From 649d52a70fd75e255437deb1798fa9f09697b78c Mon Sep 17 00:00:00 2001 From: Fuad Muhic Date: Wed, 18 Jul 2018 12:43:20 +0200 Subject: [PATCH] remove trailing white space from all files Arvados-DCO-1.1-Signed-off-by: Fuad Muhic --- sdk/R/R/Arvados.R | 2796 +++++++++---------- sdk/R/R/ArvadosFile.R | 16 +- sdk/R/R/Collection.R | 22 +- sdk/R/R/CollectionTree.R | 10 +- sdk/R/R/HttpParser.R | 6 +- sdk/R/R/HttpRequest.R | 4 +- sdk/R/R/RESTService.R | 6 +- sdk/R/R/Subcollection.R | 14 +- sdk/R/R/autoGenAPI.R | 16 +- sdk/R/tests/testthat/fakes/FakeHttpParser.R | 6 +- sdk/R/tests/testthat/test-ArvadosFile.R | 46 +- sdk/R/tests/testthat/test-Collection.R | 6 +- sdk/R/tests/testthat/test-CollectionTree.R | 20 +- sdk/R/tests/testthat/test-HttpParser.R | 10 +- sdk/R/tests/testthat/test-Subcollection.R | 62 +- sdk/R/tests/testthat/test-util.R | 20 +- 16 files changed, 1530 insertions(+), 1530 deletions(-) diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R index 0ec2d11529..4b65546912 100644 --- a/sdk/R/R/Arvados.R +++ b/sdk/R/R/Arvados.R @@ -3,9 +3,9 @@ # SPDX-License-Identifier: Apache-2.0 #' users.get -#' +#' #' users.get is a method defined in Arvados class. -#' +#' #' @usage arv$users.get(uuid) #' @param uuid The UUID of the User in question. #' @return User object. @@ -13,9 +13,9 @@ NULL #' users.create -#' +#' #' users.create is a method defined in Arvados class. -#' +#' #' @usage arv$users.create(user, ensure_unique_name = "false") #' @param user User object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -24,9 +24,9 @@ NULL NULL #' users.update -#' +#' #' users.update is a method defined in Arvados class. -#' +#' #' @usage arv$users.update(user, uuid) #' @param user User object. #' @param uuid The UUID of the User in question. @@ -35,9 +35,9 @@ NULL NULL #' users.delete -#' +#' #' users.delete is a method defined in Arvados class. -#' +#' #' @usage arv$users.delete(uuid) #' @param uuid The UUID of the User in question. #' @return User object. @@ -45,93 +45,93 @@ NULL NULL #' users.current -#' +#' #' users.current is a method defined in Arvados class. -#' +#' #' @usage arv$users.current(NULL) #' @return User object. #' @name users.current NULL #' users.system -#' +#' #' users.system is a method defined in Arvados class. -#' +#' #' @usage arv$users.system(NULL) #' @return User object. #' @name users.system NULL #' users.activate -#' +#' #' users.activate is a method defined in Arvados class. -#' +#' #' @usage arv$users.activate(uuid) -#' @param uuid +#' @param uuid #' @return User object. #' @name users.activate NULL #' users.setup -#' +#' #' users.setup is a method defined in Arvados class. -#' +#' #' @usage arv$users.setup(user = NULL, openid_prefix = NULL, #' repo_name = NULL, vm_uuid = NULL, send_notification_email = "false") -#' @param user -#' @param openid_prefix -#' @param repo_name -#' @param vm_uuid -#' @param send_notification_email +#' @param user +#' @param openid_prefix +#' @param repo_name +#' @param vm_uuid +#' @param send_notification_email #' @return User object. #' @name users.setup NULL #' users.unsetup -#' +#' #' users.unsetup is a method defined in Arvados class. -#' +#' #' @usage arv$users.unsetup(uuid) -#' @param uuid +#' @param uuid #' @return User object. #' @name users.unsetup NULL #' users.update_uuid -#' +#' #' users.update_uuid is a method defined in Arvados class. -#' +#' #' @usage arv$users.update_uuid(uuid, new_uuid) -#' @param uuid -#' @param new_uuid +#' @param uuid +#' @param new_uuid #' @return User object. #' @name users.update_uuid NULL #' users.list -#' +#' #' users.list is a method defined in Arvados class. -#' +#' #' @usage arv$users.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return UserList object. #' @name users.list NULL #' api_client_authorizations.get -#' +#' #' api_client_authorizations.get is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.get(uuid) #' @param uuid The UUID of the ApiClientAuthorization in question. #' @return ApiClientAuthorization object. @@ -139,9 +139,9 @@ NULL NULL #' api_client_authorizations.create -#' +#' #' api_client_authorizations.create is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.create(apiclientauthorization, #' ensure_unique_name = "false") #' @param apiClientAuthorization ApiClientAuthorization object. @@ -151,9 +151,9 @@ NULL NULL #' api_client_authorizations.update -#' +#' #' api_client_authorizations.update is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.update(apiclientauthorization, #' uuid) #' @param apiClientAuthorization ApiClientAuthorization object. @@ -163,9 +163,9 @@ NULL NULL #' api_client_authorizations.delete -#' +#' #' api_client_authorizations.delete is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.delete(uuid) #' @param uuid The UUID of the ApiClientAuthorization in question. #' @return ApiClientAuthorization object. @@ -173,50 +173,50 @@ NULL NULL #' api_client_authorizations.create_system_auth -#' +#' #' api_client_authorizations.create_system_auth is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.create_system_auth(api_client_id = NULL, #' scopes = NULL) -#' @param api_client_id -#' @param scopes +#' @param api_client_id +#' @param scopes #' @return ApiClientAuthorization object. #' @name api_client_authorizations.create_system_auth NULL #' api_client_authorizations.current -#' +#' #' api_client_authorizations.current is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.current(NULL) #' @return ApiClientAuthorization object. #' @name api_client_authorizations.current NULL #' api_client_authorizations.list -#' +#' #' api_client_authorizations.list is a method defined in Arvados class. -#' +#' #' @usage arv$api_client_authorizations.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return ApiClientAuthorizationList object. #' @name api_client_authorizations.list NULL #' containers.get -#' +#' #' containers.get is a method defined in Arvados class. -#' +#' #' @usage arv$containers.get(uuid) #' @param uuid The UUID of the Container in question. #' @return Container object. @@ -224,9 +224,9 @@ NULL NULL #' containers.create -#' +#' #' containers.create is a method defined in Arvados class. -#' +#' #' @usage arv$containers.create(container, #' ensure_unique_name = "false") #' @param container Container object. @@ -236,9 +236,9 @@ NULL NULL #' containers.update -#' +#' #' containers.update is a method defined in Arvados class. -#' +#' #' @usage arv$containers.update(container, #' uuid) #' @param container Container object. @@ -248,9 +248,9 @@ NULL NULL #' containers.delete -#' +#' #' containers.delete is a method defined in Arvados class. -#' +#' #' @usage arv$containers.delete(uuid) #' @param uuid The UUID of the Container in question. #' @return Container object. @@ -258,78 +258,78 @@ NULL NULL #' containers.auth -#' +#' #' containers.auth is a method defined in Arvados class. -#' +#' #' @usage arv$containers.auth(uuid) -#' @param uuid +#' @param uuid #' @return Container object. #' @name containers.auth NULL #' containers.lock -#' +#' #' containers.lock is a method defined in Arvados class. -#' +#' #' @usage arv$containers.lock(uuid) -#' @param uuid +#' @param uuid #' @return Container object. #' @name containers.lock NULL #' containers.unlock -#' +#' #' containers.unlock is a method defined in Arvados class. -#' +#' #' @usage arv$containers.unlock(uuid) -#' @param uuid +#' @param uuid #' @return Container object. #' @name containers.unlock NULL #' containers.secret_mounts -#' +#' #' containers.secret_mounts is a method defined in Arvados class. -#' +#' #' @usage arv$containers.secret_mounts(uuid) -#' @param uuid +#' @param uuid #' @return Container object. #' @name containers.secret_mounts NULL #' containers.current -#' +#' #' containers.current is a method defined in Arvados class. -#' +#' #' @usage arv$containers.current(NULL) #' @return Container object. #' @name containers.current NULL #' containers.list -#' +#' #' containers.list is a method defined in Arvados class. -#' +#' #' @usage arv$containers.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return ContainerList object. #' @name containers.list NULL #' api_clients.get -#' +#' #' api_clients.get is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.get(uuid) #' @param uuid The UUID of the ApiClient in question. #' @return ApiClient object. @@ -337,9 +337,9 @@ NULL NULL #' api_clients.create -#' +#' #' api_clients.create is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.create(apiclient, #' ensure_unique_name = "false") #' @param apiClient ApiClient object. @@ -349,9 +349,9 @@ NULL NULL #' api_clients.update -#' +#' #' api_clients.update is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.update(apiclient, #' uuid) #' @param apiClient ApiClient object. @@ -361,9 +361,9 @@ NULL NULL #' api_clients.delete -#' +#' #' api_clients.delete is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.delete(uuid) #' @param uuid The UUID of the ApiClient in question. #' @return ApiClient object. @@ -371,29 +371,29 @@ NULL NULL #' api_clients.list -#' +#' #' api_clients.list is a method defined in Arvados class. -#' +#' #' @usage arv$api_clients.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return ApiClientList object. #' @name api_clients.list NULL #' authorized_keys.get -#' +#' #' authorized_keys.get is a method defined in Arvados class. -#' +#' #' @usage arv$authorized_keys.get(uuid) #' @param uuid The UUID of the AuthorizedKey in question. #' @return AuthorizedKey object. @@ -401,9 +401,9 @@ NULL NULL #' authorized_keys.create -#' +#' #' authorized_keys.create is a method defined in Arvados class. -#' +#' #' @usage arv$authorized_keys.create(authorizedkey, #' ensure_unique_name = "false") #' @param authorizedKey AuthorizedKey object. @@ -413,9 +413,9 @@ NULL NULL #' authorized_keys.update -#' +#' #' authorized_keys.update is a method defined in Arvados class. -#' +#' #' @usage arv$authorized_keys.update(authorizedkey, #' uuid) #' @param authorizedKey AuthorizedKey object. @@ -425,9 +425,9 @@ NULL NULL #' authorized_keys.delete -#' +#' #' authorized_keys.delete is a method defined in Arvados class. -#' +#' #' @usage arv$authorized_keys.delete(uuid) #' @param uuid The UUID of the AuthorizedKey in question. #' @return AuthorizedKey object. @@ -435,29 +435,29 @@ NULL NULL #' authorized_keys.list -#' +#' #' authorized_keys.list is a method defined in Arvados class. -#' +#' #' @usage arv$authorized_keys.