Added project manipulation methods to autogenerated 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 c629a70ca0cb2cef31c790c32f88fc8486045c33..c69fe08490f462d01df52ff820f1aadd08e12127 100644 (file)
--- a/sdk/R/R/Arvados.R
+++ b/sdk/R/R/Arvados.R
@@ -241,17 +241,17 @@ NULL
 #' @name api_client_authorizations.destroy
 NULL
 
-#' api_clients.get is a method defined in Arvados class.
+#' containers.get is a method defined in Arvados class.
 #' 
-#' @usage arv$api_clients.get(uuid)
-#' @param uuid The UUID of the ApiClient in question.
-#' @return ApiClient object.
-#' @name api_clients.get
+#' @usage arv$containers.get(uuid)
+#' @param uuid The UUID of the Container in question.
+#' @return Container object.
+#' @name containers.get
 NULL
 
-#' api_clients.index is a method defined in Arvados class.
+#' containers.index is a method defined in Arvados class.
 #' 
-#' @usage arv$api_clients.index(filters = NULL,
+#' @usage arv$containers.index(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
 #'     count = "exact")
@@ -263,41 +263,80 @@ NULL
 #' @param limit 
 #' @param offset 
 #' @param count 
-#' @return ApiClientList object.
-#' @name api_clients.index
+#' @return ContainerList object.
+#' @name containers.index
 NULL
 
-#' api_clients.create is a method defined in Arvados class.
+#' containers.create is a method defined in Arvados class.
 #' 
-#' @usage arv$api_clients.create(apiclient,
+#' @usage arv$containers.create(container,
 #'     ensure_unique_name = "false")
-#' @param apiClient ApiClient object.
+#' @param container Container object.
 #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @return ApiClient object.
-#' @name api_clients.create
+#' @return Container object.
+#' @name containers.create
 NULL
 
-#' api_clients.update is a method defined in Arvados class.
+#' containers.update is a method defined in Arvados class.
 #' 
-#' @usage arv$api_clients.update(apiclient,
+#' @usage arv$containers.update(container,
 #'     uuid)
-#' @param apiClient ApiClient object.
-#' @param uuid The UUID of the ApiClient in question.
-#' @return ApiClient object.
-#' @name api_clients.update
+#' @param container Container object.
+#' @param uuid The UUID of the Container in question.
+#' @return Container object.
+#' @name containers.update
 NULL
 
-#' api_clients.delete is a method defined in Arvados class.
+#' containers.delete is a method defined in Arvados class.
 #' 
-#' @usage arv$api_clients.delete(uuid)
-#' @param uuid The UUID of the ApiClient in question.
-#' @return ApiClient object.
-#' @name api_clients.delete
+#' @usage arv$containers.delete(uuid)
+#' @param uuid The UUID of the Container in question.
+#' @return Container object.
+#' @name containers.delete
 NULL
 
-#' api_clients.list is a method defined in Arvados class.
+#' containers.auth is a method defined in Arvados class.
 #' 
-#' @usage arv$api_clients.list(filters = NULL,
+#' @usage arv$containers.auth(uuid)
+#' @param uuid 
+#' @return Container object.
+#' @name containers.auth
+NULL
+
+#' containers.lock is a method defined in Arvados class.
+#' 
+#' @usage arv$containers.lock(uuid)
+#' @param uuid 
+#' @return Container object.
+#' @name containers.lock
+NULL
+
+#' containers.unlock is a method defined in Arvados class.
+#' 
+#' @usage arv$containers.unlock(uuid)
+#' @param uuid 
+#' @return Container object.
+#' @name containers.unlock
+NULL
+
+#' containers.secret_mounts is a method defined in Arvados class.
+#' 
+#' @usage arv$containers.secret_mounts(uuid)
+#' @param uuid 
+#' @return Container object.
+#' @name containers.secret_mounts
+NULL
+
+#' containers.current is a method defined in Arvados class.
+#' 
+#' @usage arv$containers.current(NULL)
+#' @return Container object.
+#' @name containers.current
+NULL
+
+#' containers.list is a method defined in Arvados class.
+#' 
+#' @usage arv$containers.list(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
 #'     count = "exact")
@@ -309,37 +348,37 @@ NULL
 #' @param limit 
 #' @param offset 
 #' @param count 
-#' @return ApiClientList object.
-#' @name api_clients.list
+#' @return ContainerList object.
+#' @name containers.list
 NULL
 
-#' api_clients.show is a method defined in Arvados class.
+#' containers.show is a method defined in Arvados class.
 #' 
-#' @usage arv$api_clients.show(uuid)
+#' @usage arv$containers.show(uuid)
 #' @param uuid 
-#' @return ApiClient object.
-#' @name api_clients.show
+#' @return Container object.
+#' @name containers.show
 NULL
 
-#' api_clients.destroy is a method defined in Arvados class.
+#' containers.destroy is a method defined in Arvados class.
 #' 
-#' @usage arv$api_clients.destroy(uuid)
+#' @usage arv$containers.destroy(uuid)
 #' @param uuid 
-#' @return ApiClient object.
-#' @name api_clients.destroy
+#' @return Container object.
+#' @name containers.destroy
 NULL
 
-#' container_requests.get is a method defined in Arvados class.
+#' api_clients.get is a method defined in Arvados class.
 #' 
-#' @usage arv$container_requests.get(uuid)
-#' @param uuid The UUID of the ContainerRequest in question.
-#' @return ContainerRequest object.
-#' @name container_requests.get
+#' @usage arv$api_clients.get(uuid)
+#' @param uuid The UUID of the ApiClient in question.
+#' @return ApiClient object.
+#' @name api_clients.get
 NULL
 
