X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f00ce9a30d252386634c79bc0a40da2e7da00de2..342c15f625fda8746e7d74510a298286b3a52196:/sdk/R/R/Arvados.R diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R index b2b40efabd..744cb3c296 100644 --- a/sdk/R/R/Arvados.R +++ b/sdk/R/R/Arvados.R @@ -1,3 +1,5 @@ +#' users.get +#' #' users.get is a method defined in Arvados class. #' #' @usage arv$users.get(uuid) @@ -6,24 +8,8 @@ #' @name users.get NULL -#' users.index is a method defined in Arvados class. +#' users.create #' -#' @usage arv$users.index(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 -#' @return UserList object. -#' @name users.index -NULL - #' users.create is a method defined in Arvados class. #' #' @usage arv$users.create(user, ensure_unique_name = "false") @@ -33,6 +19,8 @@ NULL #' @name users.create NULL +#' users.update +#' #' users.update is a method defined in Arvados class. #' #' @usage arv$users.update(user, uuid) @@ -42,6 +30,8 @@ NULL #' @name users.update NULL +#' users.delete +#' #' users.delete is a method defined in Arvados class. #' #' @usage arv$users.delete(uuid) @@ -50,6 +40,8 @@ NULL #' @name users.delete NULL +#' users.current +#' #' users.current is a method defined in Arvados class. #' #' @usage arv$users.current(NULL) @@ -57,6 +49,8 @@ NULL #' @name users.current NULL +#' users.system +#' #' users.system is a method defined in Arvados class. #' #' @usage arv$users.system(NULL) @@ -64,6 +58,8 @@ NULL #' @name users.system NULL +#' users.activate +#' #' users.activate is a method defined in Arvados class. #' #' @usage arv$users.activate(uuid) @@ -72,6 +68,8 @@ NULL #' @name users.activate NULL +#' users.setup +#' #' users.setup is a method defined in Arvados class. #' #' @usage arv$users.setup(user = NULL, openid_prefix = NULL, @@ -85,6 +83,8 @@ NULL #' @name users.setup NULL +#' users.unsetup +#' #' users.unsetup is a method defined in Arvados class. #' #' @usage arv$users.unsetup(uuid) @@ -93,6 +93,8 @@ NULL #' @name users.unsetup NULL +#' users.update_uuid +#' #' users.update_uuid is a method defined in Arvados class. #' #' @usage arv$users.update_uuid(uuid, new_uuid) @@ -102,6 +104,21 @@ NULL #' @name users.update_uuid NULL +#' users.merge +#' +#' users.merge is a method defined in Arvados class. +#' +#' @usage arv$users.merge(new_owner_uuid, +#' new_user_token, redirect_to_new_user = NULL) +#' @param new_owner_uuid +#' @param new_user_token +#' @param redirect_to_new_user +#' @return User object. +#' @name users.merge +NULL + +#' users.list +#' #' users.list is a method defined in Arvados class. #' #' @usage arv$users.list(filters = NULL, @@ -120,22 +137,8 @@ NULL #' @name users.list NULL -#' users.show is a method defined in Arvados class. -#' -#' @usage arv$users.show(uuid) -#' @param uuid -#' @return User object. -#' @name users.show -NULL - -#' users.destroy is a method defined in Arvados class. +#' api_client_authorizations.get #' -#' @usage arv$users.destroy(uuid) -#' @param uuid -#' @return User object. -#' @name users.destroy -NULL - #' api_client_authorizations.get is a method defined in Arvados class. #' #' @usage arv$api_client_authorizations.get(uuid) @@ -144,24 +147,8 @@ NULL #' @name api_client_authorizations.get NULL -#' api_client_authorizations.index is a method defined in Arvados class. +#' api_client_authorizations.create #' -#' @usage arv$api_client_authorizations.index(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return ApiClientAuthorizationList object. -#' @name api_client_authorizations.index -NULL - #' api_client_authorizations.create is a method defined in Arvados class. #' #' @usage arv$api_client_authorizations.create(apiclientauthorization, @@ -172,6 +159,8 @@ NULL #' @name api_client_authorizations.create NULL +#' api_client_authorizations.update +#' #' api_client_authorizations.update is a method defined in Arvados class. #' #' @usage arv$api_client_authorizations.update(apiclientauthorization, @@ -182,6 +171,8 @@ NULL #' @name api_client_authorizations.update NULL +#' api_client_authorizations.delete +#' #' api_client_authorizations.delete is a method defined in Arvados class. #' #' @usage arv$api_client_authorizations.delete(uuid) @@ -190,6 +181,8 @@ NULL #' @name api_client_authorizations.delete NULL +#' api_client_authorizations.create_system_auth +#' #' api_client_authorizations.create_system_auth is a method defined in Arvados class. #' #' @usage arv$api_client_authorizations.create_system_auth(api_client_id = NULL, @@ -200,6 +193,8 @@ NULL #' @name api_client_authorizations.create_system_auth NULL +#' api_client_authorizations.current +#' #' api_client_authorizations.current is a method defined in Arvados class. #' #' @usage arv$api_client_authorizations.current(NULL) @@ -207,6 +202,8 @@ NULL #' @name api_client_authorizations.current NULL +#' api_client_authorizations.list +#' #' api_client_authorizations.list is a method defined in Arvados class. #' #' @usage arv$api_client_authorizations.list(filters = NULL, @@ -225,33 +222,104 @@ NULL #' @name api_client_authorizations.list NULL -#' api_client_authorizations.show is a method defined in Arvados class. +#' containers.get +#' +#' containers.get is a method defined in Arvados class. +#' +#' @usage arv$containers.get(uuid) +#' @param uuid The UUID of the Container in question. +#' @return Container object. +#' @name containers.get +NULL + +#' containers.create +#' +#' containers.create is a method defined in Arvados class. +#' +#' @usage arv$containers.create(container, +#' ensure_unique_name = "false") +#' @param container Container object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Container object. +#' @name containers.create +NULL + +#' containers.update +#' +#' containers.update is a method defined in Arvados class. +#' +#' @usage arv$containers.update(container, +#' uuid) +#' @param container Container object. +#' @param uuid The UUID of the Container in question. +#' @return Container object. +#' @name containers.update +NULL + +#' containers.delete +#' +#' containers.delete is a method defined in Arvados class. +#' +#' @usage arv$containers.delete(uuid) +#' @param uuid The UUID of the Container in question. +#' @return Container object. +#' @name containers.delete +NULL + +#' containers.auth +#' +#' containers.auth is a method defined in Arvados class. #' -#' @usage arv$api_client_authorizations.show(uuid) +#' @usage arv$containers.auth(uuid) #' @param uuid -#' @return ApiClientAuthorization object. -#' @name api_client_authorizations.show +#' @return Container object. +#' @name containers.auth NULL -#' api_client_authorizations.destroy is a method defined in Arvados class. +#' containers.lock +#' +#' containers.lock is a method defined in Arvados class. #' -#' @usage arv$api_client_authorizations.destroy(uuid) +#' @usage arv$containers.lock(uuid) #' @param uuid -#' @return ApiClientAuthorization object. -#' @name api_client_authorizations.destroy +#' @return Container object. +#' @name containers.lock NULL -#' api_clients.get is a method defined in Arvados class. +#' containers.unlock #' -#' @usage arv$api_clients.get(uuid) -#' @param uuid The UUID of the ApiClient in question. -#' @return ApiClient object. -#' @name api_clients.get +#' containers.unlock is a method defined in Arvados class. +#' +#' @usage arv$containers.unlock(uuid) +#' @param uuid +#' @return Container object. +#' @name containers.unlock +NULL + +#' containers.secret_mounts +#' +#' containers.secret_mounts is a method defined in Arvados class. +#' +#' @usage arv$containers.secret_mounts(uuid) +#' @param uuid +#' @return Container object. +#' @name containers.secret_mounts +NULL + +#' containers.current +#' +#' containers.current is a method defined in Arvados class. +#' +#' @usage arv$containers.current(NULL) +#' @return Container object. +#' @name containers.current NULL -#' api_clients.index is a method defined in Arvados class. +#' containers.list +#' +#' containers.list is a method defined in Arvados class. #' -#' @usage arv$api_clients.index(filters = NULL, +#' @usage arv$containers.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") @@ -263,10 +331,22 @@ NULL #' @param limit #' @param offset #' @param count -#' @return ApiClientList object. -#' @name api_clients.index +#' @return ContainerList object. +#' @name containers.list +NULL + +#' api_clients.get +#' +#' api_clients.get is a method defined in Arvados class. +#' +#' @usage arv$api_clients.get(uuid) +#' @param uuid The UUID of the ApiClient in question. +#' @return ApiClient object. +#' @name api_clients.get NULL +#' api_clients.create +#' #' api_clients.create is a method defined in Arvados class. #' #' @usage arv$api_clients.create(apiclient, @@ -277,6 +357,8 @@ NULL #' @name api_clients.create NULL +#' api_clients.update +#' #' api_clients.update is a method defined in Arvados class. #' #' @usage arv$api_clients.update(apiclient, @@ -287,6 +369,8 @@ NULL #' @name api_clients.update NULL +#' api_clients.delete +#' #' api_clients.delete is a method defined in Arvados class. #' #' @usage arv$api_clients.delete(uuid) @@ -295,6 +379,8 @@ NULL #' @name api_clients.delete NULL +#' api_clients.list +#' #' api_clients.list is a method defined in Arvados class. #' #' @usage arv$api_clients.list(filters = NULL, @@ -313,22 +399,8 @@ NULL #' @name api_clients.list NULL -#' api_clients.show is a method defined in Arvados class. -#' -#' @usage arv$api_clients.show(uuid) -#' @param uuid -#' @return ApiClient object. -#' @name api_clients.show -NULL - -#' api_clients.destroy is a method defined in Arvados class. +#' container_requests.get #' -#' @usage arv$api_clients.destroy(uuid) -#' @param uuid -#' @return ApiClient object. -#' @name api_clients.destroy -NULL - #' container_requests.get is a method defined in Arvados class. #' #' @usage arv$container_requests.get(uuid) @@ -337,24 +409,8 @@ NULL #' @name container_requests.get NULL -#' container_requests.index is a method defined in Arvados class. +#' container_requests.create #' -#' @usage arv$container_requests.index(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 -#' @return ContainerRequestList object. -#' @name container_requests.index -NULL - #' container_requests.create is a method defined in Arvados class. #' #' @usage arv$container_requests.create(containerrequest, @@ -365,6 +421,8 @@ NULL #' @name container_requests.create NULL +#' container_requests.update +#' #' container_requests.update is a method defined in Arvados class. #' #' @usage arv$container_requests.update(containerrequest, @@ -375,6 +433,8 @@ NULL #' @name container_requests.update NULL +#' container_requests.delete +#' #' container_requests.delete is a method defined in Arvados class. #' #' @usage arv$container_requests.delete(uuid) @@ -383,6 +443,8 @@ NULL #' @name container_requests.delete NULL +#' container_requests.list +#' #' container_requests.list is a method defined in Arvados class. #' #' @usage arv$container_requests.list(filters = NULL, @@ -401,22 +463,8 @@ NULL #' @name container_requests.list NULL -#' container_requests.show is a method defined in Arvados class. -#' -#' @usage arv$container_requests.show(uuid) -#' @param uuid -#' @return ContainerRequest object. -#' @name container_requests.show -NULL - -#' container_requests.destroy is a method defined in Arvados class. +#' authorized_keys.get #' -#' @usage arv$container_requests.destroy(uuid) -#' @param uuid -#' @return ContainerRequest object. -#' @name container_requests.destroy -NULL - #' authorized_keys.get is a method defined in Arvados class. #' #' @usage arv$authorized_keys.get(uuid) @@ -425,24 +473,8 @@ NULL #' @name authorized_keys.get NULL -#' authorized_keys.index is a method defined in Arvados class. +#' authorized_keys.create #' -#' @usage arv$authorized_keys.index(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 -#' @return AuthorizedKeyList object. -#' @name authorized_keys.index -NULL - #' authorized_keys.create is a method defined in Arvados class. #' #' @usage arv$authorized_keys.create(authorizedkey, @@ -453,6 +485,8 @@ NULL #' @name authorized_keys.create NULL +#' authorized_keys.update +#' #' authorized_keys.update is a method defined in Arvados class. #' #' @usage arv$authorized_keys.update(authorizedkey, @@ -463,6 +497,8 @@ NULL #' @name authorized_keys.update NULL +#' authorized_keys.delete +#' #' authorized_keys.delete is a method defined in Arvados class. #' #' @usage arv$authorized_keys.delete(uuid) @@ -471,6 +507,8 @@ NULL #' @name authorized_keys.delete NULL +#' authorized_keys.list +#' #' authorized_keys.list is a method defined in Arvados class. #' #' @usage arv$authorized_keys.list(filters = NULL, @@ -489,22 +527,8 @@ NULL #' @name authorized_keys.list NULL -#' authorized_keys.show is a method defined in Arvados class. -#' -#' @usage arv$authorized_keys.show(uuid) -#' @param uuid -#' @return AuthorizedKey object. -#' @name authorized_keys.show -NULL - -#' authorized_keys.destroy is a method defined in Arvados class. +#' collections.get #' -#' @usage arv$authorized_keys.destroy(uuid) -#' @param uuid -#' @return AuthorizedKey object. -#' @name authorized_keys.destroy -NULL - #' collections.get is a method defined in Arvados class. #' #' @usage arv$collections.get(uuid) @@ -513,25 +537,8 @@ NULL #' @name collections.get NULL -#' collections.index is a method defined in Arvados class. +#' collections.create #' -#' @usage arv$collections.index(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 include_trash Include collections whose is_trashed attribute is true. -#' @return CollectionList object. -#' @name collections.index -NULL - #' collections.create is a method defined in Arvados class. #' #' @usage arv$collections.create(collection, @@ -542,6 +549,8 @@ NULL #' @name collections.create NULL +#' collections.update +#' #' collections.update is a method defined in Arvados class. #' #' @usage arv$collections.update(collection, @@ -552,6 +561,8 @@ NULL #' @name collections.update NULL +#' collections.delete +#' #' collections.delete is a method defined in Arvados class. #' #' @usage arv$collections.delete(uuid) @@ -560,6 +571,8 @@ NULL #' @name collections.delete NULL +#' collections.provenance +#' #' collections.provenance is a method defined in Arvados class. #' #' @usage arv$collections.provenance(uuid) @@ -568,6 +581,8 @@ NULL #' @name collections.provenance NULL +#' collections.used_by +#' #' collections.used_by is a method defined in Arvados class. #' #' @usage arv$collections.used_by(uuid) @@ -576,6 +591,8 @@ NULL #' @name collections.used_by NULL +#' collections.trash +#' #' collections.trash is a method defined in Arvados class. #' #' @usage arv$collections.trash(uuid) @@ -584,6 +601,8 @@ NULL #' @name collections.trash NULL +#' collections.untrash +#' #' collections.untrash is a method defined in Arvados class. #' #' @usage arv$collections.untrash(uuid) @@ -592,6 +611,8 @@ NULL #' @name collections.untrash NULL +#' collections.list +#' #' collections.list is a method defined in Arvados class. #' #' @usage arv$collections.list(filters = NULL, @@ -611,176 +632,29 @@ NULL #' @name collections.list NULL -#' collections.show is a method defined in Arvados class. +#' humans.get #' -#' @usage arv$collections.show(uuid) -#' @param uuid -#' @return Collection object. -#' @name collections.show +#' humans.get is a method defined in Arvados class. +#' +#' @usage arv$humans.get(uuid) +#' @param uuid The UUID of the Human in question. +#' @return Human object. +#' @name humans.get NULL -#' collections.destroy is a method defined in Arvados class. +#' humans.create #' -#' @usage arv$collections.destroy(uuid) -#' @param uuid -#' @return Collection object. -#' @name collections.destroy +#' humans.create is a method defined in Arvados class. +#' +#' @usage arv$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. +#' @return Human object. +#' @name humans.create NULL -#' containers.get is a method defined in Arvados class. +#' humans.update #' -#' @usage arv$containers.get(uuid) -#' @param uuid The UUID of the Container in question. -#' @return Container object. -#' @name containers.get -NULL - -#' containers.index is a method defined in Arvados class. -#' -#' @usage arv$containers.index(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 -#' @return ContainerList object. -#' @name containers.index -NULL - -#' containers.create is a method defined in Arvados class. -#' -#' @usage arv$containers.create(container, -#' ensure_unique_name = "false") -#' @param container Container object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return Container object. -#' @name containers.create -NULL - -#' containers.update is a method defined in Arvados class. -#' -#' @usage arv$containers.update(container, -#' uuid) -#' @param