Added auto-generated documentation for Arvados class.

Arvados-DCO-1.1-Signed-off-by: Fuad Muhic <fmuhic@capeannenterprises.com>

diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R
index 66e2794c7ed688ad8a88e6356ecd1971b2172222..368ca52237c9ef079d3024eca4f5869cfb684789 100644 (file)
--- a/sdk/R/R/Arvados.R
+++ b/sdk/R/R/Arvados.R
@@ -1593,6 +1593,204 @@ NULL
 #' @name user_agreements.new
 NULL
 
+#' Arvados
+#'
+#' Arvados class gives users ability to manipulate collections and projects.
+#'
+#' @section Usage:
+#' \preformatted{arv = Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)}
+#'
+#' @section Arguments:
+#' \describe{
+#'     \item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.}
+#'     \item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.}
+#'     \item{numRetries}{Number which specifies how many times to retry failed service requests.}
+#' }
+#'
+#' @section Methods:
+#' \describe{
+#'     \item{}{\code{\link{api_client_authorizations.create}}}
+#'     \item{}{\code{\link{api_client_authorizations.create_system_auth}}}
+#'     \item{}{\code{\link{api_client_authorizations.current}}}
+#'     \item{}{\code{\link{api_client_authorizations.delete}}}
+#'     \item{}{\code{\link{api_client_authorizations.get}}}
+#'     \item{}{\code{\link{api_client_authorizations.list}}}
+#'     \item{}{\code{\link{api_client_authorizations.update}}}
+#'     \item{}{\code{\link{api_clients.create}}}
+#'     \item{}{\code{\link{api_clients.delete}}}
+#'     \item{}{\code{\link{api_clients.get}}}
+#'     \item{}{\code{\link{api_clients.list}}}
+#'     \item{}{\code{\link{api_clients.update}}}
+#'     \item{}{\code{\link{authorized_keys.create}}}
+#'     \item{}{\code{\link{authorized_keys.delete}}}
+#'     \item{}{\code{\link{authorized_keys.get}}}
+#'     \item{}{\code{\link{authorized_keys.list}}}
+#'     \item{}{\code{\link{authorized_keys.update}}}
+#'     \item{}{\code{\link{collections.create}}}
+#'     \item{}{\code{\link{collections.delete}}}
+#'     \item{}{\code{\link{collections.get}}}
+#'     \item{}{\code{\link{collections.list}}}
+#'     \item{}{\code{\link{collections.provenance}}}
+#'     \item{}{\code{\link{collections.trash}}}
+#'     \item{}{\code{\link{collections.untrash}}}
+#'     \item{}{\code{\link{collections.update}}}
+#'     \item{}{\code{\link{collections.used_by}}}
+#'     \item{}{\code{\link{container_requests.create}}}
+#'     \item{}{\code{\link{container_requests.delete}}}
+#'     \item{}{\code{\link{container_requests.get}}}
+#'     \item{}{\code{\link{container_requests.list}}}
+#'     \item{}{\code{\link{container_requests.update}}}
+#'     \item{}{\code{\link{containers.auth}}}
+#'     \item{}{\code{\link{containers.create}}}
+#'     \item{}{\code{\link{containers.current}}}
+#'     \item{}{\code{\link{containers.delete}}}
+#'     \item{}{\code{\link{containers.get}}}
+#'     \item{}{\code{\link{containers.list}}}
+#'     \item{}{\code{\link{containers.lock}}}
+#'     \item{}{\code{\link{containers.secret_mounts}}}
+#'     \item{}{\code{\link{containers.unlock}}}
+#'     \item{}{\code{\link{containers.update}}}
+#'     \item{}{\code{\link{groups.contents}}}
+#'     \item{}{\code{\link{groups.create}}}
+#'     \item{}{\code{\link{groups.delete}}}
+#'     \item{}{\code{\link{groups.get}}}