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return AuthorizedKeyList object. #' @name authorized_keys.list NULL #' container_requests.get -#' +#' #' container_requests.get is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.get(uuid) #' @param uuid The UUID of the ContainerRequest in question. #' @return ContainerRequest object. @@ -465,9 +465,9 @@ NULL NULL #' container_requests.create -#' +#' #' container_requests.create is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.create(containerrequest, #' ensure_unique_name = "false") #' @param containerRequest ContainerRequest object. @@ -477,9 +477,9 @@ NULL NULL #' container_requests.update -#' +#' #' container_requests.update is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.update(containerrequest, #' uuid) #' @param containerRequest ContainerRequest object. @@ -489,9 +489,9 @@ NULL NULL #' container_requests.delete -#' +#' #' container_requests.delete is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.delete(uuid) #' @param uuid The UUID of the ContainerRequest in question. #' @return ContainerRequest object. @@ -499,29 +499,29 @@ NULL NULL #' container_requests.list -#' +#' #' container_requests.list is a method defined in Arvados class. -#' +#' #' @usage arv$container_requests.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return ContainerRequestList object. #' @name container_requests.list NULL #' collections.get -#' +#' #' collections.get is a method defined in Arvados class. -#' +#' #' @usage arv$collections.get(uuid) #' @param uuid The UUID of the Collection in question. #' @return Collection object. @@ -529,9 +529,9 @@ NULL NULL #' collections.create -#' +#' #' collections.create is a method defined in Arvados class. -#' +#' #' @usage arv$collections.create(collection, #' ensure_unique_name = "false") #' @param collection Collection object. @@ -541,9 +541,9 @@ NULL NULL #' collections.update -#' +#' #' collections.update is a method defined in Arvados class. -#' +#' #' @usage arv$collections.update(collection, #' uuid) #' @param collection Collection object. @@ -553,9 +553,9 @@ NULL NULL #' collections.delete -#' +#' #' collections.delete is a method defined in Arvados class. -#' +#' #' @usage arv$collections.delete(uuid) #' @param uuid The UUID of the Collection in question. #' @return Collection object. @@ -563,70 +563,70 @@ NULL NULL #' collections.provenance -#' +#' #' collections.provenance is a method defined in Arvados class. -#' +#' #' @usage arv$collections.provenance(uuid) -#' @param uuid +#' @param uuid #' @return Collection object. #' @name collections.provenance NULL #' collections.used_by -#' +#' #' collections.used_by is a method defined in Arvados class. -#' +#' #' @usage arv$collections.used_by(uuid) -#' @param uuid +#' @param uuid #' @return Collection object. #' @name collections.used_by NULL #' collections.trash -#' +#' #' collections.trash is a method defined in Arvados class. -#' +#' #' @usage arv$collections.trash(uuid) -#' @param uuid +#' @param uuid #' @return Collection object. #' @name collections.trash NULL #' collections.untrash -#' +#' #' collections.untrash is a method defined in Arvados class. -#' +#' #' @usage arv$collections.untrash(uuid) -#' @param uuid +#' @param uuid #' @return Collection object. #' @name collections.untrash NULL #' collections.list -#' +#' #' collections.list is a method defined in Arvados class. -#' +#' #' @usage arv$collections.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact", include_trash = NULL) -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @param include_trash Include collections whose is_trashed attribute is true. #' @return CollectionList object. #' @name collections.list NULL #' humans.get -#' +#' #' humans.get is a method defined in Arvados class. -#' +#' #' @usage arv$humans.get(uuid) #' @param uuid The UUID of the Human in question. #' @return Human object. @@ -634,9 +634,9 @@ NULL NULL #' humans.create -#' +#' #' humans.create is a method defined in Arvados class. -#' +#' #' @usage arv$humans.create(human, ensure_unique_name = "false") #' @param human Human object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -645,9 +645,9 @@ NULL NULL #' humans.update -#' +#' #' humans.update is a method defined in Arvados class. -#' +#' #' @usage arv$humans.update(human, uuid) #' @param human Human object. #' @param uuid The UUID of the Human in question. @@ -656,9 +656,9 @@ NULL NULL #' humans.delete -#' +#' #' humans.delete is a method defined in Arvados class. -#' +#' #' @usage arv$humans.delete(uuid) #' @param uuid The UUID of the Human in question. #' @return Human object. @@ -666,29 +666,29 @@ NULL NULL #' humans.list -#' +#' #' humans.list is a method defined in Arvados class. -#' +#' #' @usage arv$humans.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return HumanList object. #' @name humans.list NULL #' job_tasks.get -#' +#' #' job_tasks.get is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.get(uuid) #' @param uuid The UUID of the JobTask in question. #' @return JobTask object. @@ -696,9 +696,9 @@ NULL NULL #' job_tasks.create -#' +#' #' job_tasks.create is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.create(jobtask, ensure_unique_name = "false") #' @param jobTask JobTask object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -707,9 +707,9 @@ NULL NULL #' job_tasks.update -#' +#' #' job_tasks.update is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.update(jobtask, uuid) #' @param jobTask JobTask object. #' @param uuid The UUID of the JobTask in question. @@ -718,9 +718,9 @@ NULL NULL #' job_tasks.delete -#' +#' #' job_tasks.delete is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.delete(uuid) #' @param uuid The UUID of the JobTask in question. #' @return JobTask object. @@ -728,29 +728,29 @@ NULL NULL #' job_tasks.list -#' +#' #' job_tasks.list is a method defined in Arvados class. -#' +#' #' @usage arv$job_tasks.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return JobTaskList object. #' @name job_tasks.list NULL #' links.get -#' +#' #' links.get is a method defined in Arvados class. -#' +#' #' @usage arv$links.get(uuid) #' @param uuid The UUID of the Link in question. #' @return Link object. @@ -758,9 +758,9 @@ NULL NULL #' links.create -#' +#' #' links.create is a method defined in Arvados class. -#' +#' #' @usage arv$links.create(link, ensure_unique_name = "false") #' @param link Link object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -769,9 +769,9 @@ NULL NULL #' links.update -#' +#' #' links.update is a method defined in Arvados class. -#' +#' #' @usage arv$links.update(link, uuid) #' @param link Link object. #' @param uuid The UUID of the Link in question. @@ -780,9 +780,9 @@ NULL NULL #' links.delete -#' +#' #' links.delete is a method defined in Arvados class. -#' +#' #' @usage arv$links.delete(uuid) #' @param uuid The UUID of the Link in question. #' @return Link object. @@ -790,39 +790,39 @@ NULL NULL #' links.list -#' +#' #' links.list is a method defined in Arvados class. -#' +#' #' @usage arv$links.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return LinkList object. #' @name links.list NULL #' links.get_permissions -#' +#' #' links.get_permissions is a method defined in Arvados class. -#' +#' #' @usage arv$links.get_permissions(uuid) -#' @param uuid +#' @param uuid #' @return Link object. #' @name links.get_permissions NULL #' jobs.get -#' +#' #' jobs.get is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.get(uuid) #' @param uuid The UUID of the Job in question. #' @return Job object. @@ -830,26 +830,26 @@ NULL NULL #' jobs.create -#' +#' #' jobs.create is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.create(job, ensure_unique_name = "false", #' find_or_create = "false", filters = NULL, #' minimum_script_version = NULL, exclude_script_versions = NULL) #' @param job Job object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @param find_or_create -#' @param filters -#' @param minimum_script_version -#' @param exclude_script_versions +#' @param find_or_create +#' @param filters +#' @param minimum_script_version +#' @param exclude_script_versions #' @return Job object. #' @name jobs.create NULL #' jobs.update -#' +#' #' jobs.update is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.update(job, uuid) #' @param job Job object. #' @param uuid The UUID of the Job in question. @@ -858,9 +858,9 @@ NULL NULL #' jobs.delete -#' +#' #' jobs.delete is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.delete(uuid) #' @param uuid The UUID of the Job in question. #' @return Job object. @@ -868,77 +868,77 @@ NULL NULL #' jobs.queue -#' +#' #' jobs.queue is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.queue(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return Job object. #' @name jobs.queue NULL #' jobs.queue_size -#' +#' #' jobs.queue_size is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.queue_size(NULL) #' @return Job object. #' @name jobs.queue_size NULL #' jobs.cancel -#' +#' #' jobs.cancel is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.cancel(uuid) -#' @param uuid +#' @param uuid #' @return Job object. #' @name jobs.cancel NULL #' jobs.lock -#' +#' #' jobs.lock is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.lock(uuid) -#' @param uuid +#' @param uuid #' @return Job object. #' @name jobs.lock NULL #' jobs.list -#' +#' #' jobs.list is a method defined in Arvados class. -#' +#' #' @usage arv$jobs.list(filters = NULL, where = NULL, #' order = NULL, select = NULL, distinct = NULL, #' limit = "100", offset = "0", count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return JobList object. #' @name jobs.list NULL #' keep_disks.get -#' +#' #' keep_disks.get is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.get(uuid) #' @param uuid The UUID of the KeepDisk in question. #' @return KeepDisk object. @@ -946,9 +946,9 @@ NULL NULL #' keep_disks.create -#' +#' #' keep_disks.create is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.create(keepdisk, #' ensure_unique_name = "false") #' @param keepDisk KeepDisk object. @@ -958,9 +958,9 @@ NULL NULL #' keep_disks.update -#' +#' #' keep_disks.update is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.update(keepdisk, #' uuid) #' @param keepDisk KeepDisk object. @@ -970,9 +970,9 @@ NULL NULL #' keep_disks.delete -#' +#' #' keep_disks.delete is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.delete(uuid) #' @param uuid The UUID of the KeepDisk in question. #' @return KeepDisk object. @@ -980,47 +980,47 @@ NULL NULL #' keep_disks.ping -#' +#' #' keep_disks.ping is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.ping(uuid = NULL, #' ping_secret, node_uuid = NULL, filesystem_uuid = NULL, #' service_host = NULL, service_port, service_ssl_flag) -#' @param uuid -#' @param ping_secret -#' @param node_uuid -#' @param filesystem_uuid -#' @param service_host -#' @param service_port -#' @param service_ssl_flag +#' @param uuid +#' @param ping_secret +#' @param node_uuid +#' @param filesystem_uuid +#' @param service_host +#' @param service_port +#' @param service_ssl_flag #' @return KeepDisk object. #' @name keep_disks.ping NULL #' keep_disks.list -#' +#' #' keep_disks.list is a method defined in Arvados class. -#' +#' #' @usage arv$keep_disks.