-#' container_requests.index is a method defined in Arvados class.
+#' api_clients.index is a method defined in Arvados class.
 #' 
-#' @usage arv$container_requests.index(filters = NULL,
+#' @usage arv$api_clients.index(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
 #'     count = "exact")
@@ -351,41 +390,41 @@ NULL
 #' @param limit 
 #' @param offset 
 #' @param count 
-#' @return ContainerRequestList object.
-#' @name container_requests.index
+#' @return ApiClientList object.
+#' @name api_clients.index
 NULL
 
-#' container_requests.create is a method defined in Arvados class.
+#' api_clients.create is a method defined in Arvados class.
 #' 
-#' @usage arv$container_requests.create(containerrequest,
+#' @usage arv$api_clients.create(apiclient,
 #'     ensure_unique_name = "false")
-#' @param containerRequest ContainerRequest object.
+#' @param apiClient ApiClient object.
 #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @return ContainerRequest object.
-#' @name container_requests.create
+#' @return ApiClient object.
+#' @name api_clients.create
 NULL
 
-#' container_requests.update is a method defined in Arvados class.
+#' api_clients.update is a method defined in Arvados class.
 #' 
-#' @usage arv$container_requests.update(containerrequest,
+#' @usage arv$api_clients.update(apiclient,
 #'     uuid)
-#' @param containerRequest ContainerRequest object.
-#' @param uuid The UUID of the ContainerRequest in question.
-#' @return ContainerRequest object.
-#' @name container_requests.update
+#' @param apiClient ApiClient object.
+#' @param uuid The UUID of the ApiClient in question.
+#' @return ApiClient object.
+#' @name api_clients.update
 NULL
 
-#' container_requests.delete is a method defined in Arvados class.
+#' api_clients.delete is a method defined in Arvados class.
 #' 
-#' @usage arv$container_requests.delete(uuid)
-#' @param uuid The UUID of the ContainerRequest in question.
-#' @return ContainerRequest object.
-#' @name container_requests.delete
+#' @usage arv$api_clients.delete(uuid)
+#' @param uuid The UUID of the ApiClient in question.
+#' @return ApiClient object.
+#' @name api_clients.delete
 NULL
 
-#' container_requests.list is a method defined in Arvados class.
+#' api_clients.list is a method defined in Arvados class.
 #' 
-#' @usage arv$container_requests.list(filters = NULL,
+#' @usage arv$api_clients.list(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
 #'     count = "exact")
@@ -397,24 +436,24 @@ NULL
 #' @param limit 
 #' @param offset 
 #' @param count 
-#' @return ContainerRequestList object.
-#' @name container_requests.list
+#' @return ApiClientList object.
+#' @name api_clients.list
 NULL
 
-#' container_requests.show is a method defined in Arvados class.
+#' api_clients.show is a method defined in Arvados class.
 #' 
-#' @usage arv$container_requests.show(uuid)
+#' @usage arv$api_clients.show(uuid)
 #' @param uuid 
-#' @return ContainerRequest object.
-#' @name container_requests.show
+#' @return ApiClient object.
+#' @name api_clients.show
 NULL
 
-#' container_requests.destroy is a method defined in Arvados class.
+#' api_clients.destroy is a method defined in Arvados class.
 #' 
-#' @usage arv$container_requests.destroy(uuid)
+#' @usage arv$api_clients.destroy(uuid)
 #' @param uuid 
-#' @return ContainerRequest object.
-#' @name container_requests.destroy
+#' @return ApiClient object.
+#' @name api_clients.destroy
 NULL
 
 #' authorized_keys.get is a method defined in Arvados class.
@@ -505,20 +544,20 @@ NULL
 #' @name authorized_keys.destroy
 NULL
 
-#' collections.get is a method defined in Arvados class.
+#' container_requests.get is a method defined in Arvados class.
 #' 
-#' @usage arv$collections.get(uuid)
-#' @param uuid The UUID of the Collection in question.
-#' @return Collection object.
-#' @name collections.get
+#' @usage arv$container_requests.get(uuid)
+#' @param uuid The UUID of the ContainerRequest in question.
+#' @return ContainerRequest object.
+#' @name container_requests.get
 NULL
 
-#' collections.index is a method defined in Arvados class.
+#' container_requests.index is a method defined in Arvados class.
 #' 
-#' @usage arv$collections.index(filters = NULL,
+#' @usage arv$container_requests.index(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
-#'     count = "exact", include_trash = NULL)
+#'     count = "exact")
 #' @param filters 
 #' @param where 
 #' @param order 
@@ -527,77 +566,44 @@ NULL
 #' @param limit 
 #' @param offset 
 #' @param count 
-#' @param include_trash Include collections whose is_trashed attribute is true.
-#' @return CollectionList object.
-#' @name collections.index
+#' @return ContainerRequestList object.
+#' @name container_requests.index
 NULL
 
-#' collections.create is a method defined in Arvados class.
+#' container_requests.create is a method defined in Arvados class.
 #' 
-#' @usage arv$collections.create(collection,
+#' @usage arv$container_requests.create(containerrequest,
 #'     ensure_unique_name = "false")
-#' @param collection Collection object.
+#' @param containerRequest ContainerRequest object.
 #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @return Collection object.
-#' @name collections.create
+#' @return ContainerRequest object.
+#' @name container_requests.create
 NULL
 