+#'     \item{}{\code{\link{groups.list}}}
+#'     \item{}{\code{\link{groups.trash}}}
+#'     \item{}{\code{\link{groups.untrash}}}
+#'     \item{}{\code{\link{groups.update}}}
+#'     \item{}{\code{\link{humans.create}}}
+#'     \item{}{\code{\link{humans.delete}}}
+#'     \item{}{\code{\link{humans.get}}}
+#'     \item{}{\code{\link{humans.list}}}
+#'     \item{}{\code{\link{humans.update}}}
+#'     \item{}{\code{\link{jobs.cancel}}}
+#'     \item{}{\code{\link{jobs.create}}}
+#'     \item{}{\code{\link{jobs.delete}}}
+#'     \item{}{\code{\link{jobs.get}}}
+#'     \item{}{\code{\link{jobs.list}}}
+#'     \item{}{\code{\link{jobs.lock}}}
+#'     \item{}{\code{\link{jobs.queue}}}
+#'     \item{}{\code{\link{jobs.queue_size}}}
+#'     \item{}{\code{\link{jobs.update}}}
+#'     \item{}{\code{\link{job_tasks.create}}}
+#'     \item{}{\code{\link{job_tasks.delete}}}
+#'     \item{}{\code{\link{job_tasks.get}}}
+#'     \item{}{\code{\link{job_tasks.list}}}
+#'     \item{}{\code{\link{job_tasks.update}}}
+#'     \item{}{\code{\link{keep_disks.create}}}
+#'     \item{}{\code{\link{keep_disks.delete}}}
+#'     \item{}{\code{\link{keep_disks.get}}}
+#'     \item{}{\code{\link{keep_disks.list}}}
+#'     \item{}{\code{\link{keep_disks.ping}}}
+#'     \item{}{\code{\link{keep_disks.update}}}
+#'     \item{}{\code{\link{keep_services.accessible}}}
+#'     \item{}{\code{\link{keep_services.create}}}
+#'     \item{}{\code{\link{keep_services.delete}}}
+#'     \item{}{\code{\link{keep_services.get}}}
+#'     \item{}{\code{\link{keep_services.list}}}
+#'     \item{}{\code{\link{keep_services.update}}}
+#'     \item{}{\code{\link{links.create}}}
+#'     \item{}{\code{\link{links.delete}}}
+#'     \item{}{\code{\link{links.get}}}
+#'     \item{}{\code{\link{links.get_permissions}}}
+#'     \item{}{\code{\link{links.list}}}
+#'     \item{}{\code{\link{links.update}}}
+#'     \item{}{\code{\link{logs.create}}}
+#'     \item{}{\code{\link{logs.delete}}}
+#'     \item{}{\code{\link{logs.get}}}
+#'     \item{}{\code{\link{logs.list}}}
+#'     \item{}{\code{\link{logs.update}}}
+#'     \item{}{\code{\link{nodes.create}}}
+#'     \item{}{\code{\link{nodes.delete}}}
+#'     \item{}{\code{\link{nodes.get}}}
+#'     \item{}{\code{\link{nodes.list}}}
+#'     \item{}{\code{\link{nodes.ping}}}
+#'     \item{}{\code{\link{nodes.update}}}
+#'     \item{}{\code{\link{pipeline_instances.cancel}}}
+#'     \item{}{\code{\link{pipeline_instances.create}}}
+#'     \item{}{\code{\link{pipeline_instances.delete}}}
+#'     \item{}{\code{\link{pipeline_instances.get}}}
+#'     \item{}{\code{\link{pipeline_instances.list}}}
+#'     \item{}{\code{\link{pipeline_instances.update}}}
+#'     \item{}{\code{\link{pipeline_templates.create}}}
+#'     \item{}{\code{\link{pipeline_templates.delete}}}
+#'     \item{}{\code{\link{pipeline_templates.get}}}
+#'     \item{}{\code{\link{pipeline_templates.list}}}
+#'     \item{}{\code{\link{pipeline_templates.update}}}
+#'     \item{}{\code{\link{projects.create}}}
+#'     \item{}{\code{\link{projects.delete}}}
+#'     \item{}{\code{\link{projects.get}}}
+#'     \item{}{\code{\link{projects.list}}}
+#'     \item{}{\code{\link{projects.update}}}
+#'     \item{}{\code{\link{repositories.create}}}
+#'     \item{}{\code{\link{repositories.delete}}}