container Container object. -#' @param uuid The UUID of the Container in question. -#' @return Container object. -#' @name containers.update -NULL - -#' containers.delete is a method defined in Arvados class. -#' -#' @usage arv$containers.delete(uuid) -#' @param uuid The UUID of the Container in question. -#' @return Container object. -#' @name containers.delete -NULL - -#' containers.auth is a method defined in Arvados class. -#' -#' @usage arv$containers.auth(uuid) -#' @param uuid -#' @return Container object. -#' @name containers.auth -NULL - -#' containers.lock is a method defined in Arvados class. -#' -#' @usage arv$containers.lock(uuid) -#' @param uuid -#' @return Container object. -#' @name containers.lock -NULL - -#' containers.unlock is a method defined in Arvados class. -#' -#' @usage arv$containers.unlock(uuid) -#' @param uuid -#' @return Container object. -#' @name containers.unlock -NULL - -#' containers.current is a method defined in Arvados class. -#' -#' @usage arv$containers.current(NULL) -#' @return Container object. -#' @name containers.current -NULL - -#' containers.list is a method defined in Arvados class. -#' -#' @usage arv$containers.list(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return ContainerList object. -#' @name containers.list -NULL - -#' containers.show is a method defined in Arvados class. -#' -#' @usage arv$containers.show(uuid) -#' @param uuid -#' @return Container object. -#' @name containers.show -NULL - -#' containers.destroy is a method defined in Arvados class. -#' -#' @usage arv$containers.destroy(uuid) -#' @param uuid -#' @return Container object. -#' @name containers.destroy -NULL - -#' humans.get is a method defined in Arvados class. -#' -#' @usage arv$humans.get(uuid) -#' @param uuid The UUID of the Human in question. -#' @return Human object. -#' @name humans.get -NULL - -#' humans.index is a method defined in Arvados class. -#' -#' @usage arv$humans.index(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 -#' @return HumanList object. -#' @name humans.index -NULL - -#' humans.create is a method defined in Arvados class. -#' -#' @usage arv$humans.create(human, ensure_unique_name = "false") -#' @param human Human object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return Human object. -#' @name humans.create -NULL - #' humans.update is a method defined in Arvados class. #' #' @usage arv$humans.update(human, uuid) @@ -790,6 +664,8 @@ NULL #' @name humans.update NULL +#' humans.delete +#' #' humans.delete is a method defined in Arvados class. #' #' @usage arv$humans.delete(uuid) @@ -798,6 +674,8 @@ NULL #' @name humans.delete NULL +#' humans.list +#' #' humans.list is a method defined in Arvados class. #' #' @usage arv$humans.list(filters = NULL, @@ -816,22 +694,8 @@ NULL #' @name humans.list NULL -#' humans.show is a method defined in Arvados class. -#' -#' @usage arv$humans.show(uuid) -#' @param uuid -#' @return Human object. -#' @name humans.show -NULL - -#' humans.destroy is a method defined in Arvados class. +#' job_tasks.get #' -#' @usage arv$humans.destroy(uuid) -#' @param uuid -#' @return Human object. -#' @name humans.destroy -NULL - #' job_tasks.get is a method defined in Arvados class. #' #' @usage arv$job_tasks.get(uuid) @@ -840,24 +704,8 @@ NULL #' @name job_tasks.get NULL -#' job_tasks.index is a method defined in Arvados class. +#' job_tasks.create #' -#' @usage arv$job_tasks.index(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 -#' @return JobTaskList object. -#' @name job_tasks.index -NULL - #' job_tasks.create is a method defined in Arvados class. #' #' @usage arv$job_tasks.create(jobtask, ensure_unique_name = "false") @@ -867,6 +715,8 @@ NULL #' @name job_tasks.create NULL +#' job_tasks.update +#' #' job_tasks.update is a method defined in Arvados class. #' #' @usage arv$job_tasks.update(jobtask, uuid) @@ -876,6 +726,8 @@ NULL #' @name job_tasks.update NULL +#' job_tasks.delete +#' #' job_tasks.delete is a method defined in Arvados class. #' #' @usage arv$job_tasks.delete(uuid) @@ -884,6 +736,8 @@ NULL #' @name job_tasks.delete NULL +#' job_tasks.list +#' #' job_tasks.list is a method defined in Arvados class. #' #' @usage arv$job_tasks.list(filters = NULL, @@ -902,77 +756,59 @@ NULL #' @name job_tasks.list NULL -#' job_tasks.show is a method defined in Arvados class. +#' jobs.get #' -#' @usage arv$job_tasks.show(uuid) -#' @param uuid -#' @return JobTask object. -#' @name job_tasks.show -NULL - -#' job_tasks.destroy is a method defined in Arvados class. +#' jobs.get is a method defined in Arvados class. #' -#' @usage arv$job_tasks.destroy(uuid) -#' @param uuid -#' @return JobTask object. -#' @name job_tasks.destroy +#' @usage arv$jobs.get(uuid) +#' @param uuid The UUID of the Job in question. +#' @return Job object. +#' @name jobs.get NULL -#' links.get is a method defined in Arvados class. +#' jobs.create #' -#' @usage arv$links.get(uuid) -#' @param uuid The UUID of the Link in question. -#' @return Link object. -#' @name links.get -NULL - -#' links.index is a method defined in Arvados class. +#' jobs.create is a method defined in Arvados class. #' -#' @usage arv$links.index(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") +#' @usage arv$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 where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return LinkList object. -#' @name links.index +#' @param minimum_script_version +#' @param exclude_script_versions +#' @return Job object. +#' @name jobs.create NULL -#' links.create is a method defined in Arvados class. +#' jobs.update #' -#' @usage arv$links.create(link, ensure_unique_name = "false") -#' @param link Link object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return Link object. -#' @name links.create -NULL - -#' links.update is a method defined in Arvados class. +#' jobs.update is a method defined in Arvados class. #' -#' @usage arv$links.update(link, uuid) -#' @param link Link object. -#' @param uuid The UUID of the Link in question. -#' @return Link object. -#' @name links.update +#' @usage arv$jobs.update(job, uuid) +#' @param job Job object. +#' @param uuid The UUID of the Job in question. +#' @return Job object. +#' @name jobs.update NULL -#' links.delete is a method defined in Arvados class. +#' jobs.delete #' -#' @usage arv$links.delete(uuid) -#' @param uuid The UUID of the Link in question. -#' @return Link object. -#' @name links.delete +#' jobs.delete is a method defined in Arvados class. +#' +#' @usage arv$jobs.delete(uuid) +#' @param uuid The UUID of the Job in question. +#' @return Job object. +#' @name jobs.delete NULL -#' links.list is a method defined in Arvados class. +#' jobs.queue #' -#' @usage arv$links.list(filters = NULL, +#' jobs.queue is a method defined in Arvados class. +#' +#' @usage arv$jobs.queue(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") @@ -984,125 +820,31 @@ NULL #' @param limit #' @param offset #' @param count -#' @return LinkList object. -#' @name links.list +#' @return Job object. +#' @name jobs.queue NULL -#' links.show is a method defined in Arvados class. +#' jobs.queue_size #' -#' @usage arv$links.show(uuid) -#' @param uuid -#' @return Link object. -#' @name links.show +#' jobs.queue_size is a method defined in Arvados class. +#' +#' @usage arv$jobs.queue_size(NULL) +#' @return Job object. +#' @name jobs.queue_size NULL -#' links.destroy is a method defined in Arvados class. +#' jobs.cancel +#' +#' jobs.cancel is a method defined in Arvados class. #' -#' @usage arv$links.destroy(uuid) -#' @param uuid -#' @return Link object. -#' @name links.destroy -NULL - -#' links.get_permissions is a method defined in Arvados class. -#' -#' @usage arv$links.get_permissions(uuid) -#' @param uuid -#' @return Link object. -#' @name links.get_permissions -NULL - -#' jobs.get is a method defined in Arvados class. -#' -#' @usage arv$jobs.get(uuid) -#' @param uuid The UUID of the Job in question. -#' @return Job object. -#' @name jobs.get -NULL - -#' jobs.index is a method defined in Arvados class. -#' -#' @usage arv$jobs.index(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return JobList object. -#' @name jobs.index -NULL - -#' jobs.create is a method defined in Arvados class. -#' -#' @usage arv$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 -#' @return Job object. -#' @name jobs.create -NULL - -#' jobs.update is a method defined in Arvados class. -#' -#' @usage arv$jobs.update(job, uuid) -#' @param job Job object. -#' @param uuid The UUID of the Job in question. -#' @return Job object. -#' @name jobs.update -NULL - -#' jobs.delete is a method defined in Arvados class. -#' -#' @usage arv$jobs.delete(uuid) -#' @param uuid The UUID of the Job in question. -#' @return Job object. -#' @name jobs.delete -NULL - -#' jobs.queue is a method defined in Arvados class. -#' -#' @usage arv$jobs.queue(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return Job object. -#' @name jobs.queue -NULL - -#' jobs.queue_size is a method defined in Arvados class. -#' -#' @usage arv$jobs.queue_size(NULL) -#' @return Job object. -#' @name jobs.queue_size -NULL - -#' jobs.cancel is a method defined in Arvados class. -#' -#' @usage arv$jobs.cancel(uuid) +#' @usage arv$jobs.cancel(uuid) #' @param uuid #' @return Job object. #' @name jobs.cancel NULL +#' jobs.lock +#' #' jobs.lock is a method defined in Arvados class. #' #' @usage arv$jobs.lock(uuid) @@ -1111,6 +853,8 @@ NULL #' @name jobs.lock NULL +#' jobs.list +#' #' jobs.list is a method defined in Arvados class. #' #' @usage arv$jobs.list(filters = NULL, where = NULL, @@ -1128,22 +872,8 @@ NULL #' @name jobs.list NULL -#' jobs.show is a method defined in Arvados class. -#' -#' @usage arv$jobs.show(uuid) -#' @param uuid -#' @return Job object. -#' @name jobs.show -NULL - -#' jobs.destroy is a method defined in Arvados class. +#' keep_disks.get #' -#' @usage arv$jobs.destroy(uuid) -#' @param uuid -#' @return Job object. -#' @name jobs.destroy -NULL - #' keep_disks.get is a method defined in Arvados class. #' #' @usage arv$keep_disks.get(uuid) @@ -1152,24 +882,8 @@ NULL #' @name keep_disks.get NULL -#' keep_disks.index is a method defined in Arvados class. +#' keep_disks.create #' -#' @usage arv$keep_disks.index(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 -#' @return KeepDiskList object. -#' @name keep_disks.index -NULL - #' keep_disks.create is a method defined in Arvados class. #' #' @usage arv$keep_disks.create(keepdisk, @@ -1180,6 +894,8 @@ NULL #' @name keep_disks.create NULL +#' keep_disks.update +#' #' keep_disks.update is a method defined in Arvados class. #' #' @usage arv$keep_disks.update(keepdisk, @@ -1190,6 +906,8 @@ NULL #' @name keep_disks.update NULL +#' keep_disks.delete +#' #' keep_disks.delete is a method defined in Arvados class. #' #' @usage arv$keep_disks.delete(uuid) @@ -1198,6 +916,8 @@ NULL #' @name keep_disks.delete NULL +#' keep_disks.ping +#' #' keep_disks.ping is a method defined in Arvados class. #' #' @usage arv$keep_disks.ping(uuid = NULL, @@ -1214,6 +934,8 @@ NULL #' @name keep_disks.ping NULL +#' keep_disks.list +#' #' keep_disks.list is a method defined in Arvados class. #' #' @usage arv$keep_disks.list(filters = NULL, @@ -1232,33 +954,67 @@ NULL #' @name keep_disks.list NULL -#' keep_disks.show is a method defined in Arvados class. +#' nodes.get #' -#' @usage arv$keep_disks.show(uuid) -#' @param uuid -#' @return KeepDisk object. -#' @name keep_disks.show +#' nodes.get is a method defined in Arvados class. +#' +#' @usage arv$nodes.get(uuid) +#' @param uuid The UUID of the Node in question. +#' @return Node object. +#' @name nodes.get NULL -#' keep_disks.destroy is a method defined in Arvados class. +#' nodes.create #' -#' @usage arv$keep_disks.destroy(uuid) -#' @param uuid -#' @return KeepDisk object. -#' @name keep_disks.destroy +#' nodes.create is a method defined in Arvados class. +#' +#' @usage arv$nodes.create(node, ensure_unique_name = "false", +#' assign_slot = NULL) +#' @param node Node object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @param assign_slot assign slot and hostname +#' @return Node object. +#' @name nodes.create NULL -#' keep_services.get is a method defined in Arvados class. +#' nodes.update #' -#' @usage arv$keep_services.get(uuid) -#' @param uuid The UUID of the KeepService in question. -#' @return KeepService object. -#' @name keep_services.get +#' nodes.update is a method defined in Arvados class. +#' +#' @usage arv$nodes.update(node, uuid, assign_slot = NULL) +#' @param node Node object. +#' @param uuid The UUID of the Node in question. +#' @param assign_slot assign slot and hostname +#' @return Node object. +#' @name nodes.update +NULL + +#' nodes.delete +#' +#' nodes.delete is a method defined in Arvados class. +#' +#' @usage arv$nodes.delete(uuid) +#' @param uuid The UUID of the Node in question. +#' @return Node object. +#' @name nodes.delete +NULL + +#' nodes.ping +#' +#' nodes.ping is a method defined in Arvados class. +#' +#' @usage arv$nodes.ping(uuid, ping_secret) +#' @param uuid +#' @param ping_secret +#' @return Node object. +#' @name nodes.ping NULL -#' keep_services.index is a method defined in Arvados class. +#' nodes.list +#' +#' nodes.list is a method defined in Arvados class. #' -#' @usage arv$keep_services.index(filters = NULL, +#' @usage arv$nodes.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") @@ -1270,48 +1026,57 @@ NULL #' @param limit #' @param offset #' @param count -#' @return KeepServiceList object. -#' @name keep_services.index +#' @return NodeList object. +#' @name nodes.list NULL -#' keep_services.create is a method defined in Arvados class. +#' links.get #' -#' @usage arv$keep_services.create(keepservice, -#' ensure_unique_name = "false") -#' @param keepService KeepService object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @return KeepService object. -#' @name keep_services.create +#' links.get is a method defined in Arvados class. +#' +#' @usage arv$links.get(uuid) +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.get NULL -#' keep_services.update is a method defined in Arvados class. +#' links.create #' -#' @usage arv$keep_services.update(keepservice, -#' uuid) -#' @param keepService KeepService object. -#' @param uuid The UUID of the KeepService in question. -#' @return KeepService object. -#' @name keep_services.update +#' links.create is a method defined in Arvados class. +#' +#' @usage arv$links.create(link, ensure_unique_name = "false") +#' @param link Link object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Link object. +#' @name links.create NULL -#' keep_services.delete is a method defined in Arvados class. +#' links.update #' -#' @usage arv$keep_services.delete(uuid) -#' @param uuid The UUID of the KeepService in question. -#' @return KeepService object. -#' @name keep_services.delete +#' links.update is a method defined in Arvados class. +#' +#' @usage arv$links.update(link, uuid) +#' @param link Link object. +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.update NULL -#' keep_services.accessible is a method defined in Arvados class. +#' links.delete #' -#' @usage arv$keep_services.accessible(NULL) -#' @return KeepService object. -#' @name keep_services.accessible +#' links.delete is a method defined in Arvados class. +#' +#' @usage arv$links.delete(uuid) +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.delete NULL -#' keep_services.list is a method defined in Arvados class. +#' links.list #' -#' @usage arv$keep_services.list(filters = NULL, +#' links.list is a method defined in Arvados class. +#' +#' @usage arv$links.