-#' collections.update is a method defined in Arvados class.
+#' container_requests.update is a method defined in Arvados class.
 #' 
-#' @usage arv$collections.update(collection,
+#' @usage arv$container_requests.update(containerrequest,
 #'     uuid)
-#' @param collection Collection object.
-#' @param uuid The UUID of the Collection in question.
-#' @return Collection object.
-#' @name collections.update
-NULL
-
-#' collections.delete is a method defined in Arvados class.
-#' 
-#' @usage arv$collections.delete(uuid)
-#' @param uuid The UUID of the Collection in question.
-#' @return Collection object.
-#' @name collections.delete
-NULL
-
-#' collections.provenance is a method defined in Arvados class.
-#' 
-#' @usage arv$collections.provenance(uuid)
-#' @param uuid 
-#' @return Collection object.
-#' @name collections.provenance
-NULL
-
-#' collections.used_by is a method defined in Arvados class.
-#' 
-#' @usage arv$collections.used_by(uuid)
-#' @param uuid 
-#' @return Collection object.
-#' @name collections.used_by
-NULL
-
-#' collections.trash is a method defined in Arvados class.
-#' 
-#' @usage arv$collections.trash(uuid)
-#' @param uuid 
-#' @return Collection object.
-#' @name collections.trash
+#' @param containerRequest ContainerRequest object.
+#' @param uuid The UUID of the ContainerRequest in question.
+#' @return ContainerRequest object.
+#' @name container_requests.update
 NULL
 
-#' collections.untrash is a method defined in Arvados class.
+#' container_requests.delete is a method defined in Arvados class.
 #' 
-#' @usage arv$collections.untrash(uuid)
-#' @param uuid 
-#' @return Collection object.
-#' @name collections.untrash
+#' @usage arv$container_requests.delete(uuid)
+#' @param uuid The UUID of the ContainerRequest in question.
+#' @return ContainerRequest object.
+#' @name container_requests.delete
 NULL
 
-#' collections.list is a method defined in Arvados class.
+#' container_requests.list is a method defined in Arvados class.
 #' 
-#' @usage arv$collections.list(filters = NULL,
+#' @usage arv$container_requests.list(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
-#'     count = "exact", include_trash = NULL)
+#'     count = "exact")
 #' @param filters 
 #' @param where 
 #' @param order 
@@ -606,41 +612,40 @@ NULL
 #' @param limit 
 #' @param offset 
 #' @param count 
-#' @param include_trash Include collections whose is_trashed attribute is true.
-#' @return CollectionList object.
-#' @name collections.list
+#' @return ContainerRequestList object.
+#' @name container_requests.list
 NULL
 
-#' collections.show is a method defined in Arvados class.
+#' container_requests.show is a method defined in Arvados class.
 #' 
-#' @usage arv$collections.show(uuid)
+#' @usage arv$container_requests.show(uuid)
 #' @param uuid 
-#' @return Collection object.
-#' @name collections.show
+#' @return ContainerRequest object.
+#' @name container_requests.show
 NULL
 
-#' collections.destroy is a method defined in Arvados class.
+#' container_requests.destroy is a method defined in Arvados class.
 #' 
-#' @usage arv$collections.destroy(uuid)
+#' @usage arv$container_requests.destroy(uuid)
 #' @param uuid 
-#' @return Collection object.
-#' @name collections.destroy
+#' @return ContainerRequest object.
+#' @name container_requests.destroy
 NULL
 
-#' containers.get is a method defined in Arvados class.
+#' collections.get is a method defined in Arvados class.
 #' 
-#' @usage arv$containers.get(uuid)
-#' @param uuid The UUID of the Container in question.
-#' @return Container object.
-#' @name containers.get
+#' @usage arv$collections.get(uuid)
+#' @param uuid The UUID of the Collection in question.
+#' @return Collection object.
+#' @name collections.get
 NULL
 
-#' containers.index is a method defined in Arvados class.
+#' collections.index is a method defined in Arvados class.
 #' 
-#' @usage arv$containers.index(filters = NULL,
+#' @usage arv$collections.index(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
-#'     count = "exact")
+#'     count = "exact", include_trash = NULL)
 #' @param filters 
 #' @param where 
 #' @param order 
@@ -649,75 +654,77 @@ NULL
 #' @param limit 
 #' @param offset 
 #' @param count 
-#' @return ContainerList object.
-#' @name containers.index
+#' @param include_trash Include collections whose is_trashed attribute is true.
+#' @return CollectionList object.
+#' @name collections.index
 NULL
 
-#' containers.create is a method defined in Arvados class.
+#' collections.create is a method defined in Arvados class.
 #' 
-#' @usage arv$containers.create(container,
+#' @usage arv$collections.create(collection,
 #'     ensure_unique_name = "false")
-#' @param container Container object.
+#' @param collection Collection object.
 #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision.
-#' @return Container object.
-#' @name containers.create
+#' @return Collection object.
+#' @name collections.create
 NULL
 
-#' containers.update is a method defined in Arvados class.
+#' collections.update is a method defined in Arvados class.
 #' 
-#' @usage arv$containers.update(container,
+#' @usage arv$collections.update(collection,
 #'     uuid)
-#' @param container Container object.
-#' @param uuid The UUID of the Container in question.
-#' @return Container object.
-#' @name containers.update
+#' @param collection Collection object.
+#' @param uuid The UUID of the Collection in question.
+#' @return Collection object.
+#' @name collections.update
 NULL
 
-#' containers.delete is a method defined in Arvados class.
+#' collections.delete is a method defined in Arvados class.
 #' 
-#' @usage arv$containers.delete(uuid)
-#' @param uuid The UUID of the Container in question.
-#' @return Container object.
-#' @name containers.delete
+#' @usage arv$collections.delete(uuid)
+#' @param uuid The UUID of the Collection in question.
+#' @return Collection object.
+#' @name collections.delete
 NULL
 