+#'     \item{}{\code{\link{repositories.get}}}
+#'     \item{}{\code{\link{repositories.get_all_permissions}}}
+#'     \item{}{\code{\link{repositories.list}}}
+#'     \item{}{\code{\link{repositories.update}}}
+#'     \item{}{\code{\link{specimens.create}}}
+#'     \item{}{\code{\link{specimens.delete}}}
+#'     \item{}{\code{\link{specimens.get}}}
+#'     \item{}{\code{\link{specimens.list}}}
+#'     \item{}{\code{\link{specimens.update}}}
+#'     \item{}{\code{\link{traits.create}}}
+#'     \item{}{\code{\link{traits.delete}}}
+#'     \item{}{\code{\link{traits.get}}}
+#'     \item{}{\code{\link{traits.list}}}
+#'     \item{}{\code{\link{traits.update}}}
+#'     \item{}{\code{\link{user_agreements.create}}}
+#'     \item{}{\code{\link{user_agreements.delete}}}
+#'     \item{}{\code{\link{user_agreements.get}}}
+#'     \item{}{\code{\link{user_agreements.list}}}
+#'     \item{}{\code{\link{user_agreements.new}}}
+#'     \item{}{\code{\link{user_agreements.sign}}}
+#'     \item{}{\code{\link{user_agreements.signatures}}}
+#'     \item{}{\code{\link{user_agreements.update}}}
+#'     \item{}{\code{\link{users.activate}}}
+#'     \item{}{\code{\link{users.create}}}
+#'     \item{}{\code{\link{users.current}}}
+#'     \item{}{\code{\link{users.delete}}}
+#'     \item{}{\code{\link{users.get}}}
+#'     \item{}{\code{\link{users.list}}}
+#'     \item{}{\code{\link{users.setup}}}
+#'     \item{}{\code{\link{users.system}}}
+#'     \item{}{\code{\link{users.unsetup}}}
+#'     \item{}{\code{\link{users.update}}}
+#'     \item{}{\code{\link{users.update_uuid}}}
+#'     \item{}{\code{\link{virtual_machines.create}}}
+#'     \item{}{\code{\link{virtual_machines.delete}}}
+#'     \item{}{\code{\link{virtual_machines.get}}}
+#'     \item{}{\code{\link{virtual_machines.get_all_logins}}}
+#'     \item{}{\code{\link{virtual_machines.list}}}
+#'     \item{}{\code{\link{virtual_machines.logins}}}
+#'     \item{}{\code{\link{virtual_machines.update}}}
+#'     \item{}{\code{\link{workflows.create}}}
+#'     \item{}{\code{\link{workflows.delete}}}
+#'     \item{}{\code{\link{workflows.get}}}
+#'     \item{}{\code{\link{workflows.list}}}
+#'     \item{}{\code{\link{workflows.update}}}
+#' }
+#'
+#' @name Arvados
+#' @examples
+#' \dontrun{
+#' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
+#'
+#' collection <- arv$collections.get("uuid")
+#'
+#' collectionList <- arv$collections.list(list(list("name", "like", "Test%")))
+#' collectionList <- listAll(arv$collections.list, list(list("name", "like", "Test%")))
+#'
+#' deletedCollection <- arv$collections.delete("uuid")
+#'
+#' updatedCollection <- arv$collections.update(list(name = "New name", description = "New description")
+#'                                            "uuid")
+#'
+#' createdCollection <- arv$collections.create(list(name = "Example",
+#'                                                  description = "This is a test collection"))
+#' }
+NULL
+
 #' @export
 Arvados <- R6::R6Class(
 

diff --git a/sdk/R/R/autoGenAPI.R b/sdk/R/R/autoGenAPI.R
index 849875204d6f224052ce3fca2a5f6d766c30a2c4..e0ad551e1e44b863a8e21cc89641a77f3b3c8bf6 100644 (file)
--- a/sdk/R/R/autoGenAPI.R
+++ b/sdk/R/R/autoGenAPI.R
@@ -15,13 +15,15 @@ generateAPI <- function()
     methodResources <- discoveryDocument$resources