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return KeepDiskList object. #' @name keep_disks.list NULL #' keep_services.get -#' +#' #' keep_services.get is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.get(uuid) #' @param uuid The UUID of the KeepService in question. #' @return KeepService object. @@ -1028,9 +1028,9 @@ NULL NULL #' keep_services.create -#' +#' #' keep_services.create is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.create(keepservice, #' ensure_unique_name = "false") #' @param keepService KeepService object. @@ -1040,9 +1040,9 @@ NULL NULL #' keep_services.update -#' +#' #' keep_services.update is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.update(keepservice, #' uuid) #' @param keepService KeepService object. @@ -1052,9 +1052,9 @@ NULL NULL #' keep_services.delete -#' +#' #' keep_services.delete is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.delete(uuid) #' @param uuid The UUID of the KeepService in question. #' @return KeepService object. @@ -1062,38 +1062,38 @@ NULL NULL #' keep_services.accessible -#' +#' #' keep_services.accessible is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.accessible(NULL) #' @return KeepService object. #' @name keep_services.accessible NULL #' keep_services.list -#' +#' #' keep_services.list is a method defined in Arvados class. -#' +#' #' @usage arv$keep_services.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return KeepServiceList object. #' @name keep_services.list NULL #' pipeline_templates.get -#' +#' #' pipeline_templates.get is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.get(uuid) #' @param uuid The UUID of the PipelineTemplate in question. #' @return PipelineTemplate object. @@ -1101,9 +1101,9 @@ NULL NULL #' pipeline_templates.create -#' +#' #' pipeline_templates.create is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.create(pipelinetemplate, #' ensure_unique_name = "false") #' @param pipelineTemplate PipelineTemplate object. @@ -1113,9 +1113,9 @@ NULL NULL #' pipeline_templates.update -#' +#' #' pipeline_templates.update is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.update(pipelinetemplate, #' uuid) #' @param pipelineTemplate PipelineTemplate object. @@ -1125,9 +1125,9 @@ NULL NULL #' pipeline_templates.delete -#' +#' #' pipeline_templates.delete is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.delete(uuid) #' @param uuid The UUID of the PipelineTemplate in question. #' @return PipelineTemplate object. @@ -1135,29 +1135,29 @@ NULL NULL #' pipeline_templates.list -#' +#' #' pipeline_templates.list is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_templates.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return PipelineTemplateList object. #' @name pipeline_templates.list NULL #' pipeline_instances.get -#' +#' #' pipeline_instances.get is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.get(uuid) #' @param uuid The UUID of the PipelineInstance in question. #' @return PipelineInstance object. @@ -1165,9 +1165,9 @@ NULL NULL #' pipeline_instances.create -#' +#' #' pipeline_instances.create is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.create(pipelineinstance, #' ensure_unique_name = "false") #' @param pipelineInstance PipelineInstance object. @@ -1177,9 +1177,9 @@ NULL NULL #' pipeline_instances.update -#' +#' #' pipeline_instances.update is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.update(pipelineinstance, #' uuid) #' @param pipelineInstance PipelineInstance object. @@ -1189,9 +1189,9 @@ NULL NULL #' pipeline_instances.delete -#' +#' #' pipeline_instances.delete is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.delete(uuid) #' @param uuid The UUID of the PipelineInstance in question. #' @return PipelineInstance object. @@ -1199,39 +1199,39 @@ NULL NULL #' pipeline_instances.cancel -#' +#' #' pipeline_instances.cancel is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.cancel(uuid) -#' @param uuid +#' @param uuid #' @return PipelineInstance object. #' @name pipeline_instances.cancel NULL #' pipeline_instances.list -#' +#' #' pipeline_instances.list is a method defined in Arvados class. -#' +#' #' @usage arv$pipeline_instances.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return PipelineInstanceList object. #' @name pipeline_instances.list NULL #' nodes.get -#' +#' #' nodes.get is a method defined in Arvados class. -#' +#' #' @usage arv$nodes.get(uuid) #' @param uuid The UUID of the Node in question. #' @return Node object. @@ -1239,9 +1239,9 @@ NULL NULL #' nodes.create -#' +#' #' nodes.create is a method defined in Arvados class. -#' +#' #' @usage arv$nodes.create(node, ensure_unique_name = "false", #' assign_slot = NULL) #' @param node Node object. @@ -1252,9 +1252,9 @@ NULL NULL #' nodes.update -#' +#' #' nodes.update is a method defined in Arvados class. -#' +#' #' @usage arv$nodes.update(node, uuid, assign_slot = NULL) #' @param node Node object. #' @param uuid The UUID of the Node in question. @@ -1264,9 +1264,9 @@ NULL NULL #' nodes.delete -#' +#' #' nodes.delete is a method defined in Arvados class. -#' +#' #' @usage arv$nodes.delete(uuid) #' @param uuid The UUID of the Node in question. #' @return Node object. @@ -1274,40 +1274,40 @@ NULL NULL #' nodes.ping -#' +#' #' nodes.ping is a method defined in Arvados class. -#' +#' #' @usage arv$nodes.ping(uuid, ping_secret) -#' @param uuid -#' @param ping_secret +#' @param uuid +#' @param ping_secret #' @return Node object. #' @name nodes.ping NULL #' nodes.list -#' +#' #' nodes.list is a method defined in Arvados class. -#' +#' #' @usage arv$nodes.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return NodeList object. #' @name nodes.list NULL #' repositories.get -#' +#' #' repositories.get is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.get(uuid) #' @param uuid The UUID of the Repository in question. #' @return Repository object. @@ -1315,9 +1315,9 @@ NULL NULL #' repositories.create -#' +#' #' repositories.create is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.create(repository, #' ensure_unique_name = "false") #' @param repository Repository object. @@ -1327,9 +1327,9 @@ NULL NULL #' repositories.update -#' +#' #' repositories.update is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.update(repository, #' uuid) #' @param repository Repository object. @@ -1339,9 +1339,9 @@ NULL NULL #' repositories.delete -#' +#' #' repositories.delete is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.delete(uuid) #' @param uuid The UUID of the Repository in question. #' @return Repository object. @@ -1349,38 +1349,38 @@ NULL NULL #' repositories.get_all_permissions -#' +#' #' repositories.get_all_permissions is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.get_all_permissions(NULL) #' @return Repository object. #' @name repositories.get_all_permissions NULL #' repositories.list -#' +#' #' repositories.list is a method defined in Arvados class. -#' +#' #' @usage arv$repositories.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return RepositoryList object. #' @name repositories.list NULL #' specimens.get -#' +#' #' specimens.get is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.get(uuid) #' @param uuid The UUID of the Specimen in question. #' @return Specimen object. @@ -1388,9 +1388,9 @@ NULL NULL #' specimens.create -#' +#' #' specimens.create is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.create(specimen, #' ensure_unique_name = "false") #' @param specimen Specimen object. @@ -1400,9 +1400,9 @@ NULL NULL #' specimens.update -#' +#' #' specimens.update is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.update(specimen, #' uuid) #' @param specimen Specimen object. @@ -1412,9 +1412,9 @@ NULL NULL #' specimens.delete -#' +#' #' specimens.delete is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.delete(uuid) #' @param uuid The UUID of the Specimen in question. #' @return Specimen object. @@ -1422,29 +1422,29 @@ NULL NULL #' specimens.list -#' +#' #' specimens.list is a method defined in Arvados class. -#' +#' #' @usage arv$specimens.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return SpecimenList object. #' @name specimens.list NULL #' logs.get -#' +#' #' logs.get is a method defined in Arvados class. -#' +#' #' @usage arv$logs.get(uuid) #' @param uuid The UUID of the Log in question. #' @return Log object. @@ -1452,9 +1452,9 @@ NULL NULL #' logs.create -#' +#' #' logs.create is a method defined in Arvados class. -#' +#' #' @usage arv$logs.create(log, ensure_unique_name = "false") #' @param log Log object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -1463,9 +1463,9 @@ NULL NULL #' logs.update -#' +#' #' logs.update is a method defined in Arvados class. -#' +#' #' @usage arv$logs.update(log, uuid) #' @param log Log object. #' @param uuid The UUID of the Log in question. @@ -1474,9 +1474,9 @@ NULL NULL #' logs.delete -#' +#' #' logs.delete is a method defined in Arvados class. -#' +#' #' @usage arv$logs.delete(uuid) #' @param uuid The UUID of the Log in question. #' @return Log object. @@ -1484,28 +1484,28 @@ NULL NULL #' logs.list -#' +#' #' logs.list is a method defined in Arvados class. -#' +#' #' @usage arv$logs.list(filters = NULL, where = NULL, #' order = NULL, select = NULL, distinct = NULL, #' limit = "100", offset = "0", count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return LogList object. #' @name logs.list NULL #' traits.get -#' +#' #' traits.get is a method defined in Arvados class. -#' +#' #' @usage arv$traits.get(uuid) #' @param uuid The UUID of the Trait in question. #' @return Trait object. @@ -1513,9 +1513,9 @@ NULL NULL #' traits.create -#' +#' #' traits.create is a method defined in Arvados class. -#' +#' #' @usage arv$traits.create(trait, ensure_unique_name = "false") #' @param trait Trait object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -1524,9 +1524,9 @@ NULL NULL #' traits.update -#' +#' #' traits.update is a method defined in Arvados class. -#' +#' #' @usage arv$traits.update(trait, uuid) #' @param trait Trait object. #' @param uuid The UUID of the Trait in question. @@ -1535,9 +1535,9 @@ NULL NULL #' traits.delete -#' +#' #' traits.delete is a method defined in Arvados class. -#' +#' #' @usage arv$traits.delete(uuid) #' @param uuid The UUID of the Trait in question. #' @return Trait object. @@ -1545,29 +1545,29 @@ NULL NULL #' traits.list -#' +#' #' traits.list is a method defined in Arvados class. -#' +#' #' @usage arv$traits.