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") @@ -1323,37 +1088,78 @@ NULL #' @param limit #' @param offset #' @param count -#' @return KeepServiceList object. -#' @name keep_services.list +#' @return LinkList object. +#' @name links.list NULL -#' keep_services.show is a method defined in Arvados class. +#' links.get_permissions +#' +#' links.get_permissions is a method defined in Arvados class. #' -#' @usage arv$keep_services.show(uuid) +#' @usage arv$links.get_permissions(uuid) #' @param uuid -#' @return KeepService object. -#' @name keep_services.show +#' @return Link object. +#' @name links.get_permissions NULL -#' keep_services.destroy is a method defined in Arvados class. +#' keep_services.get #' -#' @usage arv$keep_services.destroy(uuid) -#' @param uuid +#' keep_services.get is a method defined in Arvados class. +#' +#' @usage arv$keep_services.get(uuid) +#' @param uuid The UUID of the KeepService in question. #' @return KeepService object. -#' @name keep_services.destroy +#' @name keep_services.get NULL -#' pipeline_templates.get is a method defined in Arvados class. +#' keep_services.create #' -#' @usage arv$pipeline_templates.get(uuid) -#' @param uuid The UUID of the PipelineTemplate in question. -#' @return PipelineTemplate object. -#' @name pipeline_templates.get +#' keep_services.create is a method defined in Arvados class. +#' +#' @usage arv$keep_services.create(keepservice, +#' ensure_unique_name = "false") +#' @param keepService KeepService object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return KeepService object. +#' @name keep_services.create +NULL + +#' keep_services.update +#' +#' keep_services.update is a method defined in Arvados class. +#' +#' @usage arv$keep_services.update(keepservice, +#' uuid) +#' @param keepService KeepService object. +#' @param uuid The UUID of the KeepService in question. +#' @return KeepService object. +#' @name keep_services.update +NULL + +#' keep_services.delete +#' +#' keep_services.delete is a method defined in Arvados class. +#' +#' @usage arv$keep_services.delete(uuid) +#' @param uuid The UUID of the KeepService in question. +#' @return KeepService object. +#' @name keep_services.delete +NULL + +#' keep_services.accessible +#' +#' keep_services.accessible is a method defined in Arvados class. +#' +#' @usage arv$keep_services.accessible(NULL) +#' @return KeepService object. +#' @name keep_services.accessible NULL -#' pipeline_templates.index is a method defined in Arvados class. +#' keep_services.list #' -#' @usage arv$pipeline_templates.index(filters = NULL, +#' keep_services.list is a method defined in Arvados class. +#' +#' @usage arv$keep_services.list(filters = NULL, #' where = NULL, order = NULL, select = NULL, #' distinct = NULL, limit = "100", offset = "0", #' count = "exact") @@ -1365,10 +1171,22 @@ NULL #' @param limit #' @param offset #' @param count -#' @return PipelineTemplateList object. -#' @name pipeline_templates.index +#' @return KeepServiceList object. +#' @name keep_services.list +NULL + +#' pipeline_templates.get +#' +#' pipeline_templates.get is a method defined in Arvados class. +#' +#' @usage arv$pipeline_templates.get(uuid) +#' @param uuid The UUID of the PipelineTemplate in question. +#' @return PipelineTemplate object. +#' @name pipeline_templates.get NULL +#' pipeline_templates.create +#' #' pipeline_templates.create is a method defined in Arvados class. #' #' @usage arv$pipeline_templates.create(pipelinetemplate, @@ -1379,6 +1197,8 @@ NULL #' @name pipeline_templates.create NULL +#' pipeline_templates.update +#' #' pipeline_templates.update is a method defined in Arvados class. #' #' @usage arv$pipeline_templates.update(pipelinetemplate, @@ -1389,6 +1209,8 @@ NULL #' @name pipeline_templates.update NULL +#' pipeline_templates.delete +#' #' pipeline_templates.delete is a method defined in Arvados class. #' #' @usage arv$pipeline_templates.delete(uuid) @@ -1397,6 +1219,8 @@ NULL #' @name pipeline_templates.delete NULL +#' pipeline_templates.list +#' #' pipeline_templates.list is a method defined in Arvados class. #' #' @usage arv$pipeline_templates.list(filters = NULL, @@ -1415,22 +1239,8 @@ NULL #' @name pipeline_templates.list NULL -#' pipeline_templates.show is a method defined in Arvados class. -#' -#' @usage arv$pipeline_templates.show(uuid) -#' @param uuid -#' @return PipelineTemplate object. -#' @name pipeline_templates.show -NULL - -#' pipeline_templates.destroy is a method defined in Arvados class. +#' pipeline_instances.get #' -#' @usage arv$pipeline_templates.destroy(uuid) -#' @param uuid -#' @return PipelineTemplate object. -#' @name pipeline_templates.destroy -NULL - #' pipeline_instances.get is a method defined in Arvados class. #' #' @usage arv$pipeline_instances.get(uuid) @@ -1439,24 +1249,8 @@ NULL #' @name pipeline_instances.get NULL -#' pipeline_instances.index is a method defined in Arvados class. +#' pipeline_instances.create #' -#' @usage arv$pipeline_instances.index(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return PipelineInstanceList object. -#' @name pipeline_instances.index -NULL - #' pipeline_instances.create is a method defined in Arvados class. #' #' @usage arv$pipeline_instances.create(pipelineinstance, @@ -1467,6 +1261,8 @@ NULL #' @name pipeline_instances.create NULL +#' pipeline_instances.update +#' #' pipeline_instances.update is a method defined in Arvados class. #' #' @usage arv$pipeline_instances.update(pipelineinstance, @@ -1477,6 +1273,8 @@ NULL #' @name pipeline_instances.update NULL +#' pipeline_instances.delete +#' #' pipeline_instances.delete is a method defined in Arvados class. #' #' @usage arv$pipeline_instances.delete(uuid) @@ -1485,6 +1283,8 @@ NULL #' @name pipeline_instances.delete NULL +#' pipeline_instances.cancel +#' #' pipeline_instances.cancel is a method defined in Arvados class. #' #' @usage arv$pipeline_instances.cancel(uuid) @@ -1493,6 +1293,8 @@ NULL #' @name pipeline_instances.cancel NULL +#' pipeline_instances.list +#' #' pipeline_instances.list is a method defined in Arvados class. #' #' @usage arv$pipeline_instances.list(filters = NULL, @@ -1511,120 +1313,8 @@ NULL #' @name pipeline_instances.list NULL -#' pipeline_instances.show is a method defined in Arvados class. -#' -#' @usage arv$pipeline_instances.show(uuid) -#' @param uuid -#' @return PipelineInstance object. -#' @name pipeline_instances.show -NULL - -#' pipeline_instances.destroy is a method defined in Arvados class. -#' -#' @usage arv$pipeline_instances.destroy(uuid) -#' @param uuid -#' @return PipelineInstance object. -#' @name pipeline_instances.destroy -NULL - -#' nodes.get is a method defined in Arvados class. -#' -#' @usage arv$nodes.get(uuid) -#' @param uuid The UUID of the Node in question. -#' @return Node object. -#' @name nodes.get -NULL - -#' nodes.index is a method defined in Arvados class. -#' -#' @usage arv$nodes.index(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 -#' @return NodeList object. -#' @name nodes.index -NULL - -#' nodes.create is a method defined in Arvados class. -#' -#' @usage arv$nodes.create(node, ensure_unique_name = "false", -#' assign_slot = NULL) -#' @param node Node object. -#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. -#' @param assign_slot assign slot and hostname -#' @return Node object. -#' @name nodes.create -NULL - -#' nodes.update is a method defined in Arvados class. -#' -#' @usage arv$nodes.update(node, uuid, assign_slot = NULL) -#' @param node Node object. -#' @param uuid The UUID of the Node in question. -#' @param assign_slot assign slot and hostname -#' @return Node object. -#' @name nodes.update -NULL - -#' nodes.delete is a method defined in Arvados class. -#' -#' @usage arv$nodes.delete(uuid) -#' @param uuid The UUID of the Node in question. -#' @return Node object. -#' @name nodes.delete -NULL - -#' nodes.ping is a method defined in Arvados class. -#' -#' @usage arv$nodes.ping(uuid, ping_secret) -#' @param uuid -#' @param ping_secret -#' @return Node object. -#' @name nodes.ping -NULL - -#' nodes.list is a method defined in Arvados class. -#' -#' @usage arv$nodes.list(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return NodeList object. -#' @name nodes.list -NULL - -#' nodes.show is a method defined in Arvados class. -#' -#' @usage arv$nodes.show(uuid) -#' @param uuid -#' @return Node object. -#' @name nodes.show -NULL - -#' nodes.destroy is a method defined in Arvados class. +#' repositories.get #' -#' @usage arv$nodes.destroy(uuid) -#' @param uuid -#' @return Node object. -#' @name nodes.destroy -NULL - #' repositories.get is a method defined in Arvados class. #' #' @usage arv$repositories.get(uuid) @@ -1633,24 +1323,8 @@ NULL #' @name repositories.get NULL -#' repositories.index is a method defined in Arvados class. +#' repositories.create #' -#' @usage arv$repositories.index(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return RepositoryList object. -#' @name repositories.index -NULL - #' repositories.create is a method defined in Arvados class. #' #' @usage arv$repositories.create(repository, @@ -1661,6 +1335,8 @@ NULL #' @name repositories.create NULL +#' repositories.update +#' #' repositories.update is a method defined in Arvados class. #' #' @usage arv$repositories.update(repository, @@ -1671,6 +1347,8 @@ NULL #' @name repositories.update NULL +#' repositories.delete +#' #' repositories.delete is a method defined in Arvados class. #' #' @usage arv$repositories.delete(uuid) @@ -1679,6 +1357,8 @@ NULL #' @name repositories.delete NULL +#' repositories.get_all_permissions +#' #' repositories.get_all_permissions is a method defined in Arvados class. #' #' @usage arv$repositories.get_all_permissions(NULL) @@ -1686,6 +1366,8 @@ NULL #' @name repositories.get_all_permissions NULL +#' repositories.list +#' #' repositories.list is a method defined in Arvados class. #' #' @usage arv$repositories.list(filters = NULL, @@ -1704,22 +1386,8 @@ NULL #' @name repositories.list NULL -#' repositories.show is a method defined in Arvados class. -#' -#' @usage arv$repositories.show(uuid) -#' @param uuid -#' @return Repository object. -#' @name repositories.show -NULL - -#' repositories.destroy is a method defined in Arvados class. +#' specimens.get #' -#' @usage arv$repositories.destroy(uuid) -#' @param uuid -#' @return Repository object. -#' @name repositories.destroy -NULL - #' specimens.get is a method defined in Arvados class. #' #' @usage arv$specimens.get(uuid) @@ -1728,24 +1396,8 @@ NULL #' @name specimens.get NULL -#' specimens.index is a method defined in Arvados class. +#' specimens.create #' -#' @usage arv$specimens.index(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 -#' @return SpecimenList object. -#' @name specimens.index -NULL - #' specimens.create is a method defined in Arvados class. #' #' @usage arv$specimens.create(specimen, @@ -1756,6 +1408,8 @@ NULL #' @name specimens.create NULL +#' specimens.update +#' #' specimens.update is a method defined in Arvados class. #' #' @usage arv$specimens.update(specimen, @@ -1766,6 +1420,8 @@ NULL #' @name specimens.update NULL +#' specimens.delete +#' #' specimens.delete is a method defined in Arvados class. #' #' @usage arv$specimens.delete(uuid) @@ -1774,6 +1430,8 @@ NULL #' @name specimens.delete NULL +#' specimens.list +#' #' specimens.list is a method defined in Arvados class. #' #' @usage arv$specimens.list(filters = NULL, @@ -1792,22 +1450,8 @@ NULL #' @name specimens.list NULL -#' specimens.show is a method defined in Arvados class. +#' logs.get #' -#' @usage arv$specimens.show(uuid) -#' @param uuid -#' @return Specimen object. -#' @name specimens.show -NULL - -#' specimens.destroy is a method defined in Arvados class. -#' -#' @usage arv$specimens.destroy(uuid) -#' @param uuid -#' @return Specimen object. -#' @name specimens.destroy -NULL - #' logs.get is a method defined in Arvados class. #' #' @usage arv$logs.get(uuid) @@ -1816,24 +1460,8 @@ NULL #' @name logs.get NULL -#' logs.index is a method defined in Arvados class. +#' logs.create #' -#' @usage arv$logs.index(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 -#' @return LogList object. -#' @name logs.index -NULL - #' logs.create is a method defined in Arvados class. #' #' @usage arv$logs.create(log, ensure_unique_name = "false") @@ -1843,6 +1471,8 @@ NULL #' @name logs.create NULL +#' logs.update +#' #' logs.update is a method defined in Arvados class. #' #' @usage arv$logs.update(log, uuid) @@ -1852,6 +1482,8 @@ NULL #' @name logs.update NULL +#' logs.delete +#' #' logs.delete is a method defined in Arvados class. #' #' @usage arv$logs.delete(uuid) @@ -1860,6 +1492,8 @@ NULL #' @name logs.delete NULL +#' logs.list +#' #' logs.list is a method defined in Arvados class. #' #' @usage arv$logs.list(filters = NULL, where = NULL, @@ -1877,23 +1511,9 @@ NULL #' @name logs.list NULL -#' logs.show is a method defined in Arvados class. +#' traits.get #' -#' @usage arv$logs.show(uuid) -#' @param uuid -#' @return Log object. -#' @name logs.show -NULL - -#' logs.destroy is a method defined in Arvados class. -#' -#' @usage arv$logs.destroy(uuid) -#' @param uuid -#' @return Log object. -#' @name logs.destroy -NULL - -#' traits.get is a method defined in Arvados class. +#' traits.get is a method defined in Arvados class. #' #' @usage arv$traits.get(uuid) #' @param uuid The UUID of the Trait in question. @@ -1901,24 +1521,8 @@ NULL #' @name traits.get NULL -#' traits.index is a method defined in Arvados class. +#' traits.create #' -#' @usage arv$traits.index(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 -#' @return TraitList object. -#' @name traits.index -NULL - #' traits.create is a method defined in Arvados class. #' #' @usage arv$traits.create(trait, ensure_unique_name = "false") @@ -1928,6 +1532,8 @@ NULL #' @name traits.create NULL +#' traits.update +#' #' traits.update is a method defined in Arvados class. #' #' @usage arv$traits.update(trait, uuid) @@ -1937,6 +1543,8 @@ NULL #' @name traits.update NULL +#' traits.delete +#' #' traits.delete is a method defined in Arvados class. #' #' @usage arv$traits.delete(uuid) @@ -1945,6 +1553,8 @@ NULL #' @name traits.delete NULL +#' traits.list +#' #' traits.list is a method defined in Arvados class. #' #' @usage arv$traits.list(filters = NULL, @@ -1963,22 +1573,8 @@ NULL #' @name traits.list NULL -#' traits.show is a method defined in Arvados class. -#' -#' @usage arv$traits.show(uuid) -#' @param uuid -#' @return Trait object. -#' @name traits.show -NULL - -#' traits.destroy is a method defined in Arvados class. +#' virtual_machines.get #' -#' @usage arv$traits.destroy(uuid) -#' @param uuid -#' @return Trait object. -#' @name traits.destroy -NULL - #' virtual_machines.get is a method defined in Arvados class. #' #' @usage arv$virtual_machines.get(uuid) @@ -1987,24 +1583,8 @@ NULL #' @name virtual_machines.get NULL -#' virtual_machines.index is a method defined in Arvados class. +#' virtual_machines.create #' -#' @usage arv$virtual_machines.index(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 -#' @return VirtualMachineList object. -#' @name virtual_machines.index -NULL - #' virtual_machines.create is a method defined in Arvados class. #' #' @usage arv$virtual_machines.create(virtualmachine, @@ -2015,6 +1595,8 @@ NULL #' @name virtual_machines.create NULL +#' virtual_machines.update +#' #' virtual_machines.update is a method defined in Arvados class. #' #' @usage arv$virtual_machines.update(virtualmachine, @@ -2025,6 +1607,8 @@ NULL #' @name virtual_machines.update NULL +#' virtual_machines.delete +#' #' virtual_machines.delete is a method defined in Arvados class. #' #' @usage arv$virtual_machines.delete(uuid) @@ -2033,6 +1617,8 @@ NULL #' @name virtual_machines.delete NULL +#' virtual_machines.logins +#' #' virtual_machines.logins is a method defined in Arvados class. #' #' @usage arv$virtual_machines.logins(uuid) @@ -2041,6 +1627,8 @@ NULL #' @name virtual_machines.logins NULL +#' virtual_machines.get_all_logins +#' #' virtual_machines.get_all_logins is a method defined in Arvados class. #' #' @usage arv$virtual_machines.get_all_logins(NULL) @@ -2048,6 +1636,8 @@ NULL #' @name virtual_machines.get_all_logins NULL +#' virtual_machines.list +#' #' virtual_machines.list is a method defined in Arvados class. #' #' @usage arv$virtual_machines.list(filters = NULL, @@ -2066,22 +1656,8 @@ NULL #' @name virtual_machines.list NULL -#' virtual_machines.show is a method defined in Arvados class. -#' -#' @usage arv$virtual_machines.show(uuid) -#' @param uuid -#' @return VirtualMachine object. -#' @name virtual_machines.show -NULL - -#' virtual_machines.destroy is a method defined in Arvados class. +#' workflows.get #' -#' @usage arv$virtual_machines.destroy(uuid) -#' @param uuid -#' @return VirtualMachine object. -#' @name virtual_machines.destroy -NULL - #' workflows.get is a method defined in Arvados class. #' #' @usage arv$workflows.get(uuid) @@ -2090,24 +1666,8 @@ NULL #' @name workflows.get NULL -#' workflows.index is a method defined in Arvados class. +#' workflows.create #' -#' @usage arv$workflows.index(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 -#' @return WorkflowList object. -#' @name workflows.index -NULL - #' workflows.create is a method defined in Arvados class. #' #' @usage arv$workflows.create(workflow, @@ -2118,6 +1678,8 @@ NULL #' @name workflows.create NULL +#' workflows.update +#' #' workflows.update is a method defined in Arvados class. #' #' @usage arv$workflows.update(workflow, @@ -2128,6 +1690,8 @@ NULL #' @name workflows.update NULL +#' workflows.delete +#' #' workflows.delete is a method defined in Arvados class. #' #' @usage arv$workflows.delete(uuid) @@ -2136,6 +1700,8 @@ NULL #' @name workflows.delete NULL +#' workflows.list +#' #' workflows.list is a method defined in Arvados class. #' #' @usage arv$workflows.list(filters = NULL, @@ -2154,22 +1720,8 @@ NULL #' @name workflows.list NULL -#' workflows.show is a method defined in Arvados class. -#' -#' @usage arv$workflows.show(uuid) -#' @param uuid -#' @return Workflow object. -#' @name workflows.show -NULL - -#' workflows.destroy is a method defined in Arvados class. +#' groups.get #' -#' @usage arv$workflows.destroy(uuid) -#' @param uuid -#' @return Workflow object. -#' @name workflows.destroy -NULL - #' groups.get is a method defined in Arvados class. #' #' @usage arv$groups.get(uuid) @@ -2178,25 +1730,8 @@ NULL #' @name groups.get NULL -#' groups.index is a method defined in Arvados class. +#' groups.create #' -#' @usage arv$groups.index(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 include_trash Include items whose is_trashed attribute is true. -#' @return GroupList object. -#' @name groups.index -NULL - #' groups.create is a method defined in Arvados class. #' #' @usage arv$groups.create(group, ensure_unique_name = "false") @@ -2206,6 +1741,8 @@ NULL #' @name groups.create NULL +#' groups.update +#' #' groups.update is a method defined in Arvados class. #' #' @usage arv$groups.update(group, uuid) @@ -2215,6 +1752,8 @@ NULL #' @name groups.update NULL +#' groups.delete +#' #' groups.delete is a method defined in Arvados class. #' #' @usage arv$groups.delete(uuid) @@ -2223,6 +1762,8 @@ NULL #' @name groups.delete NULL +#' groups.contents +#' #' groups.contents is a method defined in Arvados class. #' #' @usage arv$groups.contents(filters = NULL, @@ -2243,6 +1784,8 @@ NULL #' @name groups.contents NULL +#' groups.trash +#' #' groups.trash is a method defined in Arvados class. #' #' @usage arv$groups.trash(uuid) @@ -2251,6 +1794,8 @@ NULL #' @name groups.trash NULL +#' groups.untrash +#' #' groups.untrash is a method defined in Arvados class. #' #' @usage arv$groups.untrash(uuid) @@ -2259,6 +1804,8 @@ NULL #' @name groups.untrash NULL +#' groups.list +#' #' groups.list is a method defined in Arvados class. #' #' @usage arv$groups.list(filters = NULL, @@ -2278,22 +1825,8 @@ NULL #' @name groups.list NULL -#' groups.show is a method defined in Arvados class. -#' -#' @usage arv$groups.show(uuid) -#' @param uuid -#' @return Group object. -#' @name groups.show -NULL - -#' groups.destroy is a method defined in Arvados class. +#' user_agreements.get #' -#' @usage arv$groups.destroy(uuid) -#' @param uuid -#' @return Group object. -#' @name groups.destroy -NULL - #' user_agreements.get is a method defined in Arvados class. #' #' @usage arv$user_agreements.get(uuid) @@ -2302,24 +1835,8 @@ NULL #' @name user_agreements.get NULL -#' user_agreements.index is a method defined in Arvados class. +#' user_agreements.create #' -#' @usage arv$user_agreements.index(filters = NULL, -#' where = NULL, order = NULL, select = NULL, -#' distinct = NULL, limit = "100", offset = "0", -#' count = "exact") -#' @param filters -#' @param where -#' @param order -#' @param select -#' @param distinct -#' @param limit -#' @param offset -#' @param count -#' @return UserAgreementList object. -#' @name user_agreements.index -NULL - #' user_agreements.create is a method defined in Arvados class. #' #' @usage arv$user_agreements.create(useragreement, @@ -2330,6 +1847,8 @@ NULL #' @name user_agreements.create NULL +#' user_agreements.update +#' #' user_agreements.update is a method defined in Arvados class. #' #' @usage arv$user_agreements.update(useragreement, @@ -2340,6 +1859,8 @@ NULL #' @name user_agreements.update NULL +#' user_agreements.delete +#' #' user_agreements.delete is a method defined in Arvados class. #' #' @usage arv$user_agreements.delete(uuid) @@ -2348,6 +1869,8 @@ NULL #' @name user_agreements.delete NULL +#' user_agreements.signatures +#' #' user_agreements.signatures is a method defined in Arvados class. #' #' @usage arv$user_agreements.signatures(NULL) @@ -2355,6 +1878,8 @@ NULL #' @name user_agreements.signatures NULL +#' user_agreements.sign +#' #' user_agreements.sign is a method defined in Arvados class. #' #' @usage arv$user_agreements.sign(NULL) @@ -2362,6 +1887,8 @@ NULL #' @name user_agreements.sign NULL +#' user_agreements.list +#' #' user_agreements.list is a method defined in Arvados class. #' #' @usage arv$user_agreements.list(filters = NULL, @@ -2380,6 +1907,8 @@ NULL #' @name user_agreements.list NULL +#' user_agreements.new +#' #' user_agreements.new is a method defined in Arvados class. #' #' @usage arv$user_agreements.new(NULL) @@ -2387,20 +1916,267 @@ NULL #' @name user_agreements.new NULL -#' user_agreements.show is a method defined in Arvados class. +#' project.get #' -#' @usage arv$user_agreements.show(uuid) -#' @param uuid -#' @return UserAgreement object. -#' @name user_agreements.show +#' projects.get is equivalent to groups.get method. +#' +#' @usage arv$projects.get(uuid) +#' @param uuid The UUID of the Group in question. +#' @return Group object. +#' @name projects.get +NULL + +#' project.create +#' +#' projects.create wrapps groups.create method by setting group_class attribute to "project". +#' +#' @usage arv$projects.create(group, ensure_unique_name = "false") +#' @param group Group object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Group object. +#' @name projects.create +NULL + +#' project.update +#' +#' projects.update wrapps groups.update method by setting group_class attribute to "project". +#' +#' @usage arv$projects.update(group, uuid) +#' @param group Group object. +#' @param uuid The UUID of the Group in question. +#' @return Group object. +#' @name projects.update +NULL + +#' project.delete +#' +#' projects.delete is equivalent to groups.delete method. +#' +#' @usage arv$project.delete(uuid) +#' @param uuid The UUID of the Group in question. +#' @return Group object. +#' @name projects.delete NULL -#' user_agreements.destroy is a method defined in Arvados class. +#' project.list #' -#' @usage arv$user_agreements.destroy(uuid) +#' projects.list wrapps groups.list method by setting group_class attribute to "project". +#' +#' @usage arv$projects.list(filters = NULL, +#' where = NULL, order = NULL, distinct = NULL, +#' limit = "100", offset = "0", count = "exact", +#' include_trash = NULL, uuid = NULL, recursive = NULL) +#' @param filters +#' @param where +#' @param order +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @param include_trash Include items whose is_trashed attribute is true. #' @param uuid -#' @return UserAgreement object. -#' @name user_agreements.destroy +#' @param recursive Include contents from child groups recursively. +#' @return Group object. +#' @name projects.list +NULL + +#' Arvados +#' +#' Arvados class gives users ability to access Arvados REST API. +#' +#' @section Usage: +#' \preformatted{arv = Arvados$new(authToken = NULL, hostName = NULL, numRetries = 0)} +#' +#' @section Arguments: +#' \describe{ +#' \item{authToken}{Authentification token. If not specified ARVADOS_API_TOKEN environment variable will be used.} +#' \item{hostName}{Host name. If not specified ARVADOS_API_HOST environment variable will be used.} +#' \item{numRetries}{Number which specifies how many times to retry failed service requests.} +#' } +#' +#' @section Methods: +#' \describe{ +#' \item{}{\code{\link{api_client_authorizations.create}}} +#' \item{}{\code{\link{api_client_authorizations.create_system_auth}}} +#' \item{}{\code{\link{api_client_authorizations.current}}} +#' \item{}{\code{\link{api_client_authorizations.delete}}} +#' \item{}{\code{\link{api_client_authorizations.get}}} +#' \item{}{\code{\link{api_client_authorizations.list}}} +#' \item{}{\code{\link{api_client_authorizations.update}}} +#' \item{}{\code{\link{api_clients.create}}} +#' \item{}{\code{\link{api_clients.delete}}} +#' \item{}{\code{\link{api_clients.get}}} +#' \item{}{\code{\link{api_clients.list}}} +#' \item{}{\code{\link{api_clients.update}}} +#' \item{}{\code{\link{authorized_keys.create}}} +#' \item{}{\code{\link{authorized_keys.delete}}} +#' \item{}{\code{\link{authorized_keys.get}}} +#' \item{}{\code{\link{authorized_keys.list}}} +#' \item{}{\code{\link{authorized_keys.update}}} +#' \item{}{\code{\link{collections.create}}} +#' \item{}{\code{\link{collections.delete}}} +#' \item{}{\code{\link{collections.get}}} +#' \item{}{\code{\link{collections.list}}} +#' \item{}{\code{\link{collections.provenance}}} +#' \item{}{\code{\link{collections.trash}}} +#' \item{}{\code{\link{collections.untrash}}} +#' \item{}{\code{\link{collections.update}}} +#' \item{}{\code{\link{collections.used_by}}} +#' \item{}{\code{\link{container_requests.create}}} +#' \item{}{\code{\link{container_requests.delete}}} +#' \item{}{\code{\link{container_requests.get}}} +#' \item{}{\code{\link{container_requests.list}}} +#' \item{}{\code{\link{container_requests.update}}} +#' \item{}{\code{\link{containers.auth}}} +#' \item{}{\code{\link{containers.create}}} +#' \item{}{\code{\link{containers.current}}} +#' \item{}{\code{\link{containers.delete}}} +#' \item{}{\code{\link{containers.get}}} +#' \item{}{\code{\link{containers.list}}} +#' \item{}{\code{\link{containers.lock}}} +#' \item{}{\code{\link{containers.secret_mounts}}} +#' \item{}{\code{\link{containers.unlock}}} +#' \item{}{\code{\link{containers.update}}} +#' \item{}{\code{\link{groups.contents}}} +#' \item{}{\code{\link{groups.create}}} +#' \item{}{\code{\link{groups.delete}}} +#' \item{}{\code{\link{groups.get}}} +#' \item{}{\code{\link{groups.list}}} +#' \item{}{\code{\link{groups.trash}}} +#' \item{}{\code{\link{groups.untrash}}} +#' \item{}{\code{\link{groups.update}}} +#' \item{}{\code{\link{humans.create}}} +#' \item{}{\code{\link{humans.delete}}} +#' \item{}{\code{\link{humans.get}}} +#' \item{}{\code{\link{humans.list}}} +#' \item{}{\code{\link{humans.update}}} +#' \item{}{\code{\link{jobs.cancel}}} +#' \item{}{\code{\link{jobs.create}}} +#' \item{}{\code{\link{jobs.delete}}} +#' \item{}{\code{\link{jobs.get}}} +#' \item{}{\code{\link{jobs.list}}} +#' \item{}{\code{\link{jobs.lock}}} +#' \item{}{\code{\link{jobs.queue}}} +#' \item{}{\code{\link{jobs.queue_size}}} +#' \item{}{\code{\link{jobs.update}}} +#' \item{}{\code{\link{job_tasks.create}}} +#' \item{}{\code{\link{job_tasks.delete}}} +#' \item{}{\code{\link{job_tasks.get}}} +#' \item{}{\code{\link{job_tasks.list}}} +#' \item{}{\code{\link{job_tasks.update}}} +#' \item{}{\code{\link{keep_disks.create}}} +#' \item{}{\code{\link{keep_disks.delete}}} +#' \item{}{\code{\link{keep_disks.get}}} +#' \item{}{\code{\link{keep_disks.list}}} +#' \item{}{\code{\link{keep_disks.ping}}} +#' \item{}{\code{\link{keep_disks.update}}} +#' \item{}{\code{\link{keep_services.accessible}}} +#' \item{}{\code{\link{keep_services.create}}} +#' \item{}{\code{\link{keep_services.delete}}} +#' \item{}{\code{\link{keep_services.get}}} +#' \item{}{\code{\link{keep_services.list}}} +#' \item{}{\code{\link{keep_services.update}}} +#' \item{}{\code{\link{links.create}}} +#' \item{}{\code{\link{links.delete}}} +#' \item{}{\code{\link{links.get}}} +#' \item{}{\code{\link{links.get_permissions}}} +#' \item{}{\code{\link{links.list}}} +#' \item{}{\code{\link{links.update}}} +#' \item{}{\code{\link{logs.create}}} +#' \item{}{\code{\link{logs.delete}}} +#' \item{}{\code{\link{logs.get}}} +#' \item{}{\code{\link{logs.list}}} +#' \item{}{\code{\link{logs.update}}} +#' \item{}{\code{\link{nodes.create}}} +#' \item{}{\code{\link{nodes.delete}}} +#' \item{}{\code{\link{nodes.get}}} +#' \item{}{\code{\link{nodes.list}}} +#' \item{}{\code{\link{nodes.ping}}} +#' \item{}{\code{\link{nodes.update}}} +#' \item{}{\code{\link{pipeline_instances.cancel}}} +#' \item{}{\code{\link{pipeline_instances.create}}} +#' \item{}{\code{\link{pipeline_instances.delete}}} +#' \item{}{\code{\link{pipeline_instances.get}}} +#' \item{}{\code{\link{pipeline_instances.list}}} +#' \item{}{\code{\link{pipeline_instances.update}}} +#' \item{}{\code{\link{pipeline_templates.create}}} +#' \item{}{\code{\link{pipeline_templates.delete}}} +#' \item{}{\code{\link{pipeline_templates.get}}} +#' \item{}{\code{\link{pipeline_templates.list}}} +#' \item{}{\code{\link{pipeline_templates.update}}} +#' \item{}{\code{\link{projects.create}}} +#' \item{}{\code{\link{projects.delete}}} +#' \item{}{\code{\link{projects.get}}} +#' \item{}{\code{\link{projects.list}}} +#' \item{}{\code{\link{projects.update}}} +#' \item{}{\code{\link{repositories.create}}} +#' \item{}{\code{\link{repositories.delete}}} +#' \item{}{\code{\link{repositories.get}}} +#' \item{}{\code{\link{repositories.get_all_permissions}}} +#' \item{}{\code{\link{repositories.list}}} +#' \item{}{\code{\link{repositories.update}}} +#' \item{}{\code{\link{specimens.create}}} +#' \item{}{\code{\link{specimens.delete}}} +#' \item{}{\code{\link{specimens.get}}} +#' \item{}{\code{\link{specimens.list}}} +#' \item{}{\code{\link{specimens.update}}} +#' \item{}{\code{\link{traits.create}}} +#' \item{}{\code{\link{traits.delete}}} +#' \item{}{\code{\link{traits.get}}} +#' \item{}{\code{\link{traits.list}}} +#' \item{}{\code{\link{traits.update}}} +#' \item{}{\code{\link{user_agreements.create}}} +#' \item{}{\code{\link{user_agreements.delete}}} +#' \item{}{\code{\link{user_agreements.get}}} +#' \item{}{\code{\link{user_agreements.list}}} +#' \item{}{\code{\link{user_agreements.new}}} +#' \item{}{\code{\link{user_agreements.sign}}} +#' \item{}{\code{\link{user_agreements.signatures}}} +#' \item{}{\code{\link{user_agreements.update}}} +#' \item{}{\code{\link{users.activate}}} +#' \item{}{\code{\link{users.create}}} +#' \item{}{\code{\link{users.current}}} +#' \item{}{\code{\link{users.delete}}} +#' \item{}{\code{\link{users.get}}} +#' \item{}{\code{\link{users.list}}} +#' \item{}{\code{\link{users.merge}}} +#' \item{}{\code{\link{users.setup}}} +#' \item{}{\code{\link{users.system}}} +#' \item{}{\code{\link{users.unsetup}}} +#' \item{}{\code{\link{users.update}}} +#' \item{}{\code{\link{users.update_uuid}}} +#' \item{}{\code{\link{virtual_machines.create}}} +#' \item{}{\code{\link{virtual_machines.delete}}} +#' \item{}{\code{\link{virtual_machines.get}}} +#' \item{}{\code{\link{virtual_machines.get_all_logins}}} +#' \item{}{\code{\link{virtual_machines.list}}} +#' \item{}{\code{\link{virtual_machines.logins}}} +#' \item{}{\code{\link{virtual_machines.update}}} +#' \item{}{\code{\link{workflows.create}}} +#' \item{}{\code{\link{workflows.delete}}} +#' \item{}{\code{\link{workflows.get}}} +#' \item{}{\code{\link{workflows.list}}} +#' \item{}{\code{\link{workflows.update}}} +#' } +#' +#' @name Arvados +#' @examples +#' \dontrun{ +#' arv <- Arvados$new("your Arvados token", "example.arvadosapi.com") +#' +#' collection <- arv$collections.get("uuid") +#' +#' collectionList <- arv$collections.list(list(list("name", "like", "Test%"))) +#' collectionList <- listAll(arv$collections.list, list(list("name", "like", "Test%"))) +#' +#' deletedCollection <- arv$collections.delete("uuid") +#' +#' updatedCollection <- arv$collections.update(list(name = "New name", description = "New description"), +#' "uuid") +#' +#' createdCollection <- arv$collections.create(list(name = "Example", +#' description = "This is a test collection")) +#' } NULL #' @export @@ -2426,1247 +2202,50 @@ Arvados <- R6::R6Class( "or set ARVADOS_API_HOST and ARVADOS_API_TOKEN", "environment variables.")) - private$token <- token - private$host <- paste0("https://", hostName, "/arvados/v1/") - private$numRetries <- numRetries - private$REST <- RESTService$new(token, hostName, - HttpRequest$new(), HttpParser$new(), - numRetries) - - }, - - users.get = function(uuid) - { - endPoint <- stringr::str_interp("users/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.index = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("users") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - 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$errors) - - resource - }, - - users.create = function(user, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("users") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(user) > 0) - body <- jsonlite::toJSON(list(user = user), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$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 - }, - - users.update = function(user, uuid) - { - endPoint <- stringr::str_interp("users/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(user) > 0) - body <- jsonlite::toJSON(list(user = user), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$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 - }, - - users.delete = function(uuid) - { - endPoint <- stringr::str_interp("users/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.current = function() - { - endPoint <- stringr::str_interp("users/current") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.system = function() - { - endPoint <- stringr::str_interp("users/system") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.activate = function(uuid) - { - endPoint <- stringr::str_interp("users/${uuid}/activate") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.setup = function(user = NULL, openid_prefix = NULL, - repo_name = NULL, vm_uuid = NULL, send_notification_email = "false") - { - endPoint <- stringr::str_interp("users/setup") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$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$errors) - - resource - }, - - users.unsetup = function(uuid) - { - endPoint <- stringr::str_interp("users/${uuid}/unsetup") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.update_uuid = function(uuid, new_uuid) - { - endPoint <- stringr::str_interp("users/${uuid}/update_uuid") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$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$errors) - - resource - }, - - users.