     resourceNames   <- names(methodResources)
 
-    doc <- generateMethodsDocumentation(methodResources, resourceNames)
+    methodDoc <- generateMethodsDocumentation(methodResources, resourceNames)
+    classDoc <- generateAPIClassDocumentation(methodResources, resourceNames)
     arvadosAPIHeader <- generateAPIClassHeader()
     arvadosProjectMethods <- generateProjectMethods()
     arvadosClassMethods <- generateClassContent(methodResources, resourceNames)
     arvadosAPIFooter <- generateAPIClassFooter()
 
-    arvadosClass <- c(doc,
+    arvadosClass <- c(methodDoc,
+                      classDoc,
                       arvadosAPIHeader,
                       arvadosProjectMethods,
                       arvadosClassMethods,
@@ -35,8 +37,7 @@ generateAPI <- function()
 
 generateAPIClassHeader <- function()
 {
-    c("#' @export",
-      "Arvados <- R6::R6Class(",
+    c("Arvados <- R6::R6Class(",
       "",
       "\t\"Arvados\",",
       "",
@@ -314,6 +315,7 @@ getReturnObject <- function()
 
 #NOTE: Arvados class documentation:
 
+
 generateMethodsDocumentation <- function(methodResources, resourceNames)
 {
     methodsDoc <- unlist(unname(Map(function(resource, resourceName)
@@ -340,6 +342,66 @@ generateMethodsDocumentation <- function(methodResources, resourceNames)
     methodsDoc
 }
 
+generateAPIClassDocumentation <- function(methodResources, resourceNames)
+{
+    c("#' Arvados",
+      "#'",
+      "#' Arvados class gives users ability to manipulate collections and projects.",
+      "#'" ,
+      "#' @section Usage:",
+      "#' \\preformatted{arv = Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)}",
+      "#'",
+      "#' @section Arguments:",
+      "#' \\describe{",
+      "#' \t\\item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.}",
+      "#' \t\\item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.}",
+      "#' \t\\item{numRetries}{Number which specifies how many times to retry failed service requests.}",
+      "#' }",
+      "#'",
+      "#' @section Methods:",
+      "#' \\describe{",
+      getAPIClassMethodList(methodResources, resourceNames),
+      "#' }",
+      "#'",
+      "#' @name Arvados",
+      "#' @examples",
+      "#' \\dontrun{",
+      "#' arv <- Arvados$new(\"your Arvados token\", \"example.arvadosapi.com\")",
+      "#'",
+      "#' collection <- arv$collections.get(\"uuid\")",
+      "#'",
+      "#' collectionList <- arv$collections.list(list(list(\"name\", \"like\", \"Test%\")))",
+      "#' collectionList <- listAll(arv$collections.list, list(list(\"name\", \"like\", \"Test%\")))",
+      "#'",
+      "#' deletedCollection <- arv$collections.delete(\"uuid\")",
+      "#'",
+      "#' updatedCollection <- arv$collections.update(list(name = \"New name\", description = \"New description\"),",
+      "#'                                             \"uuid\")",
+      "#'",
+      "#' createdCollection <- arv$collections.create(list(name = \"Example\",",
+      "#'                                                  description = \"This is a test collection\"))",
+      "#' }",
+      "NULL",
+      "",
+      "#' @export")
+}
+
+getAPIClassMethodList <- function(methodResources, resourceNames)
+{
+    methodList <- unlist(unname(Map(function(resource, resourceName)
+    {