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return TraitList object. #' @name traits.list NULL #' virtual_machines.get -#' +#' #' virtual_machines.get is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.get(uuid) #' @param uuid The UUID of the VirtualMachine in question. #' @return VirtualMachine object. @@ -1575,9 +1575,9 @@ NULL NULL #' virtual_machines.create -#' +#' #' virtual_machines.create is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.create(virtualmachine, #' ensure_unique_name = "false") #' @param virtualMachine VirtualMachine object. @@ -1587,9 +1587,9 @@ NULL NULL #' virtual_machines.update -#' +#' #' virtual_machines.update is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.update(virtualmachine, #' uuid) #' @param virtualMachine VirtualMachine object. @@ -1599,9 +1599,9 @@ NULL NULL #' virtual_machines.delete -#' +#' #' virtual_machines.delete is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.delete(uuid) #' @param uuid The UUID of the VirtualMachine in question. #' @return VirtualMachine object. @@ -1609,48 +1609,48 @@ NULL NULL #' virtual_machines.logins -#' +#' #' virtual_machines.logins is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.logins(uuid) -#' @param uuid +#' @param uuid #' @return VirtualMachine object. #' @name virtual_machines.logins NULL #' virtual_machines.get_all_logins -#' +#' #' virtual_machines.get_all_logins is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.get_all_logins(NULL) #' @return VirtualMachine object. #' @name virtual_machines.get_all_logins NULL #' virtual_machines.list -#' +#' #' virtual_machines.list is a method defined in Arvados class. -#' +#' #' @usage arv$virtual_machines.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return VirtualMachineList object. #' @name virtual_machines.list NULL #' workflows.get -#' +#' #' workflows.get is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.get(uuid) #' @param uuid The UUID of the Workflow in question. #' @return Workflow object. @@ -1658,9 +1658,9 @@ NULL NULL #' workflows.create -#' +#' #' workflows.create is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.create(workflow, #' ensure_unique_name = "false") #' @param workflow Workflow object. @@ -1670,9 +1670,9 @@ NULL NULL #' workflows.update -#' +#' #' workflows.update is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.update(workflow, #' uuid) #' @param workflow Workflow object. @@ -1682,9 +1682,9 @@ NULL NULL #' workflows.delete -#' +#' #' workflows.delete is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.delete(uuid) #' @param uuid The UUID of the Workflow in question. #' @return Workflow object. @@ -1692,29 +1692,29 @@ NULL NULL #' workflows.list -#' +#' #' workflows.list is a method defined in Arvados class. -#' +#' #' @usage arv$workflows.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return WorkflowList object. #' @name workflows.list NULL #' groups.get -#' +#' #' groups.get is a method defined in Arvados class. -#' +#' #' @usage arv$groups.get(uuid) #' @param uuid The UUID of the Group in question. #' @return Group object. @@ -1722,9 +1722,9 @@ NULL NULL #' groups.create -#' +#' #' groups.create is a method defined in Arvados class. -#' +#' #' @usage arv$groups.create(group, ensure_unique_name = "false") #' @param group Group object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -1733,9 +1733,9 @@ NULL NULL #' groups.update -#' +#' #' groups.update is a method defined in Arvados class. -#' +#' #' @usage arv$groups.update(group, uuid) #' @param group Group object. #' @param uuid The UUID of the Group in question. @@ -1744,9 +1744,9 @@ NULL NULL #' groups.delete -#' +#' #' groups.delete is a method defined in Arvados class. -#' +#' #' @usage arv$groups.delete(uuid) #' @param uuid The UUID of the Group in question. #' @return Group object. @@ -1754,72 +1754,72 @@ NULL NULL #' groups.contents -#' +#' #' groups.contents is a method defined in Arvados class. -#' +#' #' @usage arv$groups.contents(filters = NULL, #' where = NULL, order = NULL, distinct = NULL, #' limit = "100", offset = "0", count = "exact", #' include_trash = NULL, uuid = NULL, recursive = NULL) -#' @param filters -#' @param where -#' @param order -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @param include_trash Include items whose is_trashed attribute is true. -#' @param uuid +#' @param uuid #' @param recursive Include contents from child groups recursively. #' @return Group object. #' @name groups.contents NULL #' groups.trash -#' +#' #' groups.trash is a method defined in Arvados class. -#' +#' #' @usage arv$groups.trash(uuid) -#' @param uuid +#' @param uuid #' @return Group object. #' @name groups.trash NULL #' groups.untrash -#' +#' #' groups.untrash is a method defined in Arvados class. -#' +#' #' @usage arv$groups.untrash(uuid) -#' @param uuid +#' @param uuid #' @return Group object. #' @name groups.untrash NULL #' groups.list -#' +#' #' groups.list is a method defined in Arvados class. -#' +#' #' @usage arv$groups.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact", include_trash = NULL) -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @param include_trash Include items whose is_trashed attribute is true. #' @return GroupList object. #' @name groups.list NULL #' user_agreements.get -#' +#' #' user_agreements.get is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.get(uuid) #' @param uuid The UUID of the UserAgreement in question. #' @return UserAgreement object. @@ -1827,9 +1827,9 @@ NULL NULL #' user_agreements.create -#' +#' #' user_agreements.create is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.create(useragreement, #' ensure_unique_name = "false") #' @param userAgreement UserAgreement object. @@ -1839,9 +1839,9 @@ NULL NULL #' user_agreements.update -#' +#' #' user_agreements.update is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.update(useragreement, #' uuid) #' @param userAgreement UserAgreement object. @@ -1851,9 +1851,9 @@ NULL NULL #' user_agreements.delete -#' +#' #' user_agreements.delete is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.delete(uuid) #' @param uuid The UUID of the UserAgreement in question. #' @return UserAgreement object. @@ -1861,56 +1861,56 @@ NULL NULL #' user_agreements.signatures -#' +#' #' user_agreements.signatures is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.signatures(NULL) #' @return UserAgreement object. #' @name user_agreements.signatures NULL #' user_agreements.sign -#' +#' #' user_agreements.sign is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.sign(NULL) #' @return UserAgreement object. #' @name user_agreements.sign NULL #' user_agreements.list -#' +#' #' user_agreements.list is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @return UserAgreementList object. #' @name user_agreements.list NULL #' user_agreements.new -#' +#' #' user_agreements.new is a method defined in Arvados class. -#' +#' #' @usage arv$user_agreements.new(NULL) #' @return UserAgreement object. #' @name user_agreements.new NULL #' project.get -#' +#' #' projects.get is equivalent to groups.get method. -#' +#' #' @usage arv$projects.get(uuid) #' @param uuid The UUID of the Group in question. #' @return Group object. @@ -1918,9 +1918,9 @@ NULL NULL #' project.create -#' +#' #' projects.create wrapps groups.create method by setting group_class attribute to "project". -#' +#' #' @usage arv$projects.create(group, ensure_unique_name = "false") #' @param group Group object. #' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. @@ -1929,9 +1929,9 @@ NULL NULL #' project.update -#' +#' #' projects.update wrapps groups.update method by setting group_class attribute to "project". -#' +#' #' @usage arv$projects.update(group, uuid) #' @param group Group object. #' @param uuid The UUID of the Group in question. @@ -1940,9 +1940,9 @@ NULL NULL #' project.delete -#' +#' #' projects.delete is equivalent to groups.delete method. -#' +#' #' @usage arv$project.delete(uuid) #' @param uuid The UUID of the Group in question. #' @return Group object. @@ -1950,22 +1950,22 @@ NULL NULL #' project.list -#' +#' #' projects.list wrapps groups.list method by setting group_class attribute to "project". -#' +#' #' @usage arv$projects.list(filters = NULL, #' where = NULL, order = NULL, distinct = NULL, #' limit = "100", offset = "0", count = "exact", #' include_trash = NULL, uuid = NULL, recursive = NULL) -#' @param filters -#' @param where -#' @param order -#' @param distinct -#' @param limit -#' @param offset -#' @param count +#' @param filters +#' @param where +#' @param order +#' @param distinct +#' @param limit +#' @param offset +#' @param count #' @param include_trash Include items whose is_trashed attribute is true. -#' @param uuid +#' @param uuid #' @param recursive Include contents from child groups recursively. #' @return Group object. #' @name projects.list @@ -2237,19 +2237,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2257,23 +2257,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(user) > 0) - body <- jsonlite::toJSON(list(user = user), + body <- jsonlite::toJSON(list(user = user), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2281,23 +2281,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(user) > 0) - body <- jsonlite::toJSON(list(user = user), + body <- jsonlite::toJSON(list(user = user), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2305,19 +2305,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2325,19 +2325,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/current") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2345,19 +2345,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/system") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2365,19 +2365,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}/activate") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2386,21 +2386,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/setup") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(user = user, openid_prefix = openid_prefix, repo_name = repo_name, vm_uuid = vm_uuid, send_notification_email = send_notification_email) - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2408,19 +2408,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}/unsetup") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2428,19 +2428,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users/${uuid}/update_uuid") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(new_uuid = new_uuid) - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2450,21 +2450,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("users") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2472,19 +2472,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2493,23 +2493,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(apiclientauthorization) > 0) - body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), + body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2517,23 +2517,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(apiclientauthorization) > 