X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/2b11ab27a8508a49bb5e2c87babbbae9e95f4e3d..add8af3272303972fceb3ec35eeedeb2ca8b4af3:/sdk/R/R/Arvados.R diff --git a/sdk/R/R/Arvados.R b/sdk/R/R/Arvados.R index 7c077c03a1..c69fe08490 100644 --- a/sdk/R/R/Arvados.R +++ b/sdk/R/R/Arvados.R @@ -1,3 +1,2416 @@ +#' users.get is a method defined in Arvados class. +#' +#' @usage arv$users.get(uuid) +#' @param uuid The UUID of the User in question. +#' @return User object. +#' @name users.get +NULL + +#' users.index is a method defined in Arvados class. +#' +#' @usage arv$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$users.create(user, ensure_unique_name = "false") +#' @param user User object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return User object. +#' @name users.create +NULL + +#' users.update is a method defined in Arvados class. +#' +#' @usage arv$users.update(user, uuid) +#' @param user User object. +#' @param uuid The UUID of the User in question. +#' @return User object. +#' @name users.update +NULL + +#' users.delete is a method defined in Arvados class. +#' +#' @usage arv$users.delete(uuid) +#' @param uuid The UUID of the User in question. +#' @return User object. +#' @name users.delete +NULL + +#' users.current is a method defined in Arvados class. +#' +#' @usage arv$users.current(NULL) +#' @return User object. +#' @name users.current +NULL + +#' users.system is a method defined in Arvados class. +#' +#' @usage arv$users.system(NULL) +#' @return User object. +#' @name users.system +NULL + +#' users.activate is a method defined in Arvados class. +#' +#' @usage arv$users.activate(uuid) +#' @param uuid +#' @return User object. +#' @name users.activate +NULL + +#' users.setup is a method defined in Arvados class. +#' +#' @usage arv$users.setup(user = NULL, openid_prefix = NULL, +#' repo_name = NULL, vm_uuid = NULL, send_notification_email = "false") +#' @param user +#' @param openid_prefix +#' @param repo_name +#' @param vm_uuid +#' @param send_notification_email +#' @return User object. +#' @name users.setup +NULL + +#' users.unsetup is a method defined in Arvados class. +#' +#' @usage arv$users.unsetup(uuid) +#' @param uuid +#' @return User object. +#' @name users.unsetup +NULL + +#' users.update_uuid is a method defined in Arvados class. +#' +#' @usage arv$users.update_uuid(uuid, new_uuid) +#' @param uuid +#' @param new_uuid +#' @return User object. +#' @name users.update_uuid +NULL + +#' users.list is a method defined in Arvados class. +#' +#' @usage arv$users.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return UserList object. +#' @name users.list +NULL + +#' users.show is a method defined in Arvados class. +#' +#' @usage arv$users.show(uuid) +#' @param uuid +#' @return User object. +#' @name users.show +NULL + +#' users.destroy is a method defined in Arvados class. +#' +#' @usage arv$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$api_client_authorizations.get(uuid) +#' @param uuid The UUID of the ApiClientAuthorization in question. +#' @return ApiClientAuthorization object. +#' @name api_client_authorizations.get +NULL + +#' api_client_authorizations.index is a method defined in Arvados class. +#' +#' @usage arv$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$api_client_authorizations.create(apiclientauthorization, +#' ensure_unique_name = "false") +#' @param apiClientAuthorization ApiClientAuthorization object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return ApiClientAuthorization object. +#' @name api_client_authorizations.create +NULL + +#' api_client_authorizations.update is a method defined in Arvados class. +#' +#' @usage arv$api_client_authorizations.update(apiclientauthorization, +#' uuid) +#' @param apiClientAuthorization ApiClientAuthorization object. +#' @param uuid The UUID of the ApiClientAuthorization in question. +#' @return ApiClientAuthorization object. +#' @name api_client_authorizations.update +NULL + +#' api_client_authorizations.delete is a method defined in Arvados class. +#' +#' @usage arv$api_client_authorizations.delete(uuid) +#' @param uuid The UUID of the ApiClientAuthorization in question. +#' @return ApiClientAuthorization object. +#' @name api_client_authorizations.delete +NULL + +#' api_client_authorizations.create_system_auth is a method defined in Arvados class. +#' +#' @usage arv$api_client_authorizations.create_system_auth(api_client_id = NULL, +#' scopes = NULL) +#' @param api_client_id +#' @param scopes +#' @return ApiClientAuthorization object. +#' @name api_client_authorizations.create_system_auth +NULL + +#' api_client_authorizations.current is a method defined in Arvados class. +#' +#' @usage arv$api_client_authorizations.current(NULL) +#' @return ApiClientAuthorization object. +#' @name api_client_authorizations.current +NULL + +#' api_client_authorizations.list is a method defined in Arvados class. +#' +#' @usage arv$api_client_authorizations.