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") - { - endPoint <- stringr::str_interp("users") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - body <- NULL - - response <- private$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 - }, - - users.show = function(uuid) - { - endPoint <- stringr::str_interp("users/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - users.destroy = function(uuid) - { - endPoint <- stringr::str_interp("users/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_client_authorizations.get = function(uuid) - { - endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_client_authorizations.index = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("api_client_authorizations") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - 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$errors) - - resource - }, - - api_client_authorizations.create = function(apiclientauthorization, - ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("api_client_authorizations") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(apiclientauthorization) > 0) - body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$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 - }, - - api_client_authorizations.update = function(apiclientauthorization, uuid) - { - endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(apiclientauthorization) > 0) - body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$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 - }, - - api_client_authorizations.delete = function(uuid) - { - endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_client_authorizations.create_system_auth = function(api_client_id = NULL, scopes = NULL) - { - endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$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$errors) - - resource - }, - - api_client_authorizations.current = function() - { - endPoint <- stringr::str_interp("api_client_authorizations/current") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_client_authorizations.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("api_client_authorizations") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - 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$errors) - - resource - }, - - api_client_authorizations.show = function(uuid) - { - endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_client_authorizations.destroy = function(uuid) - { - endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - api_clients.get = function(uuid) - { - endPoint <- stringr::str_interp("api_clients/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - 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$errors) - - resource - }, - - api_clients.index = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("api_clients") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - body <- NULL - - response <- private$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 - }, - - api_clients.create = function(apiclient, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("api_clients") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(apiclient) > 0) - 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$errors) - - resource - }, - - api_clients.update = function(apiclient, uuid) - { - endPoint <- stringr::str_interp("api_clients/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(apiclient) > 0) - 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$errors) - - resource - }, - - api_clients.delete = function(uuid) - { - endPoint <- stringr::str_interp("api_clients/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - 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$errors) - - resource - }, - - api_clients.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("api_clients") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - body <- NULL - - response <- private$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 - }, - - api_clients.show = function(uuid) - { - endPoint <- stringr::str_interp("api_clients/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$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 - }, - - api_clients.destroy = function(uuid) - { - endPoint <- stringr::str_interp("api_clients/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$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 - }, - - container_requests.get = function(uuid) - { - endPoint <- stringr::str_interp("container_requests/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$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 - }, - - container_requests.index = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("container_requests") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - 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$errors) - - resource - }, - - container_requests.create = function(containerrequest, - ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("container_requests") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(containerrequest) > 0) - body <- jsonlite::toJSON(list(containerrequest = containerrequest), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$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 - }, - - container_requests.update = function(containerrequest, uuid) - { - endPoint <- stringr::str_interp("container_requests/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(containerrequest) > 0) - body <- jsonlite::toJSON(list(containerrequest = containerrequest), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$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 - }, - - container_requests.delete = function(uuid) - { - endPoint <- stringr::str_interp("container_requests/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$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 - }, - - container_requests.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("container_requests") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - 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$errors) - - resource - }, - - container_requests.show = function(uuid) - { - endPoint <- stringr::str_interp("container_requests/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - 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$errors) - - resource - }, - - container_requests.destroy = function(uuid) - { - endPoint <- stringr::str_interp("container_requests/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - 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$errors) - - resource - }, - - authorized_keys.get = function(uuid) - { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - authorized_keys.index = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("authorized_keys") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - body <- NULL - - response <- private$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 - }, - - authorized_keys.create = function(authorizedkey, - ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("authorized_keys") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(authorizedkey) > 0) - 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$errors) - - resource - }, - - authorized_keys.update = function(authorizedkey, uuid) - { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(authorizedkey) > 0) - 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$errors) - - resource - }, - - authorized_keys.delete = function(uuid) - { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - authorized_keys.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("authorized_keys") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - body <- NULL - - response <- private$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 - }, - - authorized_keys.show = function(uuid) - { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - authorized_keys.destroy = function(uuid) - { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - collections.get = function(uuid) - { - endPoint <- stringr::str_interp("collections/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - collections.index = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact", include_trash = NULL) - { - endPoint <- stringr::str_interp("collections") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count, - 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$errors) - - resource - }, - - collections.create = function(collection, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("collections") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(collection) > 0) - body <- jsonlite::toJSON(list(collection = collection), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$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 - }, - - collections.update = function(collection, uuid) - { - endPoint <- stringr::str_interp("collections/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - if(length(collection) > 0) - body <- jsonlite::toJSON(list(collection = collection), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$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 - }, - - collections.delete = function(uuid) - { - endPoint <- stringr::str_interp("collections/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$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 + private$token <- token + private$host <- paste0("https://", hostName, "/arvados/v1/") + private$numRetries <- numRetries + private$REST <- RESTService$new(token, hostName, + HttpRequest$new(), HttpParser$new(), + numRetries) + }, - collections.provenance = function(uuid) + projects.get = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}/provenance") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource + self$groups.get(uuid) }, - collections.used_by = function(uuid) + projects.create = function(group, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("collections/${uuid}/used_by") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource + group <- c("group_class" = "project", group) + self$groups.create(group, ensure_unique_name) }, - collections.trash = function(uuid) + projects.update = function(group, uuid) { - endPoint <- stringr::str_interp("collections/${uuid}/trash") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource + group <- c("group_class" = "project", group) + self$groups.update(group, uuid) }, - collections.untrash = function(uuid) + projects.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact", + include_trash = NULL) { - endPoint <- stringr::str_interp("collections/${uuid}/untrash") + filters[[length(filters) + 1]] <- list("group_class", "=", "project") + self$groups.list(filters, where, order, select, distinct, + limit, offset, count, include_trash) + }, + + projects.delete = function(uuid) + { + self$groups.delete(uuid) + }, + + users.get = function(uuid) + { + endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -3674,7 +2253,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -3684,23 +2263,21 @@ Arvados <- R6::R6Class( resource }, - collections.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact", include_trash = NULL) + users.create = function(user, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("collections") + endPoint <- stringr::str_interp("users") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count, - include_trash = include_trash) + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(user) > 0) + body <- jsonlite::toJSON(list(user = user), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -3710,17 +2287,21 @@ Arvados <- R6::R6Class( resource }, - collections.show = function(uuid) + users.update = function(user, uuid) { - endPoint <- stringr::str_interp("collections/${uuid}") + endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL + if(length(user) > 0) + body <- jsonlite::toJSON(list(user = user), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -3730,9 +2311,9 @@ Arvados <- R6::R6Class( resource }, - collections.destroy = function(uuid) + users.delete = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}") + endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -3750,9 +2331,9 @@ Arvados <- R6::R6Class( resource }, - containers.get = function(uuid) + users.current = function() { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("users/current") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -3770,18 +2351,13 @@ Arvados <- R6::R6Class( resource }, - containers.index = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + users.system = function() { - endPoint <- stringr::str_interp("containers") + endPoint <- stringr::str_interp("users/system") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL body <- NULL @@ -3795,19 +2371,15 @@ Arvados <- R6::R6Class( resource }, - containers.create = function(container, ensure_unique_name = "false") + users.activate = function(uuid) { - endPoint <- stringr::str_interp("containers") + endPoint <- stringr::str_interp("users/${uuid}/activate") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- NULL - if(length(container) > 0) - body <- jsonlite::toJSON(list(container = container), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -3819,21 +2391,20 @@ Arvados <- R6::R6Class( resource }, - containers.update = function(container, uuid) + users.setup = function(user = NULL, openid_prefix = NULL, + repo_name = NULL, vm_uuid = NULL, send_notification_email = "false") { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("users/setup") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(user = user, openid_prefix = openid_prefix, + repo_name = repo_name, vm_uuid = vm_uuid, + send_notification_email = send_notification_email) - if(length(container) > 0) - body <- jsonlite::toJSON(list(container = container), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -3843,9 +2414,9 @@ Arvados <- R6::R6Class( resource }, - containers.delete = function(uuid) + users.unsetup = function(uuid) { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("users/${uuid}/unsetup") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -3853,7 +2424,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -3863,17 +2434,17 @@ Arvados <- R6::R6Class( resource }, - containers.auth = function(uuid) + users.update_uuid = function(uuid, new_uuid) { - endPoint <- stringr::str_interp("containers/${uuid}/auth") + endPoint <- stringr::str_interp("users/${uuid}/update_uuid") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(new_uuid = new_uuid) body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -3883,13 +2454,15 @@ Arvados <- R6::R6Class( resource }, - containers.lock = function(uuid) + users.merge = function(new_owner_uuid, new_user_token, + redirect_to_new_user = NULL) { - endPoint <- stringr::str_interp("containers/${uuid}/lock") + endPoint <- stringr::str_interp("users/merge") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(new_owner_uuid = new_owner_uuid, + new_user_token = new_user_token, redirect_to_new_user = redirect_to_new_user) body <- NULL @@ -3903,17 +2476,21 @@ Arvados <- R6::R6Class( resource }, - containers.unlock = function(uuid) + users.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("containers/${uuid}/unlock") + endPoint <- stringr::str_interp("users") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -3923,9 +2500,9 @@ Arvados <- R6::R6Class( resource }, - containers.current = function() + api_client_authorizations.get = function(uuid) { - endPoint <- stringr::str_interp("containers/current") + endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -3943,22 +2520,22 @@ Arvados <- R6::R6Class( resource }, - containers.