{\code{Subcollection$get()}}
+\item \href{#method-Subcollection-getFirst}{\code{Subcollection$getFirst()}}
+\item \href{#method-Subcollection-setCollection}{\code{Subcollection$setCollection()}}
+\item \href{#method-Subcollection-getCollection}{\code{Subcollection$getCollection()}}
+\item \href{#method-Subcollection-getParent}{\code{Subcollection$getParent()}}
+\item \href{#method-Subcollection-setParent}{\code{Subcollection$setParent()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-Subcollection-new"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-new}{}}}
\subsection{Method \code{new()}}{
Initialize new enviroment.
\subsection{Usage}{
@@ -49,8 +49,8 @@ A new `Subcollection` object.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getName"></a>}}
-\if{latex}{\out{\hypertarget{method-getName}{}}}
+\if{html}{\out{<a id="method-Subcollection-getName"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-getName}{}}}
\subsection{Method \code{getName()}}{
Returns name of the file.
\subsection{Usage}{
@@ -59,8 +59,8 @@ Returns name of the file.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getRelativePath"></a>}}
-\if{latex}{\out{\hypertarget{method-getRelativePath}{}}}
+\if{html}{\out{<a id="method-Subcollection-getRelativePath"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-getRelativePath}{}}}
\subsection{Method \code{getRelativePath()}}{
Returns Subcollection's path relative to the root.
\subsection{Usage}{
@@ -69,8 +69,8 @@ Returns Subcollection's path relative to the root.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add"></a>}}
-\if{latex}{\out{\hypertarget{method-add}{}}}
+\if{html}{\out{<a id="method-Subcollection-add"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-add}{}}}
\subsection{Method \code{add()}}{
Adds ArvadosFile or Subcollection specified by content to the Subcollection.
\subsection{Usage}{
@@ -86,8 +86,8 @@ Adds ArvadosFile or Subcollection specified by content to the Subcollection.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-remove"></a>}}
-\if{latex}{\out{\hypertarget{method-remove}{}}}
+\if{html}{\out{<a id="method-Subcollection-remove"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-remove}{}}}
\subsection{Method \code{remove()}}{
Removes ArvadosFile or Subcollection specified by name from the Subcollection.
\subsection{Usage}{
@@ -103,8 +103,8 @@ Removes ArvadosFile or Subcollection specified by name from the Subcollection.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getFileListing"></a>}}
-\if{latex}{\out{\hypertarget{method-getFileListing}{}}}
+\if{html}{\out{<a id="method-Subcollection-getFileListing"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-getFileListing}{}}}
\subsection{Method \code{getFileListing()}}{
Returns Subcollections file content as character vector.
\subsection{Usage}{
@@ -120,8 +120,8 @@ Returns Subcollections file content as character vector.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getSizeInBytes"></a>}}
-\if{latex}{\out{\hypertarget{method-getSizeInBytes}{}}}
+\if{html}{\out{<a id="method-Subcollection-getSizeInBytes"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-getSizeInBytes}{}}}
\subsection{Method \code{getSizeInBytes()}}{
Returns subcollections content size in bytes.
\subsection{Usage}{
@@ -130,8 +130,8 @@ Returns subcollections content size in bytes.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-move"></a>}}
-\if{latex}{\out{\hypertarget{method-move}{}}}
+\if{html}{\out{<a id="method-Subcollection-move"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-move}{}}}
\subsection{Method \code{move()}}{
Moves Subcollection to a new location inside collection.
\subsection{Usage}{
@@ -147,8 +147,8 @@ Moves Subcollection to a new location inside collection.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-copy"></a>}}
-\if{latex}{\out{\hypertarget{method-copy}{}}}
+\if{html}{\out{<a id="method-Subcollection-copy"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-copy}{}}}
\subsection{Method \code{copy()}}{
Copies Subcollection to a new location inside collection.
\subsection{Usage}{
@@ -164,8 +164,8 @@ Copies Subcollection to a new location inside collection.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-duplicate"></a>}}
-\if{latex}{\out{\hypertarget{method-duplicate}{}}}
+\if{html}{\out{<a id="method-Subcollection-duplicate"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-duplicate}{}}}
\subsection{Method \code{duplicate()}}{
Duplicate Subcollection and gives it a new name.