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return ApiClientAuthorizationList object. +#' @name api_client_authorizations.list +NULL + +#' api_client_authorizations.show is a method defined in Arvados class. +#' +#' @usage arv$api_client_authorizations.show(uuid) +#' @param uuid +#' @return ApiClientAuthorization object. +#' @name api_client_authorizations.show +NULL + +#' api_client_authorizations.destroy is a method defined in Arvados class. +#' +#' @usage arv$api_client_authorizations.destroy(uuid) +#' @param uuid +#' @return ApiClientAuthorization object. +#' @name api_client_authorizations.destroy +NULL + +#' containers.get is a method defined in Arvados class. +#' +#' @usage arv$containers.get(uuid) +#' @param uuid The UUID of the Container in question. +#' @return Container object. +#' @name containers.get +NULL + +#' containers.index is a method defined in Arvados class. +#' +#' @usage arv$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.secret_mounts is a method defined in Arvados class. +#' +#' @usage arv$containers.secret_mounts(uuid) +#' @param uuid +#' @return Container object. +#' @name containers.secret_mounts +NULL + +#' containers.current is a method defined in Arvados class. +#' +#' @usage arv$containers.current(NULL) +#' @return Container object. +#' @name containers.current +NULL + +#' containers.list is a method defined in Arvados class. +#' +#' @usage arv$containers.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return ContainerList object. +#' @name containers.list +NULL + +#' containers.show is a method defined in Arvados class. +#' +#' @usage arv$containers.show(uuid) +#' @param uuid +#' @return Container object. +#' @name containers.show +NULL + +#' containers.destroy is a method defined in Arvados class. +#' +#' @usage arv$containers.destroy(uuid) +#' @param uuid +#' @return Container object. +#' @name containers.destroy +NULL + +#' api_clients.get is a method defined in Arvados class. +#' +#' @usage arv$api_clients.get(uuid) +#' @param uuid The UUID of the ApiClient in question. +#' @return ApiClient object. +#' @name api_clients.get +NULL + +#' api_clients.index is a method defined in Arvados class. +#' +#' @usage arv$api_clients.index(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return ApiClientList object. +#' @name api_clients.index +NULL + +#' api_clients.create is a method defined in Arvados class. +#' +#' @usage arv$api_clients.create(apiclient, +#' ensure_unique_name = "false") +#' @param apiClient ApiClient object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return ApiClient object. +#' @name api_clients.create +NULL + +#' api_clients.update is a method defined in Arvados class. +#' +#' @usage arv$api_clients.update(apiclient, +#' uuid) +#' @param apiClient ApiClient object. +#' @param uuid The UUID of the ApiClient in question. +#' @return ApiClient object. +#' @name api_clients.update +NULL + +#' api_clients.delete is a method defined in Arvados class. +#' +#' @usage arv$api_clients.delete(uuid) +#' @param uuid The UUID of the ApiClient in question. +#' @return ApiClient object. +#' @name api_clients.delete +NULL + +#' api_clients.list is a method defined in Arvados class. +#' +#' @usage arv$api_clients.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return ApiClientList object. +#' @name api_clients.list +NULL + +#' api_clients.show is a method defined in Arvados class. +#' +#' @usage arv$api_clients.show(uuid) +#' @param uuid +#' @return ApiClient object. +#' @name api_clients.show +NULL + +#' api_clients.destroy is a method defined in Arvados class. +#' +#' @usage arv$api_clients.destroy(uuid) +#' @param uuid +#' @return ApiClient object. +#' @name api_clients.destroy +NULL + +#' authorized_keys.get is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.get(uuid) +#' @param uuid The UUID of the AuthorizedKey in question. +#' @return AuthorizedKey object. +#' @name authorized_keys.get +NULL + +#' authorized_keys.index is a method defined in Arvados