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + api_client_authorizations.create = function(apiclientauthorization, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("containers") + endPoint <- stringr::str_interp("api_client_authorizations") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(apiclientauthorization) > 0) + body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -3968,17 +2545,21 @@ Arvados <- R6::R6Class( resource }, - containers.show = function(uuid) + api_client_authorizations.update = function(apiclientauthorization, uuid) { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL + if(length(apiclientauthorization) > 0) + body <- jsonlite::toJSON(list(apiclientauthorization = apiclientauthorization), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -3988,9 +2569,9 @@ Arvados <- R6::R6Class( resource }, - containers.destroy = function(uuid) + api_client_authorizations.delete = function(uuid) { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("api_client_authorizations/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -4008,17 +2589,18 @@ Arvados <- R6::R6Class( resource }, - humans.get = function(uuid) + api_client_authorizations.create_system_auth = function(api_client_id = NULL, scopes = NULL) { - endPoint <- stringr::str_interp("humans/${uuid}") + endPoint <- stringr::str_interp("api_client_authorizations/create_system_auth") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(api_client_id = api_client_id, + scopes = scopes) body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4028,17 +2610,13 @@ Arvados <- R6::R6Class( resource }, - humans.index = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + api_client_authorizations.current = function() { - endPoint <- stringr::str_interp("humans") + endPoint <- stringr::str_interp("api_client_authorizations/current") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL body <- NULL @@ -4052,45 +2630,22 @@ Arvados <- R6::R6Class( resource }, - humans.create = function(human, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("humans") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(human) > 0) - body <- jsonlite::toJSON(list(human = human), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$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 - }, - - humans.update = function(human, uuid) + api_client_authorizations.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("humans/${uuid}") + endPoint <- stringr::str_interp("api_client_authorizations") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - if(length(human) > 0) - body <- jsonlite::toJSON(list(human = human), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4100,9 +2655,9 @@ Arvados <- R6::R6Class( resource }, - humans.delete = function(uuid) + containers.get = function(uuid) { - endPoint <- stringr::str_interp("humans/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -4110,7 +2665,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4120,21 +2675,21 @@ Arvados <- R6::R6Class( resource }, - humans.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + containers.create = function(container, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("humans") + endPoint <- stringr::str_interp("containers") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(container) > 0) + body <- jsonlite::toJSON(list(container = container), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4144,17 +2699,21 @@ Arvados <- R6::R6Class( resource }, - humans.show = function(uuid) + containers.update = function(container, uuid) { - endPoint <- stringr::str_interp("humans/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL + if(length(container) > 0) + body <- jsonlite::toJSON(list(container = container), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4164,9 +2723,9 @@ Arvados <- R6::R6Class( resource }, - humans.destroy = function(uuid) + containers.delete = function(uuid) { - endPoint <- stringr::str_interp("humans/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -4184,9 +2743,9 @@ Arvados <- R6::R6Class( resource }, - job_tasks.get = function(uuid) + containers.auth = function(uuid) { - endPoint <- stringr::str_interp("job_tasks/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}/auth") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -4204,22 +2763,17 @@ Arvados <- R6::R6Class( resource }, - job_tasks.index = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + containers.lock = function(uuid) { - endPoint <- stringr::str_interp("job_tasks") + endPoint <- stringr::str_interp("containers/${uuid}/lock") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4229,19 +2783,15 @@ Arvados <- R6::R6Class( resource }, - job_tasks.create = function(jobtask, ensure_unique_name = "false") + containers.unlock = function(uuid) { - endPoint <- stringr::str_interp("job_tasks") + endPoint <- stringr::str_interp("containers/${uuid}/unlock") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- NULL - if(length(jobtask) > 0) - body <- jsonlite::toJSON(list(jobtask = jobtask), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -4253,21 +2803,17 @@ Arvados <- R6::R6Class( resource }, - job_tasks.update = function(jobtask, uuid) + containers.secret_mounts = function(uuid) { - endPoint <- stringr::str_interp("job_tasks/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(jobtask) > 0) - body <- jsonlite::toJSON(list(jobtask = jobtask), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4277,9 +2823,9 @@ Arvados <- R6::R6Class( resource }, - job_tasks.delete = function(uuid) + containers.current = function() { - endPoint <- stringr::str_interp("job_tasks/${uuid}") + endPoint <- stringr::str_interp("containers/current") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -4287,7 +2833,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4297,18 +2843,18 @@ Arvados <- R6::R6Class( resource }, - job_tasks.list = function(filters = NULL, + containers.list = function(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("job_tasks") + endPoint <- stringr::str_interp("containers") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL @@ -4322,9 +2868,9 @@ Arvados <- R6::R6Class( resource }, - job_tasks.show = function(uuid) + api_clients.get = function(uuid) { - endPoint <- stringr::str_interp("job_tasks/${uuid}") + endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -4342,17 +2888,21 @@ Arvados <- R6::R6Class( resource }, - job_tasks.destroy = function(uuid) + api_clients.create = function(apiclient, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("job_tasks/${uuid}") + endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(apiclient) > 0) + body <- jsonlite::toJSON(list(apiclient = apiclient), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4362,17 +2912,21 @@ Arvados <- R6::R6Class( resource }, - links.get = function(uuid) + api_clients.update = function(apiclient, uuid) { - endPoint <- stringr::str_interp("links/${uuid}") + endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL + if(length(apiclient) > 0) + body <- jsonlite::toJSON(list(apiclient = apiclient), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4382,21 +2936,17 @@ Arvados <- R6::R6Class( resource }, - links.index = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + api_clients.delete = function(uuid) { - endPoint <- stringr::str_interp("links") + endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4406,21 +2956,22 @@ Arvados <- R6::R6Class( resource }, - links.create = function(link, ensure_unique_name = "false") + api_clients.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("links") + endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - if(length(link) > 0) - body <- jsonlite::toJSON(list(link = link), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4430,21 +2981,17 @@ Arvados <- R6::R6Class( resource }, - links.update = function(link, uuid) + container_requests.get = function(uuid) { - endPoint <- stringr::str_interp("links/${uuid}") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(link) > 0) - body <- jsonlite::toJSON(list(link = link), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4454,17 +3001,22 @@ Arvados <- R6::R6Class( resource }, - links.delete = function(uuid) + container_requests.create = function(containerrequest, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("links/${uuid}") + endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(containerrequest) > 0) + body <- jsonlite::toJSON(list(containerrequest = containerrequest), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4474,21 +3026,21 @@ Arvados <- R6::R6Class( resource }, - links.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + container_requests.update = function(containerrequest, uuid) { - endPoint <- stringr::str_interp("links") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL - body <- NULL + if(length(containerrequest) > 0) + body <- jsonlite::toJSON(list(containerrequest = containerrequest), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4498,9 +3050,9 @@ Arvados <- R6::R6Class( resource }, - links.show = function(uuid) + container_requests.delete = function(uuid) { - endPoint <- stringr::str_interp("links/${uuid}") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -4508,7 +3060,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4518,17 +3070,22 @@ Arvados <- R6::R6Class( resource }, - links.destroy = function(uuid) + container_requests.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("links/${uuid}") + endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4538,9 +3095,9 @@ Arvados <- R6::R6Class( resource }, - links.get_permissions = function(uuid) + authorized_keys.get = function(uuid) { - endPoint <- stringr::str_interp("permissions/${uuid}") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -4558,17 +3115,22 @@ Arvados <- R6::R6Class( resource }, - jobs.get = function(uuid) + authorized_keys.create = function(authorizedkey, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("jobs/${uuid}") + endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(authorizedkey) > 0) + body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4578,21 +3140,21 @@ Arvados <- R6::R6Class( resource }, - jobs.index = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + authorized_keys.update = function(authorizedkey, uuid) { - endPoint <- stringr::str_interp("jobs") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL - body <- NULL + if(length(authorizedkey) > 0) + body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4602,26 +3164,17 @@ Arvados <- R6::R6Class( resource }, - jobs.create = function(job, ensure_unique_name = "false", - find_or_create = "false", filters = NULL, - minimum_script_version = NULL, exclude_script_versions = NULL) + authorized_keys.delete = function(uuid) { - endPoint <- stringr::str_interp("jobs") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$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) + queryArgs <- NULL - if(length(job) > 0) - body <- jsonlite::toJSON(list(job = job), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4631,21 +3184,22 @@ Arvados <- R6::R6Class( resource }, - jobs.update = function(job, uuid) + authorized_keys.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("jobs/${uuid}") + endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - if(length(job) > 0) - body <- jsonlite::toJSON(list(job = job), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4655,9 +3209,9 @@ Arvados <- R6::R6Class( resource }, - jobs.delete = function(uuid) + collections.get = function(uuid) { - endPoint <- stringr::str_interp("jobs/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -4665,7 +3219,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4673,23 +3227,23 @@ Arvados <- R6::R6Class( stop(resource$errors) resource - }, - - jobs.queue = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + }, + + collections.create = function(collection, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("jobs/queue") + endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(collection) > 0) + body <- jsonlite::toJSON(list(collection = collection), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4699,17 +3253,21 @@ Arvados <- R6::R6Class( resource }, - jobs.queue_size = function() + collections.update = function(collection, uuid) { - endPoint <- stringr::str_interp("jobs/queue_size") + endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL + if(length(collection) > 0) + body <- jsonlite::toJSON(list(collection = collection), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4719,9 +3277,9 @@ Arvados <- R6::R6Class( resource }, - jobs.cancel = function(uuid) + collections.delete = function(uuid) { - endPoint <- stringr::str_interp("jobs/${uuid}/cancel") + endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -4729,7 +3287,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4739,9 +3297,9 @@ Arvados <- R6::R6Class( resource }, - jobs.lock = function(uuid) + collections.provenance = function(uuid) { - endPoint <- stringr::str_interp("jobs/${uuid}/lock") + endPoint <- stringr::str_interp("collections/${uuid}/provenance") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -4749,7 +3307,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4759,17 +3317,13 @@ Arvados <- R6::R6Class( resource }, - jobs.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + collections.used_by = function(uuid) { - endPoint <- stringr::str_interp("jobs") + endPoint <- stringr::str_interp("collections/${uuid}/used_by") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL body <- NULL @@ -4783,9 +3337,9 @@ Arvados <- R6::R6Class( resource }, - jobs.show = function(uuid) + collections.trash = function(uuid) { - endPoint <- stringr::str_interp("jobs/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}/trash") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -4793,7 +3347,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4803,9 +3357,9 @@ Arvados <- R6::R6Class( resource }, - jobs.destroy = function(uuid) + collections.untrash = function(uuid) { - endPoint <- stringr::str_interp("jobs/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}/untrash") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -4813,7 +3367,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4823,13 +3377,19 @@ Arvados <- R6::R6Class( resource }, - keep_disks.get = function(uuid) + collections.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact", include_trash = NULL) { - endPoint <- stringr::str_interp("keep_disks/${uuid}") + endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count, + include_trash = include_trash) body <- NULL @@ -4843,18 +3403,13 @@ Arvados <- R6::R6Class( resource }, - keep_disks.index = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + humans.get = function(uuid) { - endPoint <- stringr::str_interp("keep_disks") + endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL body <- NULL @@ -4868,17 +3423,17 @@ Arvados <- R6::R6Class( resource }, - keep_disks.create = function(keepdisk, ensure_unique_name = "false") + humans.create = function(human, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("keep_disks") + endPoint <- stringr::str_interp("humans") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - if(length(keepdisk) > 0) - body <- jsonlite::toJSON(list(keepdisk = keepdisk), - auto_unbox = TRUE) + if(length(human) > 0) + body <- jsonlite::toJSON(list(human = human), + auto_unbox = TRUE) else body <- NULL @@ -4892,17 +3447,17 @@ Arvados <- R6::R6Class( resource }, - keep_disks.update = function(keepdisk, uuid) + humans.update = function(human, uuid) { - endPoint <- stringr::str_interp("keep_disks/${uuid}") + endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(keepdisk) > 0) - body <- jsonlite::toJSON(list(keepdisk = keepdisk), - auto_unbox = TRUE) + if(length(human) > 0) + body <- jsonlite::toJSON(list(human = human), + auto_unbox = TRUE) else body <- NULL @@ -4916,9 +3471,9 @@ Arvados <- R6::R6Class( resource }, - keep_disks.delete = function(uuid) + humans.delete = function(uuid) { - endPoint <- stringr::str_interp("keep_disks/${uuid}") + endPoint <- stringr::str_interp("humans/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -4936,22 +3491,21 @@ Arvados <- R6::R6Class( resource }, - keep_disks.ping = function(uuid = NULL, ping_secret, - node_uuid = NULL, filesystem_uuid = NULL, - service_host = NULL, service_port, service_ssl_flag) + humans.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("keep_disks/ping") + endPoint <- stringr::str_interp("humans") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$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) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -4961,18 +3515,13 @@ Arvados <- R6::R6Class( resource }, - keep_disks.