-#' containers.auth is a method defined in Arvados class.
+#' collections.provenance is a method defined in Arvados class.
 #' 
-#' @usage arv$containers.auth(uuid)
+#' @usage arv$collections.provenance(uuid)
 #' @param uuid 
-#' @return Container object.
-#' @name containers.auth
+#' @return Collection object.
+#' @name collections.provenance
 NULL
 
-#' containers.lock is a method defined in Arvados class.
+#' collections.used_by is a method defined in Arvados class.
 #' 
-#' @usage arv$containers.lock(uuid)
+#' @usage arv$collections.used_by(uuid)
 #' @param uuid 
-#' @return Container object.
-#' @name containers.lock
+#' @return Collection object.
+#' @name collections.used_by
 NULL
 
-#' containers.unlock is a method defined in Arvados class.
+#' collections.trash is a method defined in Arvados class.
 #' 
-#' @usage arv$containers.unlock(uuid)
+#' @usage arv$collections.trash(uuid)
 #' @param uuid 
-#' @return Container object.
-#' @name containers.unlock
+#' @return Collection object.
+#' @name collections.trash
 NULL
 
-#' containers.current is a method defined in Arvados class.
+#' collections.untrash is a method defined in Arvados class.
 #' 
-#' @usage arv$containers.current(NULL)
-#' @return Container object.
-#' @name containers.current
+#' @usage arv$collections.untrash(uuid)
+#' @param uuid 
+#' @return Collection object.
+#' @name collections.untrash
 NULL
 
-#' containers.list is a method defined in Arvados class.
+#' collections.list is a method defined in Arvados class.
 #' 
-#' @usage arv$containers.list(filters = NULL,
+#' @usage arv$collections.list(filters = NULL,
 #'     where = NULL, order = NULL, select = NULL,
 #'     distinct = NULL, limit = "100", offset = "0",
-#'     count = "exact")
+#'     count = "exact", include_trash = NULL)
 #' @param filters 
 #' @param where 
 #' @param order 
@@ -726,24 +733,25 @@ NULL
 #' @param limit 
 #' @param offset 
 #' @param count 
-#' @return ContainerList object.
-#' @name containers.list
+#' @param include_trash Include collections whose is_trashed attribute is true.
+#' @return CollectionList object.
+#' @name collections.list
 NULL
 
-#' containers.show is a method defined in Arvados class.
+#' collections.show is a method defined in Arvados class.
 #' 
-#' @usage arv$containers.show(uuid)
+#' @usage arv$collections.show(uuid)
 #' @param uuid 
-#' @return Container object.
-#' @name containers.show
+#' @return Collection object.
+#' @name collections.show
 NULL
 
-#' containers.destroy is a method defined in Arvados class.
+#' collections.destroy is a method defined in Arvados class.
 #' 
-#' @usage arv$containers.destroy(uuid)
+#' @usage arv$collections.destroy(uuid)
 #' @param uuid 
-#' @return Container object.
-#' @name containers.destroy
+#' @return Collection object.
+#' @name collections.destroy
 NULL
 
 #' humans.get is a method defined in Arvados class.
@@ -2435,6 +2443,38 @@ Arvados <- R6::R6Class(
 
                },
 
+               project.get = function(uuid)
+               {
+                       self$groups.get(uuid)
+               },
+
+               project.create = function(group, ensure_unique_name = "false")
+               {
+                       group <- c("group_class" = "project", group)
+                       self$groups.create(group, ensure_unique_name)
+               },
+
+               project.update = function(group, uuid)
+               {
+                       group <- c("group_class" = "project", group)
+                       self$groups.update(group, uuid)
+               },
+
+               project.list = function(filters = NULL, where = NULL,
+                       order = NULL, select = NULL, distinct = NULL,
+                       limit = "100", offset = "0", count = "exact",
+                       include_trash = NULL)
+               {
+                       filters[[length(filters) + 1]] <- list("group_class", "=", "project")
+                       self$groups.list(filters, where, order, select, distinct,
+                                        limit, offset, count, include_trash)
+               },
+
+               project.delete = function(uuid)
+               {
+                       self$groups.delete(uuid)
+               },
+
                users.get = function(uuid)
                {
                        endPoint <- stringr::str_interp("users/${uuid}")
@@ -2954,9 +2994,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               api_clients.get = function(uuid)
+               containers.get = function(uuid)
                {
-                       endPoint <- stringr::str_interp("api_clients/${uuid}")
+                       endPoint <- stringr::str_interp("containers/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -2974,12 +3014,12 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               api_clients.index = function(filters = NULL,
+               containers.index = function(filters = NULL,
                        where = NULL, order = NULL, select = NULL,
                        distinct = NULL, limit = "100", offset = "0",
                        count = "exact")
                {
-                       endPoint <- stringr::str_interp("api_clients")
+                       endPoint <- stringr::str_interp("containers")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -2999,16 +3039,16 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               api_clients.create = function(apiclient, ensure_unique_name = "false")
+               containers.create = function(container, ensure_unique_name = "false")
                {
-                       endPoint <- stringr::str_interp("api_clients")
+                       endPoint <- stringr::str_interp("containers")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
                        
-                       if(length(apiclient) > 0)
-                               body <- jsonlite::toJSON(list(apiclient = apiclient), 
+                       if(length(container) > 0)
+                               body <- jsonlite::toJSON(list(container = container), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
@@ -3023,16 +3063,16 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               api_clients.update = function(apiclient, uuid)
+               containers.update = function(container, uuid)
                {
-                       endPoint <- stringr::str_interp("api_clients/${uuid}")
+                       endPoint <- stringr::str_interp("containers/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
                        