+        methodNames <- names(resource$methods)
+        paste0(resourceName,
+               ".",
+               methodNames[!(methodNames %in% c("index", "show", "destroy"))])
+
+    }, methodResources, resourceNames)))
+    
+    hardcodedMethods <- c("projects.create", "projects.get",
+                          "projects.list", "projects.update", "projects.delete")
+    paste0("#' \t\\item{}{\\code{\\link{", sort(c(methodList, hardcodedMethods)), "}}}") 
+}
+
 getMethodDocumentation <- function(methodName, methodMetaData)
 {
     name        <- paste("#' @name", methodName)

diff --git a/sdk/R/man/Arvados.Rd b/sdk/R/man/Arvados.Rd
new file mode 100644 (file)
index 0000000..0128173
--- /dev/null
+++ b/sdk/R/man/Arvados.Rd
@@ -0,0 +1,206 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Arvados.R
+\name{Arvados}
+\alias{Arvados}
+\title{Arvados}
+\description{
+Arvados class gives users ability to manipulate collections and projects.
+}
+\section{Usage}{
+
+\preformatted{arv = Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)}
+}
+
+\section{Arguments}{
+
+\describe{
+       \item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.}
+       \item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.}
+       \item{numRetries}{Number which specifies how many times to retry failed service requests.}
+}
+}
+
+\section{Methods}{
+
+\describe{
+       \item{}{\code{\link{api_client_authorizations.create}}}
+       \item{}{\code{\link{api_client_authorizations.create_system_auth}}}
+       \item{}{\code{\link{api_client_authorizations.current}}}
+       \item{}{\code{\link{api_client_authorizations.delete}}}
+       \item{}{\code{\link{api_client_authorizations.get}}}
+       \item{}{\code{\link{api_client_authorizations.list}}}
+       \item{}{\code{\link{api_client_authorizations.update}}}
+       \item{}{\code{\link{api_clients.create}}}
+       \item{}{\code{\link{api_clients.delete}}}
+       \item{}{\code{\link{api_clients.get}}}
+       \item{}{\code{\link{api_clients.list}}}
+       \item{}{\code{\link{api_clients.update}}}
+       \item{}{\code{\link{authorized_keys.create}}}
+       \item{}{\code{\link{authorized_keys.delete}}}
+       \item{}{\code{\link{authorized_keys.get}}}
+       \item{}{\code{\link{authorized_keys.list}}}
+       \item{}{\code{\link{authorized_keys.update}}}
+       \item{}{\code{\link{collections.create}}}
+       \item{}{\code{\link{collections.delete}}}
+       \item{}{\code{\link{collections.get}}}
+       \item{}{\code{\link{collections.list}}}
+       \item{}{\code{\link{collections.provenance}}}
+       \item{}{\code{\link{collections.trash}}}
+       \item{}{\code{\link{collections.untrash}}}
+       \item{}{\code{\link{collections.update}}}
+       \item{}{\code{\link{collections.used_by}}}
+       \item{}{\code{\link{container_requests.create}}}
+       \item{}{\code{\link{container_requests.delete}}}
+       \item{}{\code{\link{container_requests.get}}}
+       \item{}{\code{\link{container_requests.list}}}
+       \item{}{\code{\link{container_requests.update}}}
+       \item{}{\code{\link{containers.auth}}}
+       \item{}{\code{\link{containers.create}}}
+       \item{}{\code{\link{containers.current}}}
+       \item{}{\code{\link{containers.delete}}}
+       \item{}{\code{\link{containers.get}}}