\subsection{Usage}{
@@ -181,8 +181,8 @@ Duplicate Subcollection and gives it a new name.
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-get"></a>}}
-\if{latex}{\out{\hypertarget{method-get}{}}}
+\if{html}{\out{<a id="method-Subcollection-get"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-get}{}}}
\subsection{Method \code{get()}}{
If name is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.
\subsection{Usage}{
@@ -198,8 +198,8 @@ If name is valid, returns ArvadosFile or Subcollection specified by relativePath
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getFirst"></a>}}
-\if{latex}{\out{\hypertarget{method-getFirst}{}}}
+\if{html}{\out{<a id="method-Subcollection-getFirst"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-getFirst}{}}}
\subsection{Method \code{getFirst()}}{
Returns files in Subcollection.
\subsection{Usage}{
@@ -208,8 +208,8 @@ Returns files in Subcollection.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-setCollection"></a>}}
-\if{latex}{\out{\hypertarget{method-setCollection}{}}}
+\if{html}{\out{<a id="method-Subcollection-setCollection"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-setCollection}{}}}
\subsection{Method \code{setCollection()}}{
Sets Collection by its UUID.
\subsection{Usage}{
@@ -218,8 +218,8 @@ Sets Collection by its UUID.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getCollection"></a>}}
-\if{latex}{\out{\hypertarget{method-getCollection}{}}}
+\if{html}{\out{<a id="method-Subcollection-getCollection"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-getCollection}{}}}
\subsection{Method \code{getCollection()}}{
Returns Collection of Subcollection.
\subsection{Usage}{
@@ -228,8 +228,8 @@ Returns Collection of Subcollection.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-getParent"></a>}}
-\if{latex}{\out{\hypertarget{method-getParent}{}}}
+\if{html}{\out{<a id="method-Subcollection-getParent"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-getParent}{}}}
\subsection{Method \code{getParent()}}{
Returns Collection UUID.
\subsection{Usage}{
@@ -238,8 +238,8 @@ Returns Collection UUID.
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-setParent"></a>}}
-\if{latex}{\out{\hypertarget{method-setParent}{}}}
+\if{html}{\out{<a id="method-Subcollection-setParent"></a>}}
+\if{latex}{\out{\hypertarget{method-Subcollection-setParent}{}}}
\subsection{Method \code{setParent()}}{
Sets new Collection.
\subsection{Usage}{
diff --git a/sdk/R/run_test.R b/sdk/R/run_test.R
index 156dde108..1384c1f8c 100644
--- a/sdk/R/run_test.R
+++ b/sdk/R/run_test.R
@@ -2,6 +2,8 @@
#
# SPDX-License-Identifier: Apache-2.0
+devtools::check()
+
results <- devtools::test()
any_error <- any(as.data.frame(results)$error)
if (any_error) {
commit 29fecfe25bbcfb357b324be6928754e74c503955
Author: AnetaSta22 <107112384+AnetaSta22 at users.noreply.github.com>
Date: Thu Jun 8 14:20:35 2023 +0200
Update README.md
correct order
Add \dontrun{} in documentation in Arvados.R
Add \dontrun{} in documentation in ArvadosFile.R
Add \dontrun{} in documentation in Collection.R
Arvados-DCO-1.1-Signed-off-by: Aneta Stanczyk <aneta.stanczyk at contractors.roche.com>
diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R
index 882e272c3..ed65d1fc4 100644
--- a/sdk/R/R/Arvados.R
+++ b/sdk/R/R/Arvados.R
@@ -51,7 +51,9 @@ Arvados <- R6::R6Class(
#' project_exist enables checking if the project with such a UUID exist.
#' @param uuid The UUID of a project or a file.
#' @examples
- #' arv$project_exist(uuid = projectUUID)
+ #' \dontrun{
+ #' arv$project_exist(uuid = "projectUUID")
+ #' }
project_exist = function(uuid)
{
proj <- self$project_list(list(list("uuid", '=', uuid)))
@@ -68,7 +70,9 @@ Arvados <- R6::R6Class(
#' project_get returns the demanded project.