-                       if(length(apiclient) > 0)
-                               body <- jsonlite::toJSON(list(apiclient = apiclient), 
+                       if(length(container) > 0)
+                               body <- jsonlite::toJSON(list(container = container), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
@@ -3047,9 +3087,109 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               api_clients.delete = function(uuid)
+               containers.delete = function(uuid)
                {
-                       endPoint <- stringr::str_interp("api_clients/${uuid}")
+                       endPoint <- stringr::str_interp("containers/${uuid}")
+                       url <- paste0(private$host, endPoint)
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
+                                       "Content-Type" = "application/json")
+                       queryArgs <- NULL
+                       
+                       body <- NULL
+                       
+                       response <- private$REST$http$exec("DELETE", url, headers, body,
+                                                          queryArgs, private$numRetries)
+                       resource <- private$REST$httpParser$parseJSONResponse(response)
+                       
+                       if(!is.null(resource$errors))
+                               stop(resource$errors)
+                       
+                       resource
+               },
+
+               containers.auth = function(uuid)
+               {
+                       endPoint <- stringr::str_interp("containers/${uuid}/auth")
+                       url <- paste0(private$host, endPoint)
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
+                                       "Content-Type" = "application/json")
+                       queryArgs <- NULL
+                       
+                       body <- NULL
+                       
+                       response <- private$REST$http$exec("GET", url, headers, body,
+                                                          queryArgs, private$numRetries)
+                       resource <- private$REST$httpParser$parseJSONResponse(response)
+                       
+                       if(!is.null(resource$errors))
+                               stop(resource$errors)
+                       
+                       resource
+               },
+
+               containers.lock = function(uuid)
+               {
+                       endPoint <- stringr::str_interp("containers/${uuid}/lock")
+                       url <- paste0(private$host, endPoint)
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
+                                       "Content-Type" = "application/json")
+                       queryArgs <- NULL
+                       
+                       body <- NULL
+                       
+                       response <- private$REST$http$exec("POST", url, headers, body,
+                                                          queryArgs, private$numRetries)
+                       resource <- private$REST$httpParser$parseJSONResponse(response)
+                       
+                       if(!is.null(resource$errors))
+                               stop(resource$errors)
+                       
+                       resource
+               },
+
+               containers.unlock = function(uuid)
+               {
+                       endPoint <- stringr::str_interp("containers/${uuid}/unlock")
+                       url <- paste0(private$host, endPoint)
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
+                                       "Content-Type" = "application/json")
+                       queryArgs <- NULL
+                       
+                       body <- NULL
+                       
+                       response <- private$REST$http$exec("POST", url, headers, body,
+                                                          queryArgs, private$numRetries)
+                       resource <- private$REST$httpParser$parseJSONResponse(response)
+                       
+                       if(!is.null(resource$errors))
+                               stop(resource$errors)
+                       
+                       resource
+               },
+
+               containers.secret_mounts = function(uuid)
+               {
+                       endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts")
+                       url <- paste0(private$host, endPoint)
+                       headers <- list(Authorization = paste("OAuth2", private$token), 
+                                       "Content-Type" = "application/json")
+                       queryArgs <- NULL
+                       
+                       body <- NULL
+                       
+                       response <- private$REST$http$exec("GET", url, headers, body,
+                                                          queryArgs, private$numRetries)
+                       resource <- private$REST$httpParser$parseJSONResponse(response)
+                       
+                       if(!is.null(resource$errors))
+                               stop(resource$errors)
+                       
+                       resource
+               },
+
+               containers.current = function()
+               {
+                       endPoint <- stringr::str_interp("containers/current")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3057,7 +3197,7 @@ Arvados <- R6::R6Class(
                        
                        body <- NULL
                        
-                       response <- private$REST$http$exec("DELETE", url, headers, body,
+                       response <- private$REST$http$exec("GET", url, headers, body,
                                                           queryArgs, private$numRetries)
                        resource <- private$REST$httpParser$parseJSONResponse(response)
                        
@@ -3067,12 +3207,12 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               api_clients.list = function(filters = NULL,
+               containers.list = function(filters = NULL,
                        where = NULL, order = NULL, select = NULL,
                        distinct = NULL, limit = "100", offset = "0",
                        count = "exact")
                {
-                       endPoint <- stringr::str_interp("api_clients")
+                       endPoint <- stringr::str_interp("containers")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3092,9 +3232,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               api_clients.show = function(uuid)
+               containers.show = function(uuid)
                {
-                       endPoint <- stringr::str_interp("api_clients/${uuid}")
+                       endPoint <- stringr::str_interp("containers/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3112,9 +3252,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               api_clients.destroy = function(uuid)
+               containers.destroy = function(uuid)
                {
-                       endPoint <- stringr::str_interp("api_clients/${uuid}")
+                       endPoint <- stringr::str_interp("containers/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3132,9 +3272,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               container_requests.get = function(uuid)
+               api_clients.get = function(uuid)
                {
-                       endPoint <- stringr::str_interp("container_requests/${uuid}")
+                       endPoint <- stringr::str_interp("api_clients/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3152,12 +3292,12 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               container_requests.index = function(filters = NULL,
+               api_clients.index = function(filters = NULL,
                        where = NULL, order = NULL, select = NULL,
                        distinct = NULL, limit = "100", offset = "0",
                        count = "exact")
                {
-                       endPoint <- stringr::str_interp("container_requests")
+                       endPoint <- stringr::str_interp("api_clients")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3177,17 +3317,16 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               container_requests.create = function(containerrequest,
-                       ensure_unique_name = "false")
+               api_clients.create = function(apiclient, ensure_unique_name = "false")
                {
-                       endPoint <- stringr::str_interp("container_requests")
+                       endPoint <- stringr::str_interp("api_clients")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
                        