+       \item{}{\code{\link{containers.list}}}
+       \item{}{\code{\link{containers.lock}}}
+       \item{}{\code{\link{containers.secret_mounts}}}
+       \item{}{\code{\link{containers.unlock}}}
+       \item{}{\code{\link{containers.update}}}
+       \item{}{\code{\link{groups.contents}}}
+       \item{}{\code{\link{groups.create}}}
+       \item{}{\code{\link{groups.delete}}}
+       \item{}{\code{\link{groups.get}}}
+       \item{}{\code{\link{groups.list}}}
+       \item{}{\code{\link{groups.trash}}}
+       \item{}{\code{\link{groups.untrash}}}
+       \item{}{\code{\link{groups.update}}}
+       \item{}{\code{\link{humans.create}}}
+       \item{}{\code{\link{humans.delete}}}
+       \item{}{\code{\link{humans.get}}}
+       \item{}{\code{\link{humans.list}}}
+       \item{}{\code{\link{humans.update}}}
+       \item{}{\code{\link{jobs.cancel}}}
+       \item{}{\code{\link{jobs.create}}}
+       \item{}{\code{\link{jobs.delete}}}
+       \item{}{\code{\link{jobs.get}}}
+       \item{}{\code{\link{jobs.list}}}
+       \item{}{\code{\link{jobs.lock}}}
+       \item{}{\code{\link{jobs.queue}}}
+       \item{}{\code{\link{jobs.queue_size}}}
+       \item{}{\code{\link{jobs.update}}}
+       \item{}{\code{\link{job_tasks.create}}}
+       \item{}{\code{\link{job_tasks.delete}}}
+       \item{}{\code{\link{job_tasks.get}}}
+       \item{}{\code{\link{job_tasks.list}}}
+       \item{}{\code{\link{job_tasks.update}}}
+       \item{}{\code{\link{keep_disks.create}}}
+       \item{}{\code{\link{keep_disks.delete}}}
+       \item{}{\code{\link{keep_disks.get}}}
+       \item{}{\code{\link{keep_disks.list}}}
+       \item{}{\code{\link{keep_disks.ping}}}
+       \item{}{\code{\link{keep_disks.update}}}
+       \item{}{\code{\link{keep_services.accessible}}}
+       \item{}{\code{\link{keep_services.create}}}
+       \item{}{\code{\link{keep_services.delete}}}
+       \item{}{\code{\link{keep_services.get}}}
+       \item{}{\code{\link{keep_services.list}}}
+       \item{}{\code{\link{keep_services.update}}}
+       \item{}{\code{\link{links.create}}}
+       \item{}{\code{\link{links.delete}}}
+       \item{}{\code{\link{links.get}}}
+       \item{}{\code{\link{links.get_permissions}}}
+       \item{}{\code{\link{links.list}}}
+       \item{}{\code{\link{links.update}}}
+       \item{}{\code{\link{logs.create}}}
+       \item{}{\code{\link{logs.delete}}}
+       \item{}{\code{\link{logs.get}}}
+       \item{}{\code{\link{logs.list}}}
+       \item{}{\code{\link{logs.update}}}
+       \item{}{\code{\link{nodes.create}}}
+       \item{}{\code{\link{nodes.delete}}}
+       \item{}{\code{\link{nodes.get}}}
+       \item{}{\code{\link{nodes.list}}}
+       \item{}{\code{\link{nodes.ping}}}
+       \item{}{\code{\link{nodes.update}}}
+       \item{}{\code{\link{pipeline_instances.cancel}}}
+       \item{}{\code{\link{pipeline_instances.create}}}
+       \item{}{\code{\link{pipeline_instances.delete}}}
+       \item{}{\code{\link{pipeline_instances.get}}}
+       \item{}{\code{\link{pipeline_instances.list}}}
+       \item{}{\code{\link{pipeline_instances.update}}}
+       \item{}{\code{\link{pipeline_templates.create}}}
+       \item{}{\code{\link{pipeline_templates.delete}}}
+       \item{}{\code{\link{pipeline_templates.get}}}
+       \item{}{\code{\link{pipeline_templates.list}}}