class. +#' +#' @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, +#' ensure_unique_name = "false") +#' @param authorizedKey AuthorizedKey object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return AuthorizedKey object. +#' @name authorized_keys.create +NULL + +#' authorized_keys.update is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.update(authorizedkey, +#' uuid) +#' @param authorizedKey AuthorizedKey object. +#' @param uuid The UUID of the AuthorizedKey in question. +#' @return AuthorizedKey object. +#' @name authorized_keys.update +NULL + +#' authorized_keys.delete is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.delete(uuid) +#' @param uuid The UUID of the AuthorizedKey in question. +#' @return AuthorizedKey object. +#' @name authorized_keys.delete +NULL + +#' authorized_keys.list is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return AuthorizedKeyList object. +#' @name authorized_keys.list +NULL + +#' authorized_keys.show is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.show(uuid) +#' @param uuid +#' @return AuthorizedKey object. +#' @name authorized_keys.show +NULL + +#' authorized_keys.destroy is a method defined in Arvados class. +#' +#' @usage arv$authorized_keys.destroy(uuid) +#' @param uuid +#' @return AuthorizedKey object. +#' @name authorized_keys.destroy +NULL + +#' container_requests.get is a method defined in Arvados class. +#' +#' @usage arv$container_requests.get(uuid) +#' @param uuid The UUID of the ContainerRequest in question. +#' @return ContainerRequest object. +#' @name container_requests.get +NULL + +#' container_requests.index is a method defined in Arvados class. +#' +#' @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, +#' ensure_unique_name = "false") +#' @param containerRequest ContainerRequest object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return ContainerRequest object. +#' @name container_requests.create +NULL + +#' container_requests.update is a method defined in Arvados class. +#' +#' @usage arv$container_requests.update(containerrequest, +#' uuid) +#' @param containerRequest ContainerRequest object. +#' @param uuid The UUID of the ContainerRequest in question. +#' @return ContainerRequest object. +#' @name container_requests.update +NULL + +#' container_requests.delete is a method defined in Arvados class. +#' +#' @usage arv$container_requests.delete(uuid) +#' @param uuid The UUID of the ContainerRequest in question. +#' @return ContainerRequest object. +#' @name container_requests.delete +NULL + +#' container_requests.list is a method defined in Arvados class. +#' +#' @usage arv$container_requests.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return ContainerRequestList object. +#' @name container_requests.list +NULL + +#' container_requests.show is a method defined in Arvados class. +#' +#' @usage arv$container_requests.show(uuid) +#' @param uuid +#' @return ContainerRequest object. +#' @name container_requests.show +NULL + +#' container_requests.destroy is a method defined in Arvados class. +#' +#' @usage arv$container_requests.destroy(uuid) +#' @param uuid +#' @return ContainerRequest object. +#' @name container_requests.destroy +NULL + +#' collections.get is a method defined in Arvados class. +#' +#' @usage arv$collections.get(uuid) +#' @param uuid The UUID of the Collection in question. +#' @return Collection object. +#' @name collections.get +NULL + +#' collections.index is a method defined in Arvados class. +#' +#' @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, +#' ensure_unique_name = "false") +#' @param collection Collection object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Collection object. +#' @name collections.create +NULL + +#' collections.update is a method defined in Arvados class. +#' +#' @usage arv$collections.update(collection, +#' uuid) +#' @param collection Collection object. +#' @param uuid The UUID of the Collection in question. +#' @return Collection object. +#' @name collections.update +NULL + +#' collections.delete is a method defined in Arvados class. +#' +#' @usage arv$collections.delete(uuid) +#' @param uuid The UUID of the Collection in question. +#' @return Collection object. +#' @name collections.delete +NULL + +#' collections.provenance is a method defined in Arvados class. +#' +#' @usage arv$collections.provenance(uuid) +#' @param uuid +#' @return Collection object. +#' @name collections.provenance +NULL + +#' collections.used_by is a method defined in Arvados class. +#' +#' @usage arv$collections.used_by(uuid) +#' @param uuid +#' @return Collection object. +#' @name collections.used_by +NULL + +#' collections.trash is a method defined in Arvados class. +#' +#' @usage arv$collections.trash(uuid) +#' @param uuid +#' @return Collection object. +#' @name collections.trash +NULL + +#' collections.untrash is a method defined in Arvados class. +#' +#' @usage arv$collections.untrash(uuid) +#' @param uuid +#' @return Collection object. +#' @name collections.untrash +NULL + +#' collections.list is a method defined in Arvados class. +#' +#' @usage arv$collections.