-                       if(length(containerrequest) > 0)
-                               body <- jsonlite::toJSON(list(containerrequest = containerrequest), 
+                       if(length(apiclient) > 0)
+                               body <- jsonlite::toJSON(list(apiclient = apiclient), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
@@ -3202,16 +3341,16 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               container_requests.update = function(containerrequest, uuid)
+               api_clients.update = function(apiclient, uuid)
                {
-                       endPoint <- stringr::str_interp("container_requests/${uuid}")
+                       endPoint <- stringr::str_interp("api_clients/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
                        
-                       if(length(containerrequest) > 0)
-                               body <- jsonlite::toJSON(list(containerrequest = containerrequest), 
+                       if(length(apiclient) > 0)
+                               body <- jsonlite::toJSON(list(apiclient = apiclient), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
@@ -3226,9 +3365,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               container_requests.delete = function(uuid)
+               api_clients.delete = function(uuid)
                {
-                       endPoint <- stringr::str_interp("container_requests/${uuid}")
+                       endPoint <- stringr::str_interp("api_clients/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3246,12 +3385,12 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               container_requests.list = function(filters = NULL,
+               api_clients.list = function(filters = NULL,
                        where = NULL, order = NULL, select = NULL,
                        distinct = NULL, limit = "100", offset = "0",
                        count = "exact")
                {
-                       endPoint <- stringr::str_interp("container_requests")
+                       endPoint <- stringr::str_interp("api_clients")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3271,9 +3410,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               container_requests.show = function(uuid)
+               api_clients.show = function(uuid)
                {
-                       endPoint <- stringr::str_interp("container_requests/${uuid}")
+                       endPoint <- stringr::str_interp("api_clients/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3291,9 +3430,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               container_requests.destroy = function(uuid)
+               api_clients.destroy = function(uuid)
                {
-                       endPoint <- stringr::str_interp("container_requests/${uuid}")
+                       endPoint <- stringr::str_interp("api_clients/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3490,9 +3629,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               collections.get = function(uuid)
+               container_requests.get = function(uuid)
                {
-                       endPoint <- stringr::str_interp("collections/${uuid}")
+                       endPoint <- stringr::str_interp("container_requests/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3510,19 +3649,18 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               collections.index = function(filters = NULL,
+               container_requests.index = function(filters = NULL,
                        where = NULL, order = NULL, select = NULL,
                        distinct = NULL, limit = "100", offset = "0",
-                       count = "exact", include_trash = NULL)
+                       count = "exact")
                {
-                       endPoint <- stringr::str_interp("collections")
+                       endPoint <- stringr::str_interp("container_requests")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
-                                                         limit = limit, offset = offset, count = count,
-                                                         include_trash = include_trash)
+                                                         limit = limit, offset = offset, count = count)
                        
                        body <- NULL
                        
@@ -3536,16 +3674,17 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               collections.create = function(collection, ensure_unique_name = "false")
+               container_requests.create = function(containerrequest,
+                       ensure_unique_name = "false")
                {
-                       endPoint <- stringr::str_interp("collections")
+                       endPoint <- stringr::str_interp("container_requests")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
                        
-                       if(length(collection) > 0)
-                               body <- jsonlite::toJSON(list(collection = collection), 
+                       if(length(containerrequest) > 0)
+                               body <- jsonlite::toJSON(list(containerrequest = containerrequest), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
@@ -3560,16 +3699,16 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               collections.update = function(collection, uuid)
+               container_requests.update = function(containerrequest, uuid)
                {
-                       endPoint <- stringr::str_interp("collections/${uuid}")
+                       endPoint <- stringr::str_interp("container_requests/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
                        
-                       if(length(collection) > 0)
-                               body <- jsonlite::toJSON(list(collection = collection), 
+                       if(length(containerrequest) > 0)
+                               body <- jsonlite::toJSON(list(containerrequest = containerrequest), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
@@ -3584,9 +3723,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               collections.delete = function(uuid)
+               container_requests.delete = function(uuid)
                {
-                       endPoint <- stringr::str_interp("collections/${uuid}")
+                       endPoint <- stringr::str_interp("container_requests/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3604,99 +3743,18 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               collections.provenance = function(uuid)
-               {
-                       endPoint <- stringr::str_interp("collections/${uuid}/provenance")
-                       url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token), 
-                                       "Content-Type" = "application/json")
-                       queryArgs <- NULL
-                       
-                       body <- NULL
-                       
-                       response <- private$REST$http$exec("GET", url, headers, body,
-                                                          queryArgs, private$numRetries)
-                       resource <- private$REST$httpParser$parseJSONResponse(response)
-                       
-                       if(!is.null(resource$errors))
-                               stop(resource$errors)
-                       
-                       resource
-               },
-
-               collections.used_by = function(uuid)
-               {
-                       endPoint <- stringr::str_interp("collections/${uuid}/used_by")
-                       url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token), 
-                                       "Content-Type" = "application/json")
-                       queryArgs <- NULL
-                       
-                       body <- NULL
-                       
-                       response <- private$REST$http$exec("GET", url, headers, body,
-                                                          queryArgs, private$numRetries)
-                       resource <- private$REST$httpParser$parseJSONResponse(response)
-                       
-                       if(!is.null(resource$errors))
-                               stop(resource$errors)
-                       
-                       resource
-               },
-
-               collections.trash = function(uuid)
-               {
-                       endPoint <- stringr::str_interp("collections/${uuid}/trash")
-                       url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token), 
-                                       "Content-Type" = "application/json")
-                       queryArgs <- NULL
-                       
-                       body <- NULL
-                       
-                       response <- private$REST$http$exec("POST", url, headers, body,
-                                                          queryArgs, private$numRetries)
-                       resource <- private$REST$httpParser$parseJSONResponse(response)
-                       
-                       if(!is.null(resource$errors))
-                               stop(resource$errors)
-                       
-                       resource
-               },
-
-               collections.untrash = function(uuid)
-               {
-                       endPoint <- stringr::str_interp("collections/${uuid}/untrash")
-                       url <- paste0(private$host, endPoint)
-                       headers <- list(Authorization = paste("OAuth2", private$token), 
-                                       "Content-Type" = "application/json")
-                       queryArgs <- NULL
-                       
-                       body <- NULL
-                       
-                       response <- private$REST$http$exec("POST", url, headers, body,
-                                                          queryArgs, private$numRetries)
-                       resource <- private$REST$httpParser$parseJSONResponse(response)
-                       
-                       if(!is.null(resource$errors))
-                               stop(resource$errors)
-                       
-                       resource
-               },
-
-               collections.list = function(filters = NULL,
+               container_requests.list = function(filters = NULL,
                        where = NULL, order = NULL, select = NULL,
                        distinct = NULL, limit = "100", offset = "0",
-                       count = "exact", include_trash = NULL)
+                       count = "exact")
                {
-                       endPoint <- stringr::str_interp("collections")
+                       endPoint <- stringr::str_interp("container_requests")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
-                                                         limit = limit, offset = offset, count = count,
-                                                         include_trash = include_trash)
+                                                         limit = limit, offset = offset, count = count)
                        