+       \item{}{\code{\link{pipeline_templates.update}}}
+       \item{}{\code{\link{projects.create}}}
+       \item{}{\code{\link{projects.delete}}}
+       \item{}{\code{\link{projects.get}}}
+       \item{}{\code{\link{projects.list}}}
+       \item{}{\code{\link{projects.update}}}
+       \item{}{\code{\link{repositories.create}}}
+       \item{}{\code{\link{repositories.delete}}}
+       \item{}{\code{\link{repositories.get}}}
+       \item{}{\code{\link{repositories.get_all_permissions}}}
+       \item{}{\code{\link{repositories.list}}}
+       \item{}{\code{\link{repositories.update}}}
+       \item{}{\code{\link{specimens.create}}}
+       \item{}{\code{\link{specimens.delete}}}
+       \item{}{\code{\link{specimens.get}}}
+       \item{}{\code{\link{specimens.list}}}
+       \item{}{\code{\link{specimens.update}}}
+       \item{}{\code{\link{traits.create}}}
+       \item{}{\code{\link{traits.delete}}}
+       \item{}{\code{\link{traits.get}}}
+       \item{}{\code{\link{traits.list}}}
+       \item{}{\code{\link{traits.update}}}
+       \item{}{\code{\link{user_agreements.create}}}
+       \item{}{\code{\link{user_agreements.delete}}}
+       \item{}{\code{\link{user_agreements.get}}}
+       \item{}{\code{\link{user_agreements.list}}}
+       \item{}{\code{\link{user_agreements.new}}}
+       \item{}{\code{\link{user_agreements.sign}}}
+       \item{}{\code{\link{user_agreements.signatures}}}
+       \item{}{\code{\link{user_agreements.update}}}
+       \item{}{\code{\link{users.activate}}}
+       \item{}{\code{\link{users.create}}}
+       \item{}{\code{\link{users.current}}}
+       \item{}{\code{\link{users.delete}}}
+       \item{}{\code{\link{users.get}}}
+       \item{}{\code{\link{users.list}}}
+       \item{}{\code{\link{users.setup}}}
+       \item{}{\code{\link{users.system}}}
+       \item{}{\code{\link{users.unsetup}}}
+       \item{}{\code{\link{users.update}}}
+       \item{}{\code{\link{users.update_uuid}}}
+       \item{}{\code{\link{virtual_machines.create}}}
+       \item{}{\code{\link{virtual_machines.delete}}}
+       \item{}{\code{\link{virtual_machines.get}}}
+       \item{}{\code{\link{virtual_machines.get_all_logins}}}
+       \item{}{\code{\link{virtual_machines.list}}}
+       \item{}{\code{\link{virtual_machines.logins}}}
+       \item{}{\code{\link{virtual_machines.update}}}
+       \item{}{\code{\link{workflows.create}}}
+       \item{}{\code{\link{workflows.delete}}}
+       \item{}{\code{\link{workflows.get}}}
+       \item{}{\code{\link{workflows.list}}}
+       \item{}{\code{\link{workflows.update}}}
+}
+}
+
+\examples{
+\dontrun{
+arv <- Arvados$new("your Arvados token", "example.arvadosapi.com")
+
+collection <- arv$collections.get("uuid")
+
+collectionList <- arv$collections.list(list(list("name", "like", "Test\%")))
+collectionList <- listAll(arv$collections.list, list(list("name", "like", "Test\%")))
+
+deletedCollection <- arv$collections.delete("uuid")
+
+updatedCollection <- arv$collections.update(list(name = "New name", description = "New description")
+                                           "uuid")
+
+createdCollection <- arv$collections.create(list(name = "Example",
+                                                 description = "This is a test collection"))
+}
+}