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact", include_trash = NULL) +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @param include_trash Include collections whose is_trashed attribute is true. +#' @return CollectionList object. +#' @name collections.list +NULL + +#' collections.show is a method defined in Arvados class. +#' +#' @usage arv$collections.show(uuid) +#' @param uuid +#' @return Collection object. +#' @name collections.show +NULL + +#' collections.destroy is a method defined in Arvados class. +#' +#' @usage arv$collections.destroy(uuid) +#' @param uuid +#' @return Collection object. +#' @name collections.destroy +NULL + +#' humans.get is a method defined in Arvados class. +#' +#' @usage arv$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$humans.update(human, uuid) +#' @param human Human object. +#' @param uuid The UUID of the Human in question. +#' @return Human object. +#' @name humans.update +NULL + +#' humans.delete is a method defined in Arvados class. +#' +#' @usage arv$humans.delete(uuid) +#' @param uuid The UUID of the Human in question. +#' @return Human object. +#' @name humans.delete +NULL + +#' humans.list is a method defined in Arvados class. +#' +#' @usage arv$humans.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return HumanList object. +#' @name humans.list +NULL + +#' humans.show is a method defined in Arvados class. +#' +#' @usage arv$humans.show(uuid) +#' @param uuid +#' @return Human object. +#' @name humans.show +NULL + +#' humans.destroy is a method defined in Arvados class. +#' +#' @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) +#' @param uuid The UUID of the JobTask in question. +#' @return JobTask object. +#' @name job_tasks.get +NULL + +#' job_tasks.index is a method defined in Arvados class. +#' +#' @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") +#' @param jobTask JobTask object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return JobTask object. +#' @name job_tasks.create +NULL + +#' job_tasks.update is a method defined in Arvados class. +#' +#' @usage arv$job_tasks.update(jobtask, uuid) +#' @param jobTask JobTask object. +#' @param uuid The UUID of the JobTask in question. +#' @return JobTask object. +#' @name job_tasks.update +NULL + +#' job_tasks.delete is a method defined in Arvados class. +#' +#' @usage arv$job_tasks.delete(uuid) +#' @param uuid The UUID of the JobTask in question. +#' @return JobTask object. +#' @name job_tasks.delete +NULL + +#' job_tasks.list is a method defined in Arvados class. +#' +#' @usage arv$job_tasks.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return JobTaskList object. +#' @name job_tasks.list +NULL + +#' job_tasks.show is a method defined in Arvados class. +#' +#' @usage arv$job_tasks.show(uuid) +#' @param uuid +#' @return JobTask object. +#' @name job_tasks.show +NULL + +#' job_tasks.destroy is a method defined in Arvados class. +#' +#' @usage arv$job_tasks.destroy(uuid) +#' @param uuid +#' @return JobTask object. +#' @name job_tasks.destroy +NULL + +#' links.get is a method defined in Arvados class. +#' +#' @usage arv$links.get(uuid) +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.get +NULL + +#' links.index is a method defined in Arvados class. +#' +#' @usage arv$links.index(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return LinkList object. +#' @name links.index +NULL + +#' links.create is a method defined in Arvados class. +#' +#' @usage arv$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 + +#' links.update is a method defined in Arvados class. +#' +#' @usage arv$links.update(link, uuid) +#' @param link Link object. +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.update +NULL + +#' links.delete is a method defined in Arvados class. +#' +#' @usage arv$links.delete(uuid) +#' @param uuid The UUID of the Link in question. +#' @return Link object. +#' @name links.delete +NULL + +#' links.list is a method defined in Arvados class. +#' +#' @usage arv$links.