#' @param uuid The UUID of the Group in question.
#' @examples
- #' project <- arv$project_get(uuid = projectUUID)
+ #' \dontrun{
+ #' project <- arv$project_get(uuid = 'projectUUID')
+ #' }
project_get = function(uuid)
{
self$groups_get(uuid)
@@ -82,8 +86,10 @@ Arvados <- R6::R6Class(
#' @param properties List of the properties of the project.
#' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
#' @examples
+ #' \dontrun{
#' Properties <- list() # should contain a list of new properties to be added
#' new_project <- arv$project_create(name = "project name", description = "project description", owner_uuid = "project UUID", properties = NULL, ensureUniqueName = "false")
+ #' }
project_create = function(name, description, ownerUUID, properties = NULL, ensureUniqueName = "false")
{
group <- list(name = name, description = description, owner_uuid = ownerUUID, properties = properties)
@@ -96,8 +102,10 @@ Arvados <- R6::R6Class(
#' @param listProperties List of new properties.
#' @param uuid The UUID of a project or a file.
#' @examples
+ #' \dontrun{
#' Properties <- list() # should contain a list of new properties to be added
#' arv$project_properties_set(Properties, uuid)
+ #' }
project_properties_set = function(listProperties, uuid)
{
group <- c("group_class" = "project", list("properties" = listProperties))
@@ -107,11 +115,13 @@ Arvados <- R6::R6Class(
#' @description
#' project_properties_append is a method defined in Arvados class that enables appending properties. Allows to add new properties.
- #' @param listOfNewProperties List of new properties.
+ #' @param properties List of new properties.
#' @param uuid The UUID of a project or a file.
#' @examples
+ #' \dontrun{
#' newProperties <- list() # should contain a list of new properties to be added
#' arv$project_properties_append(properties = newProperties, uuid)
+ #' }
project_properties_append = function(properties, uuid)
{
proj <- self$project_list(list(list('uuid', '=', uuid)))
@@ -130,7 +140,9 @@ Arvados <- R6::R6Class(
#' project_properties_get is a method defined in Arvados class that returns properties.
#' @param uuid The UUID of a project or a file.
#' @examples
+ #' \dontrun{
#' arv$project_properties_get(projectUUID)
+ #' }
project_properties_get = function(uuid)
{
proj <- self$project_list(list(list('uuid', '=', uuid)))
@@ -142,8 +154,10 @@ Arvados <- R6::R6Class(
#' @param oneProp Property to be deleted.
#' @param uuid The UUID of a project or a file.
#' @examples
+ #' \dontrun{
#' Properties <- list() # should contain a list of new properties to be added
#' arv$project_properties_delete(Properties, projectUUID)
+ #' }
project_properties_delete = function(oneProp, uuid)
{
proj <- self$project_list(list(list('uuid', '=', uuid))) # find project
@@ -162,8 +176,10 @@ Arvados <- R6::R6Class(
#' @param ... Feature to be updated (name, description, properties).
#' @param uuid The UUID of a project in question.
#' @examples
+ #' \dontrun{
#' newProperties <- list() # should contain a list of new properties to be added
#' arv$project_update(name = "new project name", properties = newProperties, uuid = projectUUID)
+ #' }
project_update = function(..., uuid) {
vec <- list(...)
for (i in 1:length(vec))
@@ -190,7 +206,9 @@ Arvados <- R6::R6Class(
#' @param uuid The UUID of a project in question.
#' @param recursive Include contents from child groups recursively.
#' @examples
+ #' \dontrun{
#' listOfprojects <- arv$project_list(list(list("owner_uuid", "=", projectUUID))) # Sample query which show projects within the project of a given UUID
+ #' }
project_list = function(filters = NULL, where = NULL,
order = NULL, select = NULL, distinct = NULL,
limit = "100", offset = "0", count = "exact",
@@ -204,6 +222,10 @@ Arvados <- R6::R6Class(
#' @description
#' project_delete trashes project of a given uuid. It can be restored from trash or deleted permanently.