0) - body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), + body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2541,19 +2541,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2561,20 +2561,20 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(api_client_id = api_client_id, scopes = scopes) - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2582,19 +2582,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations/current") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2605,21 +2605,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_client_authorizations") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2627,19 +2627,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2647,23 +2647,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(container) > 0) - body <- jsonlite::toJSON(list(container = container), + body <- jsonlite::toJSON(list(container = container), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2671,23 +2671,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(container) > 0) - body <- jsonlite::toJSON(list(container = container), + body <- jsonlite::toJSON(list(container = container), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2695,19 +2695,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2715,19 +2715,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}/auth") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2735,19 +2735,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}/lock") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2755,19 +2755,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}/unlock") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2775,19 +2775,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2795,19 +2795,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers/current") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2818,21 +2818,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("containers") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2840,19 +2840,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2860,23 +2860,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(apiclient) > 0) - body <- jsonlite::toJSON(list(apiclient = apiclient), + body <- jsonlite::toJSON(list(apiclient = apiclient), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2884,23 +2884,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(apiclient) > 0) - body <- jsonlite::toJSON(list(apiclient = apiclient), + body <- jsonlite::toJSON(list(apiclient = apiclient), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2908,19 +2908,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2931,21 +2931,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2953,19 +2953,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2974,23 +2974,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(authorizedkey) > 0) - body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), + body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -2998,23 +2998,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(authorizedkey) > 0) - body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), + body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3022,19 +3022,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3045,21 +3045,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3067,19 +3067,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3088,23 +3088,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(containerrequest) > 0) - body <- jsonlite::toJSON(list(containerrequest = containerrequest), + body <- jsonlite::toJSON(list(containerrequest = containerrequest), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3112,23 +3112,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(containerrequest) > 0) - body <- jsonlite::toJSON(list(containerrequest = containerrequest), + body <- jsonlite::toJSON(list(containerrequest = containerrequest), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3136,19 +3136,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3159,21 +3159,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3181,19 +3181,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3201,23 +3201,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(collection) > 0) - body <- jsonlite::toJSON(list(collection = collection), + body <- jsonlite::toJSON(list(collection = collection), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3225,23 +3225,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(collection) > 0) - body <- jsonlite::toJSON(list(collection = collection), + body <- jsonlite::toJSON(list(collection = collection), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3249,19 +3249,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3269,19 +3269,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}/provenance") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3289,19 +3289,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}/used_by") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3309,19 +3309,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}/trash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3329,19 +3329,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections/${uuid}/untrash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3352,22 +3352,22 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count, include_trash = include_trash) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3375,19 +3375,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3395,23 +3395,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(human) > 0) - body <- jsonlite::toJSON(list(human = human), + body <- jsonlite::toJSON(list(human = human), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3419,23 +3419,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(human) > 0) - body <- jsonlite::toJSON(list(human = human), + body <- jsonlite::toJSON(list(human = human), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3443,19 +3443,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3465,21 +3465,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("humans") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3487,19 +3487,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3507,23 +3507,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(jobtask) > 0) - body <- jsonlite::toJSON(list(jobtask = jobtask), + body <- jsonlite::toJSON(list(jobtask = jobtask), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3531,23 +3531,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(jobtask) > 0) - body <- jsonlite::toJSON(list(jobtask = jobtask), + body <- jsonlite::toJSON(list(jobtask = jobtask), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3555,19 +3555,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3578,21 +3578,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("job_tasks") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3600,19 +3600,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3620,23 +3620,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("links") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(link) > 0) - body <- jsonlite::toJSON(list(link = link), + body <- jsonlite::toJSON(list(link = link), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3644,23 +3644,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(link) > 0) - body <- jsonlite::toJSON(list(link = link), + body <- jsonlite::toJSON(list(link = link), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3668,19 +3668,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3690,21 +3690,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("links") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3712,19 +3712,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("permissions/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3732,19 +3732,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3754,26 +3754,26 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name, find_or_create = find_or_create, filters = filters, minimum_script_version = minimum_script_version, exclude_script_versions = exclude_script_versions) - + if(length(job) > 0) - body <- jsonlite::toJSON(list(job = job), + body <- jsonlite::toJSON(list(job = job), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3781,23 +3781,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(job) > 0) - body <- jsonlite::toJSON(list(job = job), + body <- jsonlite::toJSON(list(job = job), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3805,19 +3805,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3827,21 +3827,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs/queue") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3849,19 +3849,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs/queue_size") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3869,19 +3869,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs/${uuid}/cancel") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3889,19 +3889,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs/${uuid}/lock") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3911,21 +3911,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("jobs") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3933,19 +3933,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3953,23 +3953,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_disks") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(keepdisk) > 0) - body <- jsonlite::toJSON(list(keepdisk = keepdisk), + body <- jsonlite::toJSON(list(keepdisk = keepdisk), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -3977,23 +3977,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(keepdisk) > 0) - body <- jsonlite::toJSON(list(keepdisk = keepdisk), + body <- jsonlite::toJSON(list(keepdisk = keepdisk), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4001,19 +4001,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4023,22 +4023,22 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_disks/ping") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(uuid = uuid, ping_secret = ping_secret, node_uuid = node_uuid, filesystem_uuid = filesystem_uuid, service_host = service_host, service_port = service_port, service_ssl_flag = service_ssl_flag) - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4049,21 +4049,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_disks") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4071,19 +4071,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4092,23 +4092,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_services") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(keepservice) > 0) - body <- jsonlite::toJSON(list(keepservice = keepservice), + body <- jsonlite::toJSON(list(keepservice = keepservice), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4116,23 +4116,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(keepservice) > 0) - body <- jsonlite::toJSON(list(keepservice = keepservice), + body <- jsonlite::toJSON(list(keepservice = keepservice), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4140,19 +4140,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4160,19 +4160,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_services/accessible") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4183,21 +4183,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("keep_services") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4205,19 +4205,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4226,23 +4226,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_templates") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(pipelinetemplate) > 0) - body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), + body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4250,23 +4250,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(pipelinetemplate) > 0) - body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), + body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4274,19 +4274,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4297,21 +4297,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_templates") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4319,19 +4319,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4340,23 +4340,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_instances") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(pipelineinstance) > 0) - body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), + body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4364,23 +4364,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(pipelineinstance) > 0) - body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), + body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4388,19 +4388,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4408,19 +4408,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_instances/${uuid}/cancel") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4431,21 +4431,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("pipeline_instances") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4453,19 +4453,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4474,24 +4474,24 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("nodes") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name, assign_slot = assign_slot) - + if(length(node) > 0) - body <- jsonlite::toJSON(list(node = node), + body <- jsonlite::toJSON(list(node = node), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4499,23 +4499,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(assign_slot = assign_slot) - + if(length(node) > 0) - body <- jsonlite::toJSON(list(node = node), + body <- jsonlite::toJSON(list(node = node), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4523,19 +4523,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4543,19 +4543,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("nodes/${uuid}/ping") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ping_secret = ping_secret) - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4565,21 +4565,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("nodes") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4587,19 +4587,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4607,23 +4607,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(repository) > 0) - body <- jsonlite::toJSON(list(repository = repository), + body <- jsonlite::toJSON(list(repository = repository), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4631,23 +4631,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(repository) > 0) - body <- jsonlite::toJSON(list(repository = repository), + body <- jsonlite::toJSON(list(repository = repository), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4655,19 +4655,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4675,19 +4675,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories/get_all_permissions") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4698,21 +4698,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("repositories") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4720,19 +4720,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4740,23 +4740,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(specimen) > 0) - body <- jsonlite::toJSON(list(specimen = specimen), + body <- jsonlite::toJSON(list(specimen = specimen), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4764,23 +4764,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(specimen) > 0) - body <- jsonlite::toJSON(list(specimen = specimen), + body <- jsonlite::toJSON(list(specimen = specimen), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4788,19 +4788,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4811,21 +4811,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("specimens") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4833,19 +4833,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4853,23 +4853,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(log) > 0) - body <- jsonlite::toJSON(list(log = log), + body <- jsonlite::toJSON(list(log = log), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4877,23 +4877,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(log) > 0) - body <- jsonlite::toJSON(list(log = log), + body <- jsonlite::toJSON(list(log = log), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4901,19 +4901,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4923,21 +4923,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("logs") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4945,19 +4945,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4965,23 +4965,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(trait) > 0) - body <- jsonlite::toJSON(list(trait = trait), + body <- jsonlite::toJSON(list(trait = trait), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -4989,23 +4989,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(trait) > 0) - body <- jsonlite::toJSON(list(trait = trait), + body <- jsonlite::toJSON(list(trait = trait), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5013,19 +5013,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5035,21 +5035,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("traits") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5057,19 +5057,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5078,23 +5078,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(virtualmachine) > 0) - body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), + body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5102,23 +5102,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(virtualmachine) > 0) - body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), + body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5126,19 +5126,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5146,19 +5146,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/${uuid}/logins") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5166,19 +5166,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines/get_all_logins") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5189,21 +5189,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("virtual_machines") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5211,19 +5211,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5231,23 +5231,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(workflow) > 0) - body <- jsonlite::toJSON(list(workflow = workflow), + body <- jsonlite::toJSON(list(workflow = workflow), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5255,23 +5255,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(workflow) > 0) - body <- jsonlite::toJSON(list(workflow = workflow), + body <- jsonlite::toJSON(list(workflow = workflow), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5279,19 +5279,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5302,21 +5302,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("workflows") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5324,19 +5324,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5344,23 +5344,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(group) > 0) - body <- jsonlite::toJSON(list(group = group), + body <- jsonlite::toJSON(list(group = group), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5368,23 +5368,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(group) > 0) - body <- jsonlite::toJSON(list(group = group), + body <- jsonlite::toJSON(list(group = group), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5392,19 +5392,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5415,22 +5415,22 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/contents") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, distinct = distinct, limit = limit, offset = offset, count = count, include_trash = include_trash, uuid = uuid, recursive = recursive) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5438,19 +5438,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}/trash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5458,19 +5458,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups/${uuid}/untrash") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5481,22 +5481,22 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("groups") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count, include_trash = include_trash) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5504,19 +5504,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5525,23 +5525,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - + if(length(useragreement) > 0) - body <- jsonlite::toJSON(list(useragreement = useragreement), + body <- jsonlite::toJSON(list(useragreement = useragreement), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5549,23 +5549,23 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + if(length(useragreement) > 0) - body <- jsonlite::toJSON(list(useragreement = useragreement), + body <- jsonlite::toJSON(list(useragreement = useragreement), auto_unbox = TRUE) else body <- NULL - + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5573,19 +5573,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/${uuid}") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5593,19 +5593,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/signatures") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5613,19 +5613,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/sign") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5636,21 +5636,21 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, order = order, select = select, distinct = distinct, limit = limit, offset = offset, count = count) - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, @@ -5658,19 +5658,19 @@ Arvados <- R6::R6Class( { endPoint <- stringr::str_interp("user_agreements/new") url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), + headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - + body <- NULL - + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) - + if(!is.null(resource$errors)) stop(resource$errors) - + resource }, diff --git a/sdk/R/R/ArvadosFile.R b/sdk/R/R/ArvadosFile.R index df323fbc48..1071302892 100644 --- a/sdk/R/R/ArvadosFile.R +++ b/sdk/R/R/ArvadosFile.R @@ -5,9 +5,9 @@ source("./R/util.R") #' ArvadosFile -#' +#' #' ArvadosFile class represents a file inside Arvados collection. -#' +#' #' @section Usage: #' \preformatted{file = ArvadosFile$new(name)} #' @@ -15,7 +15,7 @@ source("./R/util.R") #' \describe{ #' \item{name}{Name of the file.