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + job_tasks.get = function(uuid) { - endPoint <- stringr::str_interp("keep_disks") + endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL body <- NULL @@ -4986,17 +3535,21 @@ Arvados <- R6::R6Class( resource }, - keep_disks.show = function(uuid) + job_tasks.create = function(jobtask, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("keep_disks/${uuid}") + endPoint <- stringr::str_interp("job_tasks") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(jobtask) > 0) + body <- jsonlite::toJSON(list(jobtask = jobtask), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5006,17 +3559,21 @@ Arvados <- R6::R6Class( resource }, - keep_disks.destroy = function(uuid) + job_tasks.update = function(jobtask, uuid) { - endPoint <- stringr::str_interp("keep_disks/${uuid}") + endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL + if(length(jobtask) > 0) + body <- jsonlite::toJSON(list(jobtask = jobtask), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5026,9 +3583,9 @@ Arvados <- R6::R6Class( resource }, - keep_services.get = function(uuid) + job_tasks.delete = function(uuid) { - endPoint <- stringr::str_interp("keep_services/${uuid}") + endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -5036,7 +3593,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5046,18 +3603,18 @@ Arvados <- R6::R6Class( resource }, - keep_services.index = function(filters = NULL, + job_tasks.list = function(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("keep_services") + endPoint <- stringr::str_interp("job_tasks") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL @@ -5071,22 +3628,17 @@ Arvados <- R6::R6Class( resource }, - keep_services.create = function(keepservice, - ensure_unique_name = "false") + jobs.get = function(uuid) { - endPoint <- stringr::str_interp("keep_services") + endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- NULL - if(length(keepservice) > 0) - body <- jsonlite::toJSON(list(keepservice = keepservice), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5096,21 +3648,26 @@ Arvados <- R6::R6Class( resource }, - keep_services.update = function(keepservice, uuid) + jobs.create = function(job, ensure_unique_name = "false", + find_or_create = "false", filters = NULL, + minimum_script_version = NULL, exclude_script_versions = NULL) { - endPoint <- stringr::str_interp("keep_services/${uuid}") + endPoint <- stringr::str_interp("jobs") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + 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(keepservice) > 0) - body <- jsonlite::toJSON(list(keepservice = keepservice), - auto_unbox = TRUE) + if(length(job) > 0) + body <- jsonlite::toJSON(list(job = job), + auto_unbox = TRUE) else body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5120,17 +3677,21 @@ Arvados <- R6::R6Class( resource }, - keep_services.delete = function(uuid) + jobs.update = function(job, uuid) { - endPoint <- stringr::str_interp("keep_services/${uuid}") + endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL + if(length(job) > 0) + body <- jsonlite::toJSON(list(job = job), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5140,9 +3701,9 @@ Arvados <- R6::R6Class( resource }, - keep_services.accessible = function() + jobs.delete = function(uuid) { - endPoint <- stringr::str_interp("keep_services/accessible") + endPoint <- stringr::str_interp("jobs/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -5150,7 +3711,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5160,18 +3721,17 @@ Arvados <- R6::R6Class( resource }, - keep_services.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + jobs.queue = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("keep_services") + endPoint <- stringr::str_interp("jobs/queue") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL @@ -5185,9 +3745,9 @@ Arvados <- R6::R6Class( resource }, - keep_services.show = function(uuid) + jobs.queue_size = function() { - endPoint <- stringr::str_interp("keep_services/${uuid}") + endPoint <- stringr::str_interp("jobs/queue_size") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -5205,9 +3765,9 @@ Arvados <- R6::R6Class( resource }, - keep_services.destroy = function(uuid) + jobs.cancel = function(uuid) { - endPoint <- stringr::str_interp("keep_services/${uuid}") + endPoint <- stringr::str_interp("jobs/${uuid}/cancel") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -5215,7 +3775,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5225,9 +3785,9 @@ Arvados <- R6::R6Class( resource }, - pipeline_templates.get = function(uuid) + jobs.lock = function(uuid) { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") + endPoint <- stringr::str_interp("jobs/${uuid}/lock") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -5235,56 +3795,6 @@ Arvados <- R6::R6Class( 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$errors) - - resource - }, - - pipeline_templates.index = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("pipeline_templates") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - body <- NULL - - response <- private$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 - }, - - pipeline_templates.create = function(pipelinetemplate, - ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("pipeline_templates") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(pipelinetemplate) > 0) - 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$parseJSONResponse(response) @@ -5295,21 +3805,21 @@ Arvados <- R6::R6Class( resource }, - pipeline_templates.update = function(pipelinetemplate, uuid) + jobs.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") + endPoint <- stringr::str_interp("jobs") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - if(length(pipelinetemplate) > 0) - body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5319,9 +3829,9 @@ Arvados <- R6::R6Class( resource }, - pipeline_templates.delete = function(uuid) + keep_disks.get = function(uuid) { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") + endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -5329,7 +3839,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5339,22 +3849,21 @@ Arvados <- R6::R6Class( resource }, - pipeline_templates.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + keep_disks.create = function(keepdisk, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("pipeline_templates") + endPoint <- stringr::str_interp("keep_disks") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(keepdisk) > 0) + body <- jsonlite::toJSON(list(keepdisk = keepdisk), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5364,17 +3873,21 @@ Arvados <- R6::R6Class( resource }, - pipeline_templates.show = function(uuid) + keep_disks.update = function(keepdisk, uuid) { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") + endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL + if(length(keepdisk) > 0) + body <- jsonlite::toJSON(list(keepdisk = keepdisk), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5384,9 +3897,9 @@ Arvados <- R6::R6Class( resource }, - pipeline_templates.destroy = function(uuid) + keep_disks.delete = function(uuid) { - endPoint <- stringr::str_interp("pipeline_templates/${uuid}") + endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -5404,17 +3917,22 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.get = function(uuid) + keep_disks.ping = function(uuid = NULL, ping_secret, + node_uuid = NULL, filesystem_uuid = NULL, + service_host = NULL, service_port, service_ssl_flag) { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("keep_disks/ping") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(uuid = uuid, ping_secret = ping_secret, + node_uuid = node_uuid, filesystem_uuid = filesystem_uuid, + service_host = service_host, service_port = service_port, + service_ssl_flag = service_ssl_flag) body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5424,18 +3942,18 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.index = function(filters = NULL, + keep_disks.list = function(filters = NULL, where = NULL, order = NULL, select = NULL, distinct = NULL, limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("pipeline_instances") + endPoint <- stringr::str_interp("keep_disks") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL @@ -5449,18 +3967,39 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.create = function(pipelineinstance, - ensure_unique_name = "false") + nodes.get = function(uuid) { - endPoint <- stringr::str_interp("pipeline_instances") + endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- NULL - if(length(pipelineinstance) > 0) - body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), - auto_unbox = TRUE) + 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$errors) + + resource + }, + + nodes.create = function(node, ensure_unique_name = "false", + assign_slot = NULL) + { + endPoint <- stringr::str_interp("nodes") + url <- paste0(private$host, endPoint) + headers <- list(Authorization = paste("OAuth2", private$token), + "Content-Type" = "application/json") + queryArgs <- list(ensure_unique_name = ensure_unique_name, + assign_slot = assign_slot) + + if(length(node) > 0) + body <- jsonlite::toJSON(list(node = node), + auto_unbox = TRUE) else body <- NULL @@ -5474,17 +4013,17 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.update = function(pipelineinstance, uuid) + nodes.update = function(node, uuid, assign_slot = NULL) { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(assign_slot = assign_slot) - if(length(pipelineinstance) > 0) - body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), - auto_unbox = TRUE) + if(length(node) > 0) + body <- jsonlite::toJSON(list(node = node), + auto_unbox = TRUE) else body <- NULL @@ -5498,9 +4037,9 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.delete = function(uuid) + nodes.delete = function(uuid) { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("nodes/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -5518,13 +4057,13 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.cancel = function(uuid) + nodes.ping = function(uuid, ping_secret) { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}/cancel") + endPoint <- stringr::str_interp("nodes/${uuid}/ping") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(ping_secret = ping_secret) body <- NULL @@ -5538,18 +4077,17 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + nodes.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("pipeline_instances") + endPoint <- stringr::str_interp("nodes") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL @@ -5563,9 +4101,9 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.show = function(uuid) + links.get = function(uuid) { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -5583,17 +4121,21 @@ Arvados <- R6::R6Class( resource }, - pipeline_instances.destroy = function(uuid) + links.create = function(link, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("pipeline_instances/${uuid}") + endPoint <- stringr::str_interp("links") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(link) > 0) + body <- jsonlite::toJSON(list(link = link), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5603,17 +4145,21 @@ Arvados <- R6::R6Class( resource }, - nodes.get = function(uuid) + links.update = function(link, uuid) { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL + if(length(link) > 0) + body <- jsonlite::toJSON(list(link = link), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5623,21 +4169,17 @@ Arvados <- R6::R6Class( resource }, - nodes.index = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + links.delete = function(uuid) { - endPoint <- stringr::str_interp("nodes") + endPoint <- stringr::str_interp("links/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5647,23 +4189,21 @@ Arvados <- R6::R6Class( resource }, - nodes.create = function(node, ensure_unique_name = "false", - assign_slot = NULL) + links.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("nodes") + endPoint <- stringr::str_interp("links") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name, - assign_slot = assign_slot) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - if(length(node) > 0) - body <- jsonlite::toJSON(list(node = node), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5673,21 +4213,17 @@ Arvados <- R6::R6Class( resource }, - nodes.update = function(node, uuid, assign_slot = NULL) + links.get_permissions = function(uuid) { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("permissions/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(assign_slot = assign_slot) + queryArgs <- NULL - if(length(node) > 0) - body <- jsonlite::toJSON(list(node = node), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5697,9 +4233,9 @@ Arvados <- R6::R6Class( resource }, - nodes.delete = function(uuid) + keep_services.get = function(uuid) { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -5707,7 +4243,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5717,15 +4253,20 @@ Arvados <- R6::R6Class( resource }, - nodes.ping = function(uuid, ping_secret) + keep_services.create = function(keepservice, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("nodes/${uuid}/ping") + endPoint <- stringr::str_interp("keep_services") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ping_secret = ping_secret) + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(keepservice) > 0) + body <- jsonlite::toJSON(list(keepservice = keepservice), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -5737,21 +4278,21 @@ Arvados <- R6::R6Class( resource }, - nodes.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + keep_services.update = function(keepservice, uuid) { - endPoint <- stringr::str_interp("nodes") + endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL - body <- NULL + if(length(keepservice) > 0) + body <- jsonlite::toJSON(list(keepservice = keepservice), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5761,9 +4302,9 @@ Arvados <- R6::R6Class( resource }, - nodes.show = function(uuid) + keep_services.delete = function(uuid) { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -5771,7 +4312,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5781,9 +4322,9 @@ Arvados <- R6::R6Class( resource }, - nodes.destroy = function(uuid) + keep_services.accessible = function() { - endPoint <- stringr::str_interp("nodes/${uuid}") + endPoint <- stringr::str_interp("keep_services/accessible") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -5791,7 +4332,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5801,13 +4342,18 @@ Arvados <- R6::R6Class( resource }, - repositories.get = function(uuid) + keep_services.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("repositories/${uuid}") + endPoint <- stringr::str_interp("keep_services") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL @@ -5821,18 +4367,13 @@ Arvados <- R6::R6Class( resource }, - repositories.index = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + pipeline_templates.get = function(uuid) { - endPoint <- stringr::str_interp("repositories") + endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL body <- NULL @@ -5846,17 +4387,18 @@ Arvados <- R6::R6Class( resource }, - repositories.create = function(repository, ensure_unique_name = "false") + pipeline_templates.create = function(pipelinetemplate, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("repositories") + endPoint <- stringr::str_interp("pipeline_templates") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - if(length(repository) > 0) - body <- jsonlite::toJSON(list(repository = repository), - auto_unbox = TRUE) + if(length(pipelinetemplate) > 0) + body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), + auto_unbox = TRUE) else body <- NULL @@ -5870,17 +4412,17 @@ Arvados <- R6::R6Class( resource }, - repositories.update = function(repository, uuid) + pipeline_templates.update = function(pipelinetemplate, uuid) { - endPoint <- stringr::str_interp("repositories/${uuid}") + endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(repository) > 0) - body <- jsonlite::toJSON(list(repository = repository), - auto_unbox = TRUE) + if(length(pipelinetemplate) > 0) + body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), + auto_unbox = TRUE) else body <- NULL @@ -5894,9 +4436,9 @@ Arvados <- R6::R6Class( resource }, - repositories.delete = function(uuid) + pipeline_templates.delete = function(uuid) { - endPoint <- stringr::str_interp("repositories/${uuid}") + endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -5914,13 +4456,18 @@ Arvados <- R6::R6Class( resource }, - repositories.get_all_permissions = function() + pipeline_templates.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("repositories/get_all_permissions") + endPoint <- stringr::str_interp("pipeline_templates") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL @@ -5934,18 +4481,13 @@ Arvados <- R6::R6Class( resource }, - repositories.