#' @param uuid The UUID of the Group in question.
+ #' @examples
+ #' \dontrun{
+ #' arv$project_delete(uuid = 'projectUUID')
+ #' }
project_delete = function(uuid)
{
self$groups_delete(uuid)
@@ -688,7 +710,10 @@ Arvados <- R6::R6Class(
#' @description
#' collections_get is a method defined in Arvados class.
#' @param uuid The UUID of the Collection in question.
+ #' @examples
+ #' \dontrun{
#' collection <- arv$collections_get(uuid = collectionUUID)
+ #' }
collections_get = function(uuid)
{
endPoint <- stringr::str_interp("collections/${uuid}")
@@ -718,8 +743,10 @@ Arvados <- R6::R6Class(
#' @param ensureUniqueName Adjust name to ensure uniqueness instead of returning an error.
#' @param clusterID Create object on a remote federated cluster instead of the current one.
#' @examples
+ #' \dontrun{
#' Properties <- list() # should contain a list of new properties to be added
#' arv$collections_create(name = "collectionTitle", description = "collectionDescription", ownerUUID = "collectionOwner", properties = Properties)
+ #' }
collections_create = function(name, description, ownerUUID = NULL, properties = NULL, # name and description are obligatory
ensureUniqueName = "false", clusterID = NULL)
{
@@ -760,7 +787,9 @@ Arvados <- R6::R6Class(
#' @param properties New list of properties of the collection.
#' @param uuid The UUID of the Collection in question.
#' @examples
+ #' \dontrun{
#' collection <- arv$collections_update(name = "newCollectionTitle", description = "newCollectionDescription", ownerUUID = "collectionOwner", properties = NULL, uuid = "collectionUUID")
+ #' }
collections_update = function(name, description, ownerUUID = NULL, properties = NULL, uuid)
{
endPoint <- stringr::str_interp("collections/${uuid}")
@@ -790,7 +819,9 @@ Arvados <- R6::R6Class(
#' collections_delete is a method defined in Arvados class.
#' @param uuid The UUID of the Collection in question.
#' @examples
+ #' \dontrun{
#' arv$collection_delete(collectionUUID)
+ #' }
collections_delete = function(uuid)
{
endPoint <- stringr::str_interp("collections/${uuid}")
@@ -815,7 +846,9 @@ Arvados <- R6::R6Class(
#' collections_provenance is a method defined in Arvados class, it returns the collection by uuid.
#' @param uuid The UUID of the Collection in question.
#' @examples
+ #' \dontrun{
#' collection <- arv$collections_provenance(collectionUUID)
+ #' }
collections_provenance = function(uuid)
{
endPoint <- stringr::str_interp("collections/${uuid}/provenance")
@@ -863,7 +896,9 @@ Arvados <- R6::R6Class(
#' collections_trash is a method defined in Arvados class, it moves collection to trash.
#' @param uuid The UUID of the Collection in question.
#' @examples
+ #' \dontrun{
#' arv$collections_trash(collectionUUID)
+ #' }
collections_trash = function(uuid)
{
endPoint <- stringr::str_interp("collections/${uuid}/trash")
@@ -888,7 +923,9 @@ Arvados <- R6::R6Class(
#' collections_untrash is a method defined in Arvados class, it moves collection from trash to project.
#' @param uuid The UUID of the Collection in question.
#' @examples
+ #' \dontrun{
#' arv$collections_untrash(collectionUUID)
+ #' }
collections_untrash = function(uuid)
{
endPoint <- stringr::str_interp("collections/${uuid}/untrash")
@@ -924,7 +961,9 @@ Arvados <- R6::R6Class(
#' @param includeTrash Include collections whose is_trashed attribute is true.
#' @param includeOldVersions Include past collection versions.
#' @examples
+ #' \dontrun{
#' collectionList <- arv$collections_list(list(list("name", "=", "Example")))
+ #' }
collections_list = function(filters = NULL,
where = NULL, order = NULL, select = NULL,
distinct = NULL, limit = "100", offset = "0",
@@ -1826,7 +1865,9 @@ Arvados <- R6::R6Class(
#' @param uuid The UUID of a project or a file.