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return LinkList object. +#' @name links.list +NULL + +#' links.show is a method defined in Arvados class. +#' +#' @usage arv$links.show(uuid) +#' @param uuid +#' @return Link object. +#' @name links.show +NULL + +#' links.destroy 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) +#' @param uuid +#' @return Job object. +#' @name jobs.cancel +NULL + +#' jobs.lock is a method defined in Arvados class. +#' +#' @usage arv$jobs.lock(uuid) +#' @param uuid +#' @return Job object. +#' @name jobs.lock +NULL + +#' jobs.list is a method defined in Arvados class. +#' +#' @usage arv$jobs.list(filters = NULL, where = NULL, +#' order = NULL, select = NULL, distinct = NULL, +#' limit = "100", offset = "0", count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return JobList object. +#' @name jobs.list +NULL + +#' jobs.show is a method defined in Arvados class. +#' +#' @usage arv$jobs.show(uuid) +#' @param uuid +#' @return Job object. +#' @name jobs.show +NULL + +#' jobs.destroy is a method defined in Arvados class. +#' +#' @usage arv$jobs.destroy(uuid) +#' @param uuid +#' @return Job object. +#' @name jobs.destroy +NULL + +#' keep_disks.get is a method defined in Arvados class. +#' +#' @usage arv$keep_disks.get(uuid) +#' @param uuid The UUID of the KeepDisk in question. +#' @return KeepDisk object. +#' @name keep_disks.get +NULL + +#' keep_disks.index is a method defined in Arvados class. +#' +#' @usage arv$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$keep_disks.create(keepdisk, +#' ensure_unique_name = "false") +#' @param keepDisk KeepDisk object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return KeepDisk object. +#' @name keep_disks.create +NULL + +#' keep_disks.update is a method defined in Arvados class. +#' +#' @usage arv$keep_disks.update(keepdisk, +#' uuid) +#' @param keepDisk KeepDisk object. +#' @param uuid The UUID of the KeepDisk in question. +#' @return KeepDisk object. +#' @name keep_disks.update +NULL + +#' keep_disks.delete is a method defined in Arvados class. +#' +#' @usage arv$keep_disks.delete(uuid) +#' @param uuid The UUID of the KeepDisk in question. +#' @return KeepDisk object. +#' @name keep_disks.delete +NULL + +#' keep_disks.ping is a method defined in Arvados class. +#' +#' @usage arv$keep_disks.ping(uuid = NULL, +#' ping_secret, node_uuid = NULL, filesystem_uuid = NULL, +#' service_host = NULL, service_port, service_ssl_flag) +#' @param uuid +#' @param ping_secret +#' @param node_uuid +#' @param filesystem_uuid +#' @param service_host +#' @param service_port +#' @param service_ssl_flag +#' @return KeepDisk object. +#' @name keep_disks.ping +NULL + +#' keep_disks.list is a method defined in Arvados class. +#' +#' @usage arv$keep_disks.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return KeepDiskList object. +#' @name keep_disks.list +NULL + +#' keep_disks.show is a method defined in Arvados class. +#' +#' @usage arv$keep_disks.show(uuid) +#' @param uuid +#' @return KeepDisk object. +#' @name keep_disks.show +NULL + +#' keep_disks.destroy is a method defined in Arvados class. +#' +#' @usage arv$keep_disks.destroy(uuid) +#' @param uuid +#' @return KeepDisk object. +#' @name keep_disks.destroy +NULL + +#' keep_services.get is a method defined in Arvados class. +#' +#' @usage arv$keep_services.get(uuid) +#' @param uuid The UUID of the KeepService in question. +#' @return KeepService object. +#' @name keep_services.get +NULL + +#' keep_services.index is a method defined in Arvados class. +#' +#' @usage arv$keep_services.index(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return KeepServiceList object. +#' @name keep_services.index +NULL + +#' keep_services.create is a method defined in Arvados class. +#' +#' @usage arv$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 is a method defined in Arvados class. +#' +#' @usage arv$keep_services.update(keepservice, +#' uuid) +#' @param keepService KeepService object. +#' @param uuid The UUID of the KeepService in question. +#' @return KeepService object. +#' @name keep_services.update +NULL + +#' keep_services.delete is a method defined in Arvados class. +#' +#' @usage arv$keep_services.delete(uuid) +#' @param uuid The UUID of the KeepService in question. +#' @return KeepService object. +#' @name keep_services.delete +NULL + +#' keep_services.accessible is a method defined in Arvados class. +#' +#' @usage arv$keep_services.accessible(NULL) +#' @return KeepService object. +#' @name keep_services.accessible +NULL + +#' keep_services.list is a method defined in Arvados class. +#' +#' @usage arv$keep_services.