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + pipeline_instances.get = function(uuid) { - endPoint <- stringr::str_interp("repositories") + endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL body <- NULL @@ -5959,17 +4501,22 @@ Arvados <- R6::R6Class( resource }, - repositories.show = function(uuid) + pipeline_instances.create = function(pipelineinstance, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("repositories/${uuid}") + endPoint <- stringr::str_interp("pipeline_instances") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(pipelineinstance) > 0) + body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5979,17 +4526,21 @@ Arvados <- R6::R6Class( resource }, - repositories.destroy = function(uuid) + pipeline_instances.update = function(pipelineinstance, uuid) { - endPoint <- stringr::str_interp("repositories/${uuid}") + endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL + if(length(pipelineinstance) > 0) + body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -5999,9 +4550,9 @@ Arvados <- R6::R6Class( resource }, - specimens.get = function(uuid) + pipeline_instances.delete = function(uuid) { - endPoint <- stringr::str_interp("specimens/${uuid}") + endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -6009,7 +4560,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6019,22 +4570,17 @@ Arvados <- R6::R6Class( resource }, - specimens.index = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + pipeline_instances.cancel = function(uuid) { - endPoint <- stringr::str_interp("specimens") + endPoint <- stringr::str_interp("pipeline_instances/${uuid}/cancel") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6044,21 +4590,22 @@ Arvados <- R6::R6Class( resource }, - specimens.create = function(specimen, ensure_unique_name = "false") + pipeline_instances.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("specimens") + endPoint <- stringr::str_interp("pipeline_instances") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - if(length(specimen) > 0) - body <- jsonlite::toJSON(list(specimen = specimen), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6068,21 +4615,17 @@ Arvados <- R6::R6Class( resource }, - specimens.update = function(specimen, uuid) + repositories.get = function(uuid) { - endPoint <- stringr::str_interp("specimens/${uuid}") + endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(specimen) > 0) - body <- jsonlite::toJSON(list(specimen = specimen), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6092,17 +4635,21 @@ Arvados <- R6::R6Class( resource }, - specimens.delete = function(uuid) + repositories.create = function(repository, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("specimens/${uuid}") + endPoint <- stringr::str_interp("repositories") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(repository) > 0) + body <- jsonlite::toJSON(list(repository = repository), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6112,22 +4659,21 @@ Arvados <- R6::R6Class( resource }, - specimens.list = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + repositories.update = function(repository, uuid) { - endPoint <- stringr::str_interp("specimens") + endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL - body <- NULL + if(length(repository) > 0) + body <- jsonlite::toJSON(list(repository = repository), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6137,9 +4683,9 @@ Arvados <- R6::R6Class( resource }, - specimens.show = function(uuid) + repositories.delete = function(uuid) { - endPoint <- stringr::str_interp("specimens/${uuid}") + endPoint <- stringr::str_interp("repositories/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -6147,7 +4693,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6157,9 +4703,9 @@ Arvados <- R6::R6Class( resource }, - specimens.destroy = function(uuid) + repositories.get_all_permissions = function() { - endPoint <- stringr::str_interp("specimens/${uuid}") + endPoint <- stringr::str_interp("repositories/get_all_permissions") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -6167,7 +4713,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6177,13 +4723,18 @@ Arvados <- R6::R6Class( resource }, - logs.get = function(uuid) + repositories.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("logs/${uuid}") + endPoint <- stringr::str_interp("repositories") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL @@ -6197,17 +4748,13 @@ Arvados <- R6::R6Class( resource }, - logs.index = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + specimens.get = function(uuid) { - endPoint <- stringr::str_interp("logs") + endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL body <- NULL @@ -6221,17 +4768,17 @@ Arvados <- R6::R6Class( resource }, - logs.create = function(log, ensure_unique_name = "false") + specimens.create = function(specimen, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("logs") + endPoint <- stringr::str_interp("specimens") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - if(length(log) > 0) - body <- jsonlite::toJSON(list(log = log), - auto_unbox = TRUE) + if(length(specimen) > 0) + body <- jsonlite::toJSON(list(specimen = specimen), + auto_unbox = TRUE) else body <- NULL @@ -6245,17 +4792,17 @@ Arvados <- R6::R6Class( resource }, - logs.update = function(log, uuid) + specimens.update = function(specimen, uuid) { - endPoint <- stringr::str_interp("logs/${uuid}") + endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - if(length(log) > 0) - body <- jsonlite::toJSON(list(log = log), - auto_unbox = TRUE) + if(length(specimen) > 0) + body <- jsonlite::toJSON(list(specimen = specimen), + auto_unbox = TRUE) else body <- NULL @@ -6269,9 +4816,9 @@ Arvados <- R6::R6Class( resource }, - logs.delete = function(uuid) + specimens.delete = function(uuid) { - endPoint <- stringr::str_interp("logs/${uuid}") + endPoint <- stringr::str_interp("specimens/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") @@ -6289,17 +4836,18 @@ Arvados <- R6::R6Class( resource }, - logs.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + specimens.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("logs") + endPoint <- stringr::str_interp("specimens") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL @@ -6313,7 +4861,7 @@ Arvados <- R6::R6Class( resource }, - logs.show = function(uuid) + logs.get = function(uuid) { endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) @@ -6333,17 +4881,21 @@ Arvados <- R6::R6Class( resource }, - logs.destroy = function(uuid) + logs.create = function(log, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("logs/${uuid}") + endPoint <- stringr::str_interp("logs") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(log) > 0) + body <- jsonlite::toJSON(list(log = log), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6353,17 +4905,21 @@ Arvados <- R6::R6Class( resource }, - traits.get = function(uuid) + logs.update = function(log, uuid) { - endPoint <- stringr::str_interp("traits/${uuid}") + endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL + if(length(log) > 0) + body <- jsonlite::toJSON(list(log = log), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6373,45 +4929,17 @@ Arvados <- R6::R6Class( resource }, - traits.index = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + logs.delete = function(uuid) { - endPoint <- stringr::str_interp("traits") + endPoint <- stringr::str_interp("logs/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + 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$errors) - - resource - }, - - traits.create = function(trait, ensure_unique_name = "false") - { - endPoint <- stringr::str_interp("traits") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - - if(length(trait) > 0) - body <- jsonlite::toJSON(list(trait = trait), - auto_unbox = TRUE) - else - body <- NULL - - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("DELETE", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6421,21 +4949,21 @@ Arvados <- R6::R6Class( resource }, - traits.update = function(trait, uuid) + logs.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("traits/${uuid}") + endPoint <- stringr::str_interp("logs") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - if(length(trait) > 0) - body <- jsonlite::toJSON(list(trait = trait), - auto_unbox = TRUE) - else - body <- NULL + body <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6445,7 +4973,7 @@ Arvados <- R6::R6Class( resource }, - traits.delete = function(uuid) + traits.get = function(uuid) { endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) @@ -6455,7 +4983,7 @@ Arvados <- R6::R6Class( body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6465,21 +4993,21 @@ Arvados <- R6::R6Class( resource }, - traits.list = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact") + traits.create = function(trait, ensure_unique_name = "false") { endPoint <- stringr::str_interp("traits") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- NULL + if(length(trait) > 0) + body <- jsonlite::toJSON(list(trait = trait), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6489,7 +5017,7 @@ Arvados <- R6::R6Class( resource }, - traits.show = function(uuid) + traits.update = function(trait, uuid) { endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) @@ -6497,9 +5025,13 @@ Arvados <- R6::R6Class( "Content-Type" = "application/json") queryArgs <- NULL - body <- NULL + if(length(trait) > 0) + body <- jsonlite::toJSON(list(trait = trait), + auto_unbox = TRUE) + else + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) @@ -6509,7 +5041,7 @@ Arvados <- R6::R6Class( resource }, - traits.destroy = function(uuid) + traits.delete = function(uuid) { endPoint <- stringr::str_interp("traits/${uuid}") url <- paste0(private$host, endPoint) @@ -6529,13 +5061,17 @@ Arvados <- R6::R6Class( resource }, - virtual_machines.get = function(uuid) + traits.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { - endPoint <- stringr::str_interp("virtual_machines/${uuid}") + endPoint <- stringr::str_interp("traits") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- NULL + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL @@ -6549,18 +5085,13 @@ Arvados <- R6::R6Class( resource }, - virtual_machines.index = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") + virtual_machines.get = function(uuid) { - endPoint <- stringr::str_interp("virtual_machines") + endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + queryArgs <- NULL body <- NULL @@ -6585,7 +5116,7 @@ Arvados <- R6::R6Class( if(length(virtualmachine) > 0) body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), - auto_unbox = TRUE) + auto_unbox = TRUE) else body <- NULL @@ -6609,7 +5140,7 @@ Arvados <- R6::R6Class( if(length(virtualmachine) > 0) body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), - auto_unbox = TRUE) + auto_unbox = TRUE) else body <- NULL @@ -6693,28 +5224,8 @@ Arvados <- R6::R6Class( 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 - }, - - virtual_machines.show = function(uuid) - { - endPoint <- stringr::str_interp("virtual_machines/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL @@ -6728,26 +5239,6 @@ Arvados <- R6::R6Class( resource }, - virtual_machines.destroy = function(uuid) - { - endPoint <- stringr::str_interp("virtual_machines/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - workflows.get = function(uuid) { endPoint <- stringr::str_interp("workflows/${uuid}") @@ -6768,31 +5259,6 @@ Arvados <- R6::R6Class( resource }, - workflows.index = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("workflows") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - 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$errors) - - resource - }, - workflows.create = function(workflow, ensure_unique_name = "false") { endPoint <- stringr::str_interp("workflows") @@ -6803,7 +5269,7 @@ Arvados <- R6::R6Class( if(length(workflow) > 0) body <- jsonlite::toJSON(list(workflow = workflow), - auto_unbox = TRUE) + auto_unbox = TRUE) else body <- NULL @@ -6827,7 +5293,7 @@ Arvados <- R6::R6Class( if(length(workflow) > 0) body <- jsonlite::toJSON(list(workflow = workflow), - auto_unbox = TRUE) + auto_unbox = TRUE) else body <- NULL @@ -6871,28 +5337,8 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$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$errors) - - resource - }, - - workflows.show = function(uuid) - { - endPoint <- stringr::str_interp("workflows/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL @@ -6906,26 +5352,6 @@ Arvados <- R6::R6Class( resource }, - workflows.destroy = function(uuid) - { - endPoint <- stringr::str_interp("workflows/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - groups.get = function(uuid) { endPoint <- stringr::str_interp("groups/${uuid}") @@ -6946,32 +5372,6 @@ Arvados <- R6::R6Class( resource }, - groups.index = function(filters = NULL, where = NULL, - order = NULL, select = NULL, distinct = NULL, - limit = "100", offset = "0", count = "exact", - include_trash = NULL) - { - endPoint <- stringr::str_interp("groups") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count, - include_trash = include_trash) - - body <- NULL - - response <- private$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 - }, - groups.create = function(group, ensure_unique_name = "false") { endPoint <- stringr::str_interp("groups") @@ -6982,7 +5382,7 @@ Arvados <- R6::R6Class( if(length(group) > 0) body <- jsonlite::toJSON(list(group = group), - auto_unbox = TRUE) + auto_unbox = TRUE) else body <- NULL @@ -7006,7 +5406,7 @@ Arvados <- R6::R6Class( if(length(group) > 0) body <- jsonlite::toJSON(list(group = group), - auto_unbox = TRUE) + auto_unbox = TRUE) else body <- NULL @@ -7050,9 +5450,9 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, - order = order, distinct = distinct, limit = limit, - offset = offset, count = count, include_trash = include_trash, - uuid = uuid, recursive = recursive) + order = order, distinct = distinct, limit = limit, + offset = offset, count = count, include_trash = include_trash, + uuid = uuid, recursive = recursive) body <- NULL @@ -7116,29 +5516,9 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$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$errors) - - resource - }, - - groups.show = function(uuid) - { - endPoint <- stringr::str_interp("groups/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count, + include_trash = include_trash) body <- NULL @@ -7152,26 +5532,6 @@ Arvados <- R6::R6Class( resource }, - groups.destroy = function(uuid) - { - endPoint <- stringr::str_interp("groups/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - user_agreements.get = function(uuid) { endPoint <- stringr::str_interp("user_agreements/${uuid}") @@ -7192,31 +5552,6 @@ Arvados <- R6::R6Class( resource }, - user_agreements.index = function(filters = NULL, - where = NULL, order = NULL, select = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact") - { - endPoint <- stringr::str_interp("user_agreements") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) - - body <- NULL - - response <- private$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 - }, - user_agreements.create = function(useragreement, ensure_unique_name = "false") { @@ -7228,7 +5563,7 @@ Arvados <- R6::R6Class( if(length(useragreement) > 0) body <- jsonlite::toJSON(list(useragreement = useragreement), - auto_unbox = TRUE) + auto_unbox = TRUE) else body <- NULL @@ -7252,7 +5587,7 @@ Arvados <- R6::R6Class( if(length(useragreement) > 0) body <- jsonlite::toJSON(list(useragreement = useragreement), - auto_unbox = TRUE) + auto_unbox = TRUE) else body <- NULL @@ -7336,8 +5671,8 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(filters = filters, where = where, - order = order, select = select, distinct = distinct, - limit = limit, offset = offset, count = count) + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) body <- NULL @@ -7371,46 +5706,6 @@ Arvados <- R6::R6Class( resource }, - user_agreements.show = function(uuid) - { - endPoint <- stringr::str_interp("user_agreements/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("GET", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - - user_agreements.destroy = function(uuid) - { - endPoint <- stringr::str_interp("user_agreements/${uuid}") - url <- paste0(private$host, endPoint) - headers <- list(Authorization = paste("OAuth2", private$token), - "Content-Type" = "application/json") - queryArgs <- NULL - - body <- NULL - - response <- private$REST$http$exec("DELETE", url, headers, body, - queryArgs, private$numRetries) - resource <- private$REST$httpParser$parseJSONResponse(response) - - if(!is.null(resource$errors)) - stop(resource$errors) - - resource - }, - getHostName = function() private$host, getToken = function() private$token, setRESTService = function(newREST) private$REST <- newREST,