#' @param user The UUID of the person that gets the permission.
#' @examples
+ #' \dontrun{
#' arv$project_permission_give(type = "can_read", uuid = objectUUID, user = userUUID)
+ #' }
project_permission_give = function(type, uuid, user)
{
endPoint <- stringr::str_interp("links")
@@ -1860,7 +1901,9 @@ Arvados <- R6::R6Class(
#' @param uuid The UUID of a project or a file.
#' @param user The UUID of a person that permissions are taken from.
#' @examples
+ #' \dontrun{
#' arv$project_permission_refuse(type = "can_read", uuid = objectUUID, user = userUUID)
+ #' }
project_permission_refuse = function(type, uuid, user)
{
examples <- self$links_list(list(list("head_uuid","=", uuid)))
@@ -1884,7 +1927,9 @@ Arvados <- R6::R6Class(
#' @param uuid The UUID of a project or a file.
#' @param user The UUID of the person that the permission is being updated.
#' @examples
+ #' \dontrun{
#' arv$project_permission_update(typeOld = "can_read", typeNew = "can_write", uuid = objectUUID, user = userUUID)
+ #' }
project_permission_update = function(typeOld, typeNew, uuid, user)
{
link <- list("name" = typeNew)
@@ -1908,7 +1953,9 @@ Arvados <- R6::R6Class(
#' @param user The UUID of the person that the permission is being updated.
#' @param type Possible options are can_read or can_write or can_manage.
#' @examples
+ #' \dontrun{
#' arv$project_permission_check(type = "can_read", uuid = objectUUID, user = userUUID)
+ #' }
project_permission_check = function(uuid, user, type = NULL)
{
examples <- self$links_list(list(list("head_uuid","=", uuid)))
diff --git a/sdk/R/R/ArvadosFile.R b/sdk/R/R/ArvadosFile.R
index 938d12a7f..f585d1f94 100644
--- a/sdk/R/R/ArvadosFile.R
+++ b/sdk/R/R/ArvadosFile.R
@@ -19,7 +19,9 @@ ArvadosFile <- R6::R6Class(
#' @param name Name of the new enviroment.
#' @return A new `ArvadosFile` object.
#' @examples
+ #' \dontrun{
#' myFile <- ArvadosFile$new("myFile")
+ #' }
initialize = function(name)
{
if(name == "")
@@ -31,14 +33,18 @@ ArvadosFile <- R6::R6Class(
#' @description
#' Returns name of the file.
#' @examples
+ #' \dontrun{
#' arvadosFile$getName()
+ #' }
getName = function() private$name,
#' @description
#' Returns collections file content as character vector.
#' @param fullPath Checking if TRUE.
#' @examples
+ #' \dontrun{
#' arvadosFile$getFileListing()
+ #' }
getFileListing = function(fullpath = TRUE)
{
self$getName()
@@ -47,7 +53,9 @@ ArvadosFile <- R6::R6Class(
#' @description
#' Returns collections content size in bytes.
#' @examples
+ #' \dontrun{
#' arvadosFile$getSizeInBytes()
+ #' }
getSizeInBytes = function()
{
if(is.null(private$collection))
@@ -112,9 +120,11 @@ ArvadosFile <- R6::R6Class(
#' @param offset Describes the location of a piece of data compared to another location
#' @param length Length of content
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, collectionUUID)
#' arvadosFile <- collection$get(fileName)
#' fileContent <- arvadosFile$read("text")
+ #' }
read = function(contentType = "raw", offset = 0, length = 0)
{
if(is.null(private$collection))
@@ -135,9 +145,11 @@ ArvadosFile <- R6::R6Class(
#' Get connection opened in "read" or "write" mode.
#' @param rw Type of connection.
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, collectionUUID)
#' arvadosFile <- collection$get(fileName)
#' arvConnection <- arvadosFile$connection("w")
+ #' }
connection = function(rw)
{
if (rw == "r" || rw == "rb")
@@ -158,10 +170,12 @@ ArvadosFile <- R6::R6Class(
#' @description
#' Write connections content to a file or override current content of the file.