} #' } -#' +#' #' @section Methods: #' \describe{ #' \item{getName()}{Returns name of the file.} @@ -37,7 +37,7 @@ source("./R/util.R") #' myFile$write("This is new file content") #' fileContent <- myFile$read() #' fileContent <- myFile$read("text") -#' fileContent <- myFile$read("raw", offset = 8, length = 4) +#' fileContent <- myFile$read("raw", offset = 8, length = 4) #' #' #Write a table: #' arvConnection <- myFile$connection("w") @@ -141,14 +141,14 @@ ArvadosFile <- R6::R6Class( connection = function(rw) { - if (rw == "r" || rw == "rb") + if (rw == "r" || rw == "rb") { REST <- private$collection$getRESTService() return(REST$getConnection(self$getRelativePath(), private$collection$uuid, rw)) } - else if (rw == "w") + else if (rw == "w") { private$buffer <- textConnection(NULL, "w") @@ -156,7 +156,7 @@ ArvadosFile <- R6::R6Class( } }, - flush = function() + flush = function() { v <- textConnectionValue(private$buffer) close(private$buffer) @@ -255,7 +255,7 @@ ArvadosFile <- R6::R6Class( #' #' @param x Instance of ArvadosFile class #' @param ... Optional arguments. -#' @export +#' @export print.ArvadosFile = function(x, ...) { collection <- NULL diff --git a/sdk/R/R/Collection.R b/sdk/R/R/Collection.R index e23da13832..833b833c80 100644 --- a/sdk/R/R/Collection.R +++ b/sdk/R/R/Collection.R @@ -8,9 +8,9 @@ source("./R/RESTService.R") source("./R/util.R") #' Collection -#' +#' #' Collection class provides interface for working with Arvados collections. -#' +#' #' @section Usage: #' \preformatted{collection = Collection$new(arv, uuid)} #' @@ -19,7 +19,7 @@ source("./R/util.R") #' \item{arv}{Arvados object.} #' \item{uuid}{UUID of a collection.} #' } -#' +#' #' @section Methods: #' \describe{ #' \item{add(content)}{Adds ArvadosFile or Subcollection specified by content to the collection.} @@ -60,7 +60,7 @@ Collection <- R6::R6Class( uuid = NULL, # api = NULL, - initialize = function(api, uuid) + initialize = function(api, uuid) { # self$api <- api private$REST <- api$getRESTService() @@ -121,7 +121,7 @@ Collection <- R6::R6Class( } else { - relativePath <- trimFromEnd(relativePath, "/") + relativePath <- trimFromEnd(relativePath, "/") subcollection <- self$get(relativePath) } @@ -148,7 +148,7 @@ Collection <- R6::R6Class( else return(arvadosFiles) } - else + else { stop(paste0("Expected character vector, got ", paste0("(", paste0(class(fileNames), collapse = ", "), ")"), @@ -181,7 +181,7 @@ Collection <- R6::R6Class( "Content removed" } - else + else { stop(paste0("Expected character vector, got ", paste0("(", paste0(class(paths), collapse = ", "), ")"), @@ -221,14 +221,14 @@ Collection <- R6::R6Class( private$tree$getElement(relativePath) }, - toJSON = function() + toJSON = function() { fields <- sapply(private$classFields, function(field) { self[[field]] }, USE.NAMES = TRUE) - - jsonlite::toJSON(list("collection" = + + jsonlite::toJSON(list("collection" = Filter(Negate(is.null), fields)), auto_unbox = TRUE) }, @@ -275,7 +275,7 @@ Collection <- R6::R6Class( #' #' @param x Instance of Collection class #' @param ... Optional arguments. -#' @export +#' @export print.Collection = function(x, ...) { cat(paste0("Type: ", "\"", "Arvados Collection", "\""), sep = "\n") diff --git a/sdk/R/R/CollectionTree.R b/sdk/R/R/CollectionTree.R index 8686f88c1a..8b2f8876b0 100644 --- a/sdk/R/R/CollectionTree.R +++ b/sdk/R/R/CollectionTree.R @@ -19,7 +19,7 @@ CollectionTree <- R6::R6Class( treeBranches <- sapply(fileContent, function(filePath) { splitPath <- unlist(strsplit(filePath, "/", fixed = TRUE)) - branch <- private$createBranch(splitPath) + branch <- private$createBranch(splitPath) }) root <- Subcollection$new("") @@ -80,7 +80,7 @@ CollectionTree <- R6::R6Class( branch <- newFolder } } - + branch }, @@ -94,10 +94,10 @@ CollectionTree <- R6::R6Class( } else { - # Note: REST always returns folder name alone before other folder + # Note: REST always returns folder name alone before other folder # content, so in first iteration we don't know if it's a file - # or folder since its just a name, so we assume it's a file. - # If we encounter that same name again we know + # or folder since its just a name, so we assume it's a file. + # If we encounter that same name again we know # it's a folder so we need to replace ArvadosFile with Subcollection. if("ArvadosFile" %in% class(child)) { diff --git a/sdk/R/R/HttpParser.R b/sdk/R/R/HttpParser.R index 8ce68f3837..cd492166a1 100644 --- a/sdk/R/R/HttpParser.R +++ b/sdk/R/R/HttpParser.R @@ -10,12 +10,12 @@ HttpParser <- R6::R6Class( validContentTypes = NULL, - initialize = function() + initialize = function() { self$validContentTypes <- c("text", "raw") }, - parseJSONResponse = function(serverResponse) + parseJSONResponse = function(serverResponse) { parsed_response <- httr::content(serverResponse, as = "parsed", @@ -41,7 +41,7 @@ HttpParser <- R6::R6Class( result[-1] }, - getFileSizesFromResponse = function(response, uri) + getFileSizesFromResponse = function(response, uri) { text <- rawToChar(response$content) doc <- XML::xmlParse(text, asText=TRUE) diff --git a/sdk/R/R/HttpRequest.R b/sdk/R/R/HttpRequest.R index d1100a2e5f..4595fef662 100644 --- a/sdk/R/R/HttpRequest.R +++ b/sdk/R/R/HttpRequest.R @@ -13,7 +13,7 @@ HttpRequest <- R6::R6Class( validContentTypes = NULL, validVerbs = NULL, - initialize = function() + initialize = function() { self$validContentTypes <- c("text", "raw") self$validVerbs <- c("GET", "POST", "PUT", "DELETE", "PROPFIND", "MOVE") @@ -60,7 +60,7 @@ HttpRequest <- R6::R6Class( return("") }, - getConnection = function(url, headers, openMode) + getConnection = function(url, headers, openMode) { h <- curl::new_handle() curl::handle_setheaders(h, .list = headers) diff --git a/sdk/R/R/RESTService.R b/sdk/R/R/RESTService.R index 108aa1969f..867665299f 100644 --- a/sdk/R/R/RESTService.R +++ b/sdk/R/R/RESTService.R @@ -66,7 +66,7 @@ RESTService <- R6::R6Class( { fileURL <- paste0(self$getWebDavHostName(), "c=", uuid, "/", relativePath); - headers <- list(Authorization = paste("OAuth2", self$token)) + headers <- list(Authorization = paste("OAuth2", self$token)) serverResponse <- self$http$exec("DELETE", fileURL, headers, retryTimes = self$numRetries) @@ -188,7 +188,7 @@ RESTService <- R6::R6Class( getConnection = function(relativePath, uuid, openMode) { - fileURL <- paste0(self$getWebDavHostName(), + fileURL <- paste0(self$getWebDavHostName(), "c=", uuid, "/", relativePath); headers <- list(Authorization = paste("OAuth2", self$token)) @@ -205,7 +205,7 @@ RESTService <- R6::R6Class( { fileURL <- paste0(self$getWebDavHostName(), "c=", uuid, "/", relativePath) - headers <- list(Authorization = paste("OAuth2", self$token), + headers <- list(Authorization = paste("OAuth2", self$token), "Content-Type" = contentType) body <- NULL diff --git a/sdk/R/R/Subcollection.R b/sdk/R/R/Subcollection.R index 60714a4ad8..45fe343479 100644 --- a/sdk/R/R/Subcollection.R +++ b/sdk/R/R/Subcollection.R @@ -5,10 +5,10 @@ source("./R/util.R") #' Subcollection -#' +#' #' Subcollection class represents a folder inside Arvados collection. #' It is essentially a composite of arvadosFiles and other subcollections. -#' +#' #' @section Usage: #' \preformatted{subcollection = Subcollection$new(name)} #' @@ -16,7 +16,7 @@ source("./R/util.R") #' \describe{ #' \item{name}{Name of the subcollection.} #' } -#' +#' #' @section Methods: #' \describe{ #' \item{getName()}{Returns name of the subcollection.} @@ -56,7 +56,7 @@ Subcollection <- R6::R6Class( }, getName = function() private$name, - + getRelativePath = function() { relativePath <- c(private$name) @@ -87,7 +87,7 @@ Subcollection <- R6::R6Class( "or Subcollection with same name.")) if(!is.null(private$collection)) - { + { if(self$getRelativePath() != "") contentPath <- paste0(self$getRelativePath(), "/", content$getFileListing()) @@ -302,7 +302,7 @@ Subcollection <- R6::R6Class( content } ), - + cloneable = FALSE ) @@ -312,7 +312,7 @@ Subcollection <- R6::R6Class( #' #' @param x Instance of Subcollection class #' @param ... Optional arguments. -#' @export +#' @export print.Subcollection = function(x, ...) { collection <- NULL diff --git a/sdk/R/R/autoGenAPI.R b/sdk/R/R/autoGenAPI.R index 3e8c2fa0cf..1aef20b6cb 100644 --- a/sdk/R/R/autoGenAPI.R +++ b/sdk/R/R/autoGenAPI.R @@ -343,7 +343,7 @@ genMethodsDoc <- function(methodResources, resourceNames) }, methodResources, resourceNames))) projectDoc <- genProjectMethodsDoc() - + c(methodsDoc, projectDoc) } @@ -401,10 +401,10 @@ getAPIClassMethodList <- function(methodResources, resourceNames) methodNames[!