                        body <- NULL
                        
@@ -3710,9 +3768,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               collections.show = function(uuid)
+               container_requests.show = function(uuid)
                {
-                       endPoint <- stringr::str_interp("collections/${uuid}")
+                       endPoint <- stringr::str_interp("container_requests/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3730,9 +3788,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               collections.destroy = function(uuid)
+               container_requests.destroy = function(uuid)
                {
-                       endPoint <- stringr::str_interp("collections/${uuid}")
+                       endPoint <- stringr::str_interp("container_requests/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3750,9 +3808,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               containers.get = function(uuid)
+               collections.get = function(uuid)
                {
-                       endPoint <- stringr::str_interp("containers/${uuid}")
+                       endPoint <- stringr::str_interp("collections/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3770,18 +3828,19 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               containers.index = function(filters = NULL,
+               collections.index = function(filters = NULL,
                        where = NULL, order = NULL, select = NULL,
                        distinct = NULL, limit = "100", offset = "0",
-                       count = "exact")
+                       count = "exact", include_trash = NULL)
                {
-                       endPoint <- stringr::str_interp("containers")
+                       endPoint <- stringr::str_interp("collections")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
-                                                         limit = limit, offset = offset, count = count)
+                                                         limit = limit, offset = offset, count = count,
+                                                         include_trash = include_trash)
                        
                        body <- NULL
                        
@@ -3795,16 +3854,16 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               containers.create = function(container, ensure_unique_name = "false")
+               collections.create = function(collection, ensure_unique_name = "false")
                {
-                       endPoint <- stringr::str_interp("containers")
+                       endPoint <- stringr::str_interp("collections")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(ensure_unique_name = ensure_unique_name)
                        
-                       if(length(container) > 0)
-                               body <- jsonlite::toJSON(list(container = container), 
+                       if(length(collection) > 0)
+                               body <- jsonlite::toJSON(list(collection = collection), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
@@ -3819,16 +3878,16 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               containers.update = function(container, uuid)
+               collections.update = function(collection, uuid)
                {
-                       endPoint <- stringr::str_interp("containers/${uuid}")
+                       endPoint <- stringr::str_interp("collections/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- NULL
                        
-                       if(length(container) > 0)
-                               body <- jsonlite::toJSON(list(container = container), 
+                       if(length(collection) > 0)
+                               body <- jsonlite::toJSON(list(collection = collection), 
                                                         auto_unbox = TRUE)
                        else
                                body <- NULL
@@ -3843,9 +3902,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               containers.delete = function(uuid)
+               collections.delete = function(uuid)
                {
-                       endPoint <- stringr::str_interp("containers/${uuid}")
+                       endPoint <- stringr::str_interp("collections/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3863,9 +3922,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               containers.auth = function(uuid)
+               collections.provenance = function(uuid)
                {
-                       endPoint <- stringr::str_interp("containers/${uuid}/auth")
+                       endPoint <- stringr::str_interp("collections/${uuid}/provenance")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3883,9 +3942,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               containers.lock = function(uuid)
+               collections.used_by = function(uuid)
                {
-                       endPoint <- stringr::str_interp("containers/${uuid}/lock")
+                       endPoint <- stringr::str_interp("collections/${uuid}/used_by")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3893,7 +3952,7 @@ Arvados <- R6::R6Class(
                        
                        body <- NULL
                        
-                       response <- private$REST$http$exec("POST", url, headers, body,
+                       response <- private$REST$http$exec("GET", url, headers, body,
                                                           queryArgs, private$numRetries)
                        resource <- private$REST$httpParser$parseJSONResponse(response)
                        
@@ -3903,9 +3962,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               containers.unlock = function(uuid)
+               collections.trash = function(uuid)
                {
-                       endPoint <- stringr::str_interp("containers/${uuid}/unlock")
+                       endPoint <- stringr::str_interp("collections/${uuid}/trash")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3923,9 +3982,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               containers.current = function()
+               collections.untrash = function(uuid)
                {
-                       endPoint <- stringr::str_interp("containers/current")
+                       endPoint <- stringr::str_interp("collections/${uuid}/untrash")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3933,7 +3992,7 @@ Arvados <- R6::R6Class(
                        
                        body <- NULL
                        
-                       response <- private$REST$http$exec("GET", url, headers, body,
+                       response <- private$REST$http$exec("POST", url, headers, body,
                                                           queryArgs, private$numRetries)
                        resource <- private$REST$httpParser$parseJSONResponse(response)
                        