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, collectionUUID)
#' arvadosFile <- collection$get(fileName)
#' myFile$write("This is new file content")
#' arvadosFile$flush()
+ #' }
flush = function()
{
v <- textConnectionValue(private$buffer)
@@ -174,9 +188,11 @@ ArvadosFile <- R6::R6Class(
#' @param content File to write.
#' @param contentType Type of content. Possible is "text", "raw".
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, collectionUUID)
#' arvadosFile <- collection$get(fileName)
#' myFile$write("This is new file content")
+ #' }
write = function(content, contentType = "text/html")
{
if(is.null(private$collection))
@@ -194,7 +210,9 @@ ArvadosFile <- R6::R6Class(
#' Moves file to a new location inside collection.
#' @param destination Path to new folder.
#' @examples
+ #' \dontrun{
#' arvadosFile$move(newPath)
+ #' }
move = function(destination)
{
if(is.null(private$collection))
@@ -231,7 +249,9 @@ ArvadosFile <- R6::R6Class(
#' Copies file to a new location inside collection.
#' @param destination Path to new folder.
#' @examples
+ #' \dontrun{
#' arvadosFile$copy("NewName.format")
+ #' }
copy = function(destination)
{
if(is.null(private$collection))
diff --git a/sdk/R/R/Collection.R b/sdk/R/R/Collection.R
index 14ab0e6f2..43a4b0b60 100644
--- a/sdk/R/R/Collection.R
+++ b/sdk/R/R/Collection.R
@@ -28,7 +28,9 @@ Collection <- R6::R6Class(
#' @param uuid The UUID Autentic for Collection UUID.
#' @return A new `Collection` object.
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, CollectionUUID)
+ #' }
initialize = function(api, uuid)
{
private$REST <- api$getRESTService()
@@ -89,6 +91,7 @@ Collection <- R6::R6Class(
#' @param Ncol Used in reading binary file to set numbers of columns in data.frame.
#' @param Nrow Used in reading binary file to set numbers of rows in data.frame size.
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, collectionUUID)
#' readFile <- collection$readArvFile(arvadosFile, istable = 'yes') # table
#' readFile <- collection$readArvFile(arvadosFile, istable = 'no') # text
@@ -96,6 +99,7 @@ Collection <- R6::R6Class(
#' readFile <- collection$readArvFile(arvadosFile, fileclass = 'fasta') # fasta
#' readFile <- collection$readArvFile(arvadosFile, Ncol= 4, Nrow = 32) # binary, only numbers
#' readFile <- collection$readArvFile(arvadosFile, Ncol = 5, Nrow = 150, istable = "factor") # binary with factor or text
+ #' }
readArvFile = function(file, con, sep = ',', istable = NULL, fileclass = "SeqFastadna", Ncol = NULL, Nrow = NULL, wantedFunction = NULL)
{
arvFile <- self$get(file)
@@ -197,6 +201,7 @@ Collection <- R6::R6Class(
#' @param file File to be saved.
#' @param istable Used in writing txt file to check if the file is table or not.
#' @examples
+ #' \dontrun{
#' collection <- Collection$new(arv, collectionUUID)
#' writeFile <- collection$writeFile(name = "myoutput.csv", file = file, fileFormat = "csv", istable = NULL, collectionUUID = collectionUUID) # csv
#' writeFile <- collection$writeFile(name = "myoutput.tsv", file = file, fileFormat = "tsv", istable = NULL, collectionUUID = collectionUUID) # tsv
@@ -205,8 +210,9 @@ Collection <- R6::R6Class(
#' writeFile <- collection$writeFile(name = "myoutputtext.txt", file = file, fileFormat = "txt", istable = "no", collectionUUID = collectionUUID) # txt text
#' writeFile <- collection$writeFile(name = "myoutputbinary.dat", file = file, fileFormat = "dat", collectionUUID = collectionUUID) # binary
#' writeFile <- collection$writeFile(name = "myoutputxlsx.xlsx", file = file, fileFormat = "xlsx", collectionUUID = collectionUUID) # xlsx
- writeFile = function(name, file, collectionUUID, fileFormat, istable = NULL, seqName = NULL) {
-
+ #' }
+ writeFile = function(name, file, collectionUUID, fileFormat, istable = NULL, seqName = NULL)
+ {
# set enviroment
ARVADOS_API_TOKEN <- Sys.getenv("ARVADOS_API_TOKEN")
ARVADOS_API_HOST <- Sys.getenv("ARVADOS_API_HOST")
@@ -247,7 +253,9 @@ Collection <- R6::R6Class(
#' Creates one or more ArvadosFiles and adds them to the collection at specified path.