(methodNames %in% c("index", "show", "destroy"))]) }, methodResources, resourceNames))) - + hardcodedMethods <- c("projects.create", "projects.get", "projects.list", "projects.update", "projects.delete") - paste0("#' \t\\item{}{\\code{\\link{", sort(c(methodList, hardcodedMethods)), "}}}") + paste0("#' \t\\item{}{\\code{\\link{", sort(c(methodList, hardcodedMethods)), "}}}") } getMethodDoc <- function(methodName, methodMetaData) @@ -447,7 +447,7 @@ getMethodDescription <- function(methodMetaData) className <- sapply(prop, function(ref) ref) objectName <- paste0(tolower(substr(className, 1, 1)), substr(className, 2, nchar(className))) - paste("#' @param", objectName, className, "object.") + paste("#' @param", objectName, className, "object.") }))) } @@ -457,7 +457,7 @@ getMethodDescription <- function(methodMetaData) { arg <- methodMetaData$parameters[[argName]] argDescription <- arg$description - paste("#' @param", argName, argDescription) + paste("#' @param", argName, argDescription) }))) c(requestDoc, argsDoc) @@ -541,7 +541,7 @@ formatArgs <- function(prependAtStart, prependToEachSplit, { if(length(args) > 1) { - args[1:(length(args) - 1)] <- paste0(args[1:(length(args) - 1)], ",") + args[1:(length(args) - 1)] <- paste0(args[1:(length(args) - 1)], ",") } args[1] <- paste0(prependAtStart, args[1]) @@ -564,12 +564,12 @@ formatArgs <- function(prependAtStart, prependToEachSplit, argLines <- c(argLines, line) } - + argLines <- unlist(argLines) argLinesLen <- length(argLines) if(argLinesLen > 1) - argLines[2:argLinesLen] <- paste0(prependToEachSplit, argLines[2:argLinesLen]) + argLines[2:argLinesLen] <- paste0(prependToEachSplit, argLines[2:argLinesLen]) argLines } diff --git a/sdk/R/tests/testthat/fakes/FakeHttpParser.R b/sdk/R/tests/testthat/fakes/FakeHttpParser.R index c97572c193..c23283989a 100644 --- a/sdk/R/tests/testthat/fakes/FakeHttpParser.R +++ b/sdk/R/tests/testthat/fakes/FakeHttpParser.R @@ -11,13 +11,13 @@ FakeHttpParser <- R6::R6Class( validContentTypes = NULL, parserCallCount = NULL, - initialize = function() + initialize = function() { self$parserCallCount <- 0 self$validContentTypes <- c("text", "raw") }, - parseJSONResponse = function(serverResponse) + parseJSONResponse = function(serverResponse) { self$parserCallCount <- self$parserCallCount + 1 @@ -47,7 +47,7 @@ FakeHttpParser <- R6::R6Class( serverResponse }, - getFileSizesFromResponse = function(serverResponse, uri) + getFileSizesFromResponse = function(serverResponse, uri) { self$parserCallCount <- self$parserCallCount + 1 diff --git a/sdk/R/tests/testthat/test-ArvadosFile.R b/sdk/R/tests/testthat/test-ArvadosFile.R index fb14888aab..1f559e999c 100644 --- a/sdk/R/tests/testthat/test-ArvadosFile.R +++ b/sdk/R/tests/testthat/test-ArvadosFile.R @@ -9,30 +9,30 @@ context("ArvadosFile") test_that("constructor raises error if file name is empty string", { expect_that(ArvadosFile$new(""), throws_error("Invalid name.")) -}) +}) test_that("getFileListing always returns file name", { dog <- ArvadosFile$new("dog") expect_that(dog$getFileListing(), equals("dog")) -}) +}) test_that("get always returns NULL", { dog <- ArvadosFile$new("dog") - + responseIsNull <- is.null(dog$get("something")) expect_that(responseIsNull, is_true()) -}) +}) test_that("getFirst always returns NULL", { dog <- ArvadosFile$new("dog") - + responseIsNull <- is.null(dog$getFirst()) expect_that(responseIsNull, is_true()) -}) +}) test_that(paste("getSizeInBytes returns zero if arvadosFile", "is not part of a collection"), { @@ -40,7 +40,7 @@ test_that(paste("getSizeInBytes returns zero if arvadosFile", dog <- ArvadosFile$new("dog") expect_that(dog$getSizeInBytes(), equals(0)) -}) +}) test_that(paste("getSizeInBytes delegates size calculation", "to REST service class"), { @@ -57,7 +57,7 @@ test_that(paste("getSizeInBytes delegates size calculation", resourceSize <- fish$getSizeInBytes() expect_that(resourceSize, equals(100)) -}) +}) test_that("getRelativePath returns path relative to the tree root", { @@ -69,7 +69,7 @@ test_that("getRelativePath returns path relative to the tree root", { fish$add(shark) expect_that(shark$getRelativePath(), equals("animal/fish/shark")) -}) +}) test_that("read raises exception if file doesn't belong to a collection", { @@ -77,7 +77,7 @@ test_that("read raises exception if file doesn't belong to a collection", { expect_that(dog$read(), throws_error("ArvadosFile doesn't belong to any collection.")) -}) +}) test_that("read raises exception offset or length is negative number", { @@ -96,7 +96,7 @@ test_that("read raises exception offset or length is negative number", { throws_error("Offset and length must be positive values.")) expect_that(fish$read(contentType = "text", offset = -1, length = -1), throws_error("Offset and length must be positive values.")) -}) +}) test_that("read delegates reading operation to REST service class", { @@ -108,15 +108,15 @@ test_that("read delegates reading operation to REST service class", { api$setRESTService(fakeREST) collection <- Collection$new(api, "myUUID") fish <- collection$get("animal/fish") - + fileContent <- fish$read("text") expect_that(fileContent, equals("my file")) expect_that(fakeREST$readCallCount, equals(1)) -}) +}) test_that(paste("connection delegates connection creation ro RESTService class", - "which returns curl connection opened in read mode when", + "which returns curl connection opened in read mode when", "'r' of 'rb' is passed as argument"), { collectionContent <- c("animal", "animal/fish") @@ -130,7 +130,7 @@ test_that(paste("connection delegates connection creation ro RESTService class", connection <- fish$connection("r") expect_that(fakeREST$getConnectionCallCount, equals(1)) -}) +}) test_that(paste("connection returns textConnection opened", "in write mode when 'w' is passed as argument"), { @@ -152,7 +152,7 @@ test_that(paste("connection returns textConnection opened", expect_that(writeResult[1], equals("file")) expect_that(writeResult[2], equals("content")) -}) +}) test_that("flush sends data stored in a connection to a REST server", { @@ -172,7 +172,7 @@ test_that("flush sends data stored in a connection to a REST server", { fish$flush() expect_that(fakeREST$writeBuffer, equals("file content")) -}) +}) test_that("write raises exception if file doesn't belong to a collection", { @@ -180,7 +180,7 @@ test_that("write raises exception if file doesn't belong to a collection", { expect_that(dog$write(), throws_error("ArvadosFile doesn't belong to any collection.")) -}) +}) test_that("write delegates writing operation to REST service class", { @@ -192,11 +192,11 @@ test_that("write delegates writing operation to REST service class", { api$setRESTService(fakeREST) collection <- Collection$new(api, "myUUID") fish <- collection$get("animal/fish") - + fileContent <- fish$write("new file content") expect_that(fakeREST$writeBuffer, equals("new file content")) -}) +}) test_that(paste("move raises exception if arvados file", "doesn't belong to any collection"), { @@ -205,7 +205,7 @@ test_that(paste("move raises exception if arvados file", expect_that(animal$move("new/location"), throws_error("ArvadosFile doesn't belong to any collection")) -}) +}) test_that(paste("move raises exception if newLocationInCollection", "parameter is invalid"), { @@ -227,7 +227,7 @@ test_that(paste("move raises exception if newLocationInCollection", expect_that(dog$move("objects/dog"), throws_error("Unable to get destination subcollection")) -}) +}) test_that("move raises exception if new location contains content with the same name", { @@ -248,7 +248,7 @@ test_that("move raises exception if new location contains content with the same expect_that(dog$move("dog"), throws_error("Destination already contains content with same name.")) -}) +}) test_that("move moves arvados file inside collection tree", { diff --git a/sdk/R/tests/testthat/test-Collection.R b/sdk/R/tests/testthat/test-Collection.R index c3c70910e4..af5fabeb73 100644 --- a/sdk/R/tests/testthat/test-Collection.R +++ b/sdk/R/tests/testthat/test-Collection.R @@ -100,7 +100,7 @@ test_that("create raises exception if passed argumet is not character vector", { collection <- Collection$new(api, "myUUID") expect_that(collection$create(10), - throws_error("Expected character vector, got (numeric).", + throws_error("Expected character vector, got (numeric).", fixed = TRUE)) }) @@ -156,7 +156,7 @@ test_that("remove raises exception if passed argumet is not character vector", { collection <- Collection$new(api, "myUUID") expect_that(collection$remove(10), - throws_error("Expected character vector, got (numeric).", + throws_error("Expected character vector, got (numeric).", fixed = TRUE)) }) @@ -238,7 +238,7 @@ test_that("getFileListing returns sorted collection content received from REST s api$setRESTService(fakeREST) collection <- Collection$new(api, "myUUID") - contentMatchExpected <- all(collection$getFileListing() == + contentMatchExpected <- all(collection$getFileListing() == c("animal", "animal/fish", "ball")) expect_that(contentMatchExpected, is_true()) diff --git a/sdk/R/tests/testthat/test-CollectionTree.R b/sdk/R/tests/testthat/test-CollectionTree.R index 5c8a405269..1a3aefecd0 100644 --- a/sdk/R/tests/testthat/test-CollectionTree.R +++ b/sdk/R/tests/testthat/test-CollectionTree.R @@ -7,7 +7,7 @@ context("CollectionTree") test_that("constructor creates file tree from character array properly", { collection <- "myCollection" - characterArray <- c("animal", + characterArray <- c("animal", "animal/dog", "boat") @@ -44,12 +44,12 @@ test_that("constructor creates file tree from character array properly", { expect_that(boatIsOfTypeArvadosFile, is_true()) expect_that(boatsParentIsRoot, is_true()) expect_that(allElementsBelongToSameCollection, is_true()) -}) +}) test_that("getElement returns element from tree if element exists on specified path", { collection <- "myCollection" - characterArray <- c("animal", + characterArray <- c("animal", "animal/dog", "boat") @@ -58,12 +58,12 @@ test_that("getElement returns element from tree if element exists on specified p dog <- collectionTree$getElement("animal/dog") expect_that(dog$getName(), equals("dog")) -}) +}) test_that("getElement returns NULL from tree if element doesn't exists on specified path", { collection <- "myCollection" - characterArray <- c("animal", + characterArray <- c("animal", "animal/dog", "boat") @@ -73,12 +73,12 @@ test_that("getElement returns NULL from tree if element doesn't exists on specif fishIsNULL <- is.null(fish) expect_that(fishIsNULL, is_true()) -}) +}) test_that("getElement trims ./ from start of relativePath", { collection <- "myCollection" - characterArray <- c("animal", + characterArray <- c("animal", "animal/dog", "boat") @@ -88,12 +88,12 @@ test_that("getElement trims ./ from start of relativePath", { dogWithDotSlash <- collectionTree$getElement("./animal/dog") expect_that(dogWithDotSlash$getName(), equals(dog$getName())) -}) +}) test_that("getElement trims / from end of relativePath", { collection <- "myCollection" - characterArray <- c("animal", + characterArray <- c("animal", "animal/dog", "boat") @@ -103,4 +103,4 @@ test_that("getElement trims / from end of relativePath", { animalWithSlash <- collectionTree$getElement("animal/") expect_that(animalWithSlash$getName(), equals(animal$getName())) -}) +}) diff --git a/sdk/R/tests/testthat/test-HttpParser.R b/sdk/R/tests/testthat/test-HttpParser.R index a119d88bf8..82c0fb0dd2 100644 --- a/sdk/R/tests/testthat/test-HttpParser.R +++ b/sdk/R/tests/testthat/test-HttpParser.R @@ -20,7 +20,7 @@ test_that("parseJSONResponse generates and returns JSON object from server respo expect_that(barExists, is_true()) expect_that(unlist(result$bar$foo), equals(10)) -}) +}) test_that(paste("parseResponse generates and returns character vector", "from server response if outputType is text"), { @@ -35,10 +35,10 @@ test_that(paste("parseResponse generates and returns character vector", parsedResponse <- parser$parseResponse(serverResponse, "text") expect_that(parsedResponse, equals("random text")) -}) +}) -webDAVResponseSample = +webDAVResponseSample = paste0("/c=aaaaa-bbbbb-ccccccccccccccc