@@ -3943,18 +4002,19 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               containers.list = function(filters = NULL,
+               collections.list = function(filters = NULL,
                        where = NULL, order = NULL, select = NULL,
                        distinct = NULL, limit = "100", offset = "0",
-                       count = "exact")
+                       count = "exact", include_trash = NULL)
                {
-                       endPoint <- stringr::str_interp("containers")
+                       endPoint <- stringr::str_interp("collections")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
                        queryArgs <- list(filters = filters, where = where,
                                                          order = order, select = select, distinct = distinct,
-                                                         limit = limit, offset = offset, count = count)
+                                                         limit = limit, offset = offset, count = count,
+                                                         include_trash = include_trash)
                        
                        body <- NULL
                        
@@ -3968,9 +4028,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               containers.show = function(uuid)
+               collections.show = function(uuid)
                {
-                       endPoint <- stringr::str_interp("containers/${uuid}")
+                       endPoint <- stringr::str_interp("collections/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")
@@ -3988,9 +4048,9 @@ Arvados <- R6::R6Class(
                        resource
                },
 
-               containers.destroy = function(uuid)
+               collections.destroy = function(uuid)
                {
-                       endPoint <- stringr::str_interp("containers/${uuid}")
+                       endPoint <- stringr::str_interp("collections/${uuid}")
                        url <- paste0(private$host, endPoint)
                        headers <- list(Authorization = paste("OAuth2", private$token), 
                                        "Content-Type" = "application/json")

diff --git a/sdk/R/R/autoGenAPI.R b/sdk/R/R/autoGenAPI.R
index 4636be0855fb20f18db0d87442abc77ab7ffc66a..8dadd75cda0eabb27bde40389a6f25053cb3f3fa 100644 (file)
--- a/sdk/R/R/autoGenAPI.R
+++ b/sdk/R/R/autoGenAPI.R
@@ -17,11 +17,13 @@ generateAPI <- function()
 
     doc <- generateMethodsDocumentation(methodResources, resourceNames)
     arvadosAPIHeader <- generateAPIClassHeader()
+    arvadosProjectMethods <- generateProjectMethods()
     arvadosClassMethods <- generateClassContent(methodResources, resourceNames)
     arvadosAPIFooter <- generateAPIClassFooter()
 
     arvadosClass <- c(doc,
                       arvadosAPIHeader,
+                      arvadosProjectMethods,
                       arvadosClassMethods,
                       arvadosAPIFooter)
 
@@ -66,6 +68,42 @@ generateAPIClassHeader <- function()
       "\t\t},\n")
 }
 
+generateProjectMethods <- function()
+{
+    c("\t\tproject.get = function(uuid)",
+      "\t\t{",
+      "\t\t\tself$groups.get(uuid)",
+      "\t\t},",
+      "",
+      "\t\tproject.create = function(group, ensure_unique_name = \"false\")",
+      "\t\t{",
+      "\t\t\tgroup <- c(\"group_class\" = \"project\", group)",
+      "\t\t\tself$groups.create(group, ensure_unique_name)",
+      "\t\t},",
+      "",
+      "\t\tproject.update = function(group, uuid)",
+      "\t\t{",
+      "\t\t\tgroup <- c(\"group_class\" = \"project\", group)",
+      "\t\t\tself$groups.update(group, uuid)",
+      "\t\t},",
+      "",
+      "\t\tproject.list = function(filters = NULL, where = NULL,",
+      "\t\t\torder = NULL, select = NULL, distinct = NULL,",
+      "\t\t\tlimit = \"100\", offset = \"0\", count = \"exact\",",
+      "\t\t\tinclude_trash = NULL)",
+      "\t\t{",
+      "\t\t\tfilters[[length(filters) + 1]] <- list(\"group_class\", \"=\", \"project\")",
+      "\t\t\tself$groups.list(filters, where, order, select, distinct,",
+      "\t\t\t                 limit, offset, count, include_trash)",
+      "\t\t},",
+      "",
+      "\t\tproject.delete = function(uuid)",
+      "\t\t{",
+      "\t\t\tself$groups.delete(uuid)",
+      "\t\t},",
+      "")
+}
+
 generateClassContent <- function(methodResources, resourceNames)
 {
     arvadosMethods <- Map(function(resource, resourceName)
@@ -118,8 +156,6 @@ createMethod <- function(name, methodMetaData)
       "\t\t},\n")
 }
 
-#TODO: Make sure that arguments that are required always go first.
-#      This is not the case if request$required is false.
 getMethodArguments <- function(methodMetaData)
 {
     request <- methodMetaData$request
@@ -181,7 +217,7 @@ getMethodBody <- function(methodMetaData)
     request          <- getRequest(methodMetaData)
     response         <- getResponse(methodMetaData)
     errorCheck       <- getErrorCheckingCode()
-    returnStatement  <- getReturnObjectValidationCode()
+    returnStatement  <- getReturnObject()
 
     body <- c(url,
               headers,
@@ -265,7 +301,7 @@ getErrorCheckingCode <- function()
       "\tstop(resource$errors)")
 }
 
-getReturnObjectValidationCode <- function()
+getReturnObject <- function()
 {
     "resource"
 }
@@ -348,6 +384,8 @@ getMethodDescription <- function(methodMetaData)
 
 #NOTE: Utility functions:
 
+# This function is used to split very long lines of code into smaller chunks.
+# This is usually the case when we pass a lot of named argumets to a function.
 formatArgs <- function(prependAtStart, prependToEachSplit,
                        args, appendAtEnd, lineLength)
 {