#' @param files Content to be created.
#' @examples
+ #' \dontrun{
#' collection <- arv$collections_create(name = collectionTitle, description = collectionDescription, owner_uuid = collectionOwner, properties = list("ROX37196928443768648" = "ROX37742976443830153"))
+ #' }
create = function(files)
{
if(is.null(private$tree))
@@ -281,7 +289,9 @@ Collection <- R6::R6Class(
#' Remove one or more files from the collection.
#' @param paths Content to be removed.
#' @examples
+ #' \dontrun{
#' collection$remove(fileName.format)
+ #' }
remove = function(paths)
{
if(is.null(private$tree))
@@ -320,7 +330,9 @@ Collection <- R6::R6Class(
#' @param content Content to be moved.
#' @param destination Path to move content.
#' @examples
+ #' \dontrun{
#' collection$move("fileName.format", path)
+ #' }
move = function(content, destination)
{
if(is.null(private$tree))
@@ -341,7 +353,9 @@ Collection <- R6::R6Class(
#' @param content Content to be moved.
#' @param destination Path to move content.
#' @examples
+ #' \dontrun{
#' copied <- collection$copy("oldName.format", "newName.format")
+ #' }
copy = function(content, destination)
{
if(is.null(private$tree))
@@ -360,7 +374,9 @@ Collection <- R6::R6Class(
#' @description
#' Refreshes the environment.
#' @examples
+ #' \dontrun{
#' collection$refresh()
+ #' }
refresh = function()
{
if(!is.null(private$tree))
@@ -373,7 +389,9 @@ Collection <- R6::R6Class(
#' @description
#' Returns collections file content as character vector.
#' @examples
+ #' \dontrun{
#' list <- collection$getFileListing()
+ #' }
getFileListing = function()
{
if(is.null(private$tree))
@@ -387,7 +405,9 @@ Collection <- R6::R6Class(
#' If relativePath is valid, returns ArvadosFile or Subcollection specified by relativePath, else returns NULL.
#' @param relativePath Path from content is taken.
#' @examples
+ #' \dontrun{
#' arvadosFile <- collection$get(fileName)
+ #' }
get = function(relativePath)
{
if(is.null(private$tree))
diff --git a/sdk/R/README.md b/sdk/R/README.md
index 939e69b80..fe98e648c 100644
--- a/sdk/R/README.md
+++ b/sdk/R/README.md
@@ -63,41 +63,56 @@ This parameter can be set at any time using `setNumRetries`
arv$setNumRetries(5)
```
-### Working with collections
+### Working with Aravdos projects
-#### Get a collection:
+##### Create project:
```r
-collection <- arv$collections_get("uuid")
+newProject <- arv$project_create(name = "project name", description = "project description", owner_uuid = "project UUID", properties = NULL, ensureUniqueName = "false")
```
-Be aware that the result from `collections_get` is not a Collection class. The object returned from this method lets you access collection fields like “name” and “description”. The Collection class lets you access the files in the collection for reading and writing, and is described in the next section.
+##### Update project:
-#### List collections:
+```r
+updatedProject <- arv$project_update(name = "new project name", properties = newProperties, uuid = "projectUUID")
+```
+
+##### Delete a project:
```r
-# offset of 0 and default limit of 100
-collectionList <- arv$collections_list(list(list("name", "like", "Test%")))
+deletedProject <- arv$project_delete("uuid")
+```
-collectionList <- arv$collections_list(list(list("name", "like", "Test%")), limit = 10, offset = 2)
+#### Find a project:
-# count of total number of items (may be more than returned due to paging)
-collectionList$items_available
+##### Get a project:
-# items which match the filter criteria
-collectionList$items
+```r
+project <- arv$project_get("uuid")
```
-#### List all collections even if the number of items is greater than maximum API limit:
+##### List projects:
```r
-collectionList <- listAll(arv$collections_list, list(list("name", "like", "Test%")))
+list subprojects of a project
+projects <- arv$project_list(list(list("owner_uuid", "=", "aaaaa-j7d0g-ccccccccccccccc")))
+
+list projects which have names beginning with Example
+examples <- arv$project_list(list(list("name","like","Example%")))
```
-#### Delete a collection:
+##### List all projects even if the number of items is greater than maximum API limit:
```r
-deletedCollection <- arv$collections_delete("uuid")
+projects <- listAll(arv$project_list, list(list("name","like","Example%")))
+```
+
+### Working with collections
+
+#### Create a new collection:
+
+```r
+newCollection <- arv$collections_create(name = "collectionTitle", description = "collectionDescription", ownerUUID = "collectionOwner", properties = Properties)
```
#### Update a collection’s metadata:
@@ -106,10 +121,41 @@ deletedCollection <- arv$collections_delete("uuid")
collection <- arv$collections_update(name = "newCollectionTitle", description = "newCollectionDescription", ownerUUID = "collectionOwner", properties = NULL, uuid = "collectionUUID")
```
-#### Create a new collection:
+#### Delete a collection:
```r
-newCollection <- arv$collections_create(name = "collectionTitle", description = "collectionDescription", ownerUUID = "collectionOwner", properties = Properties)
+deletedCollection <- arv$collections_delete("uuid")
+```
+
+#### Find a collection:
+
+#### Get a collection:
+
+```r
+collection <- arv$collections_get("uuid")
+```
+
+Be aware that the result from `collections_get` is not a Collection class. The object returned from this method lets you access collection fields like “name” and “description”. The Collection class lets you access the files in the collection for reading and writing, and is described in the next section.
+
+#### List collections:
+
+```r
+# offset of 0 and default limit of 100
+collectionList <- arv$collections_list(list(list("name", "like", "Test%")))
+
+collectionList <- arv$collections_list(list(list("name", "like", "Test%")), limit = 10, offset = 2)
+
+# count of total number of items (may be more than returned due to paging)
+collectionList$items_available
+
+# items which match the filter criteria
+collectionList$items
+```
+
+#### List all collections even if the number of items is greater than maximum API limit:
+
+```r
+collectionList <- listAll(arv$collections_list, list(list("name", "like", "Test%")))
```
### Manipulating collection content
@@ -284,47 +330,6 @@ subcollection <- collection$get("location/to/folder")
subcollection$copy("destination/folder")
```
-### Working with Aravdos projects
-
-#### Get a project:
-
-```r
-project <- arv$project_get("uuid")
-```
-
-#### List projects:
-
-```r
-list subprojects of a project
-projects <- arv$project_list(list(list("owner_uuid", "=", "aaaaa-j7d0g-ccccccccccccccc")))
-
-list projects which have names beginning with Example
-examples <- arv$project_list(list(list("name","like","Example%")))
-```
-
-#### List all projects even if the number of items is greater than maximum API limit:
-
-```r
-projects <- listAll(arv$project_list, list(list("name","like","Example%")))
-```
-
-##### Delete a project:
-
-```r
-deletedProject <- arv$project_delete("uuid")
-```
-
-##### Update project:
-
-```r
-updatedProject <- arv$project_update(name = "new project name", properties = newProperties, uuid = "projectUUID")
-```
-
-##### Create project:
-
-```r
-newProject <- arv$project_create(name = "project name", description = "project description", owner_uuid = "project UUID", properties = NULL, ensureUniqueName = "false")
-```
### Help
-----------------------------------------------------------------------
hooks/post-receive
--
More information about the arvados-commits
mailing list