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return KeepServiceList object. +#' @name keep_services.list +NULL + +#' keep_services.show is a method defined in Arvados class. +#' +#' @usage arv$keep_services.show(uuid) +#' @param uuid +#' @return KeepService object. +#' @name keep_services.show +NULL + +#' keep_services.destroy is a method defined in Arvados class. +#' +#' @usage arv$keep_services.destroy(uuid) +#' @param uuid +#' @return KeepService object. +#' @name keep_services.destroy +NULL + +#' pipeline_templates.get is a method defined in Arvados class. +#' +#' @usage arv$pipeline_templates.get(uuid) +#' @param uuid The UUID of the PipelineTemplate in question. +#' @return PipelineTemplate object. +#' @name pipeline_templates.get +NULL + +#' pipeline_templates.index is a method defined in Arvados class. +#' +#' @usage arv$pipeline_templates.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 PipelineTemplateList object. +#' @name pipeline_templates.index +NULL + +#' pipeline_templates.create is a method defined in Arvados class. +#' +#' @usage arv$pipeline_templates.create(pipelinetemplate, +#' ensure_unique_name = "false") +#' @param pipelineTemplate PipelineTemplate object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return PipelineTemplate object. +#' @name pipeline_templates.create +NULL + +#' pipeline_templates.update is a method defined in Arvados class. +#' +#' @usage arv$pipeline_templates.update(pipelinetemplate, +#' uuid) +#' @param pipelineTemplate PipelineTemplate object. +#' @param uuid The UUID of the PipelineTemplate in question. +#' @return PipelineTemplate object. +#' @name pipeline_templates.update +NULL + +#' pipeline_templates.delete is a method defined in Arvados class. +#' +#' @usage arv$pipeline_templates.delete(uuid) +#' @param uuid The UUID of the PipelineTemplate in question. +#' @return PipelineTemplate object. +#' @name pipeline_templates.delete +NULL + +#' pipeline_templates.list is a method defined in Arvados class. +#' +#' @usage arv$pipeline_templates.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return PipelineTemplateList object. +#' @name pipeline_templates.list +NULL + +#' pipeline_templates.show is a method defined in Arvados class. +#' +#' @usage arv$pipeline_templates.show(uuid) +#' @param uuid +#' @return PipelineTemplate object. +#' @name pipeline_templates.show +NULL + +#' pipeline_templates.destroy is a method defined in Arvados class. +#' +#' @usage arv$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$pipeline_instances.get(uuid) +#' @param uuid The UUID of the PipelineInstance in question. +#' @return PipelineInstance object. +#' @name pipeline_instances.get +NULL + +#' pipeline_instances.index is a method defined in Arvados class. +#' +#' @usage arv$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$pipeline_instances.create(pipelineinstance, +#' ensure_unique_name = "false") +#' @param pipelineInstance PipelineInstance object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return PipelineInstance object. +#' @name pipeline_instances.create +NULL + +#' pipeline_instances.update is a method defined in Arvados class. +#' +#' @usage arv$pipeline_instances.update(pipelineinstance, +#' uuid) +#' @param pipelineInstance PipelineInstance object. +#' @param uuid The UUID of the PipelineInstance in question. +#' @return PipelineInstance object. +#' @name pipeline_instances.update +NULL + +#' pipeline_instances.delete is a method defined in Arvados class. +#' +#' @usage arv$pipeline_instances.delete(uuid) +#' @param uuid The UUID of the PipelineInstance in question. +#' @return PipelineInstance object. +#' @name pipeline_instances.delete +NULL + +#' pipeline_instances.cancel is a method defined in Arvados class. +#' +#' @usage arv$pipeline_instances.cancel(uuid) +#' @param uuid +#' @return PipelineInstance object. +#' @name pipeline_instances.cancel +NULL + +#' pipeline_instances.list is a method defined in Arvados class. +#' +#' @usage arv$pipeline_instances.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return PipelineInstanceList object. +#' @name pipeline_instances.list +NULL + +#' pipeline_instances.show is a method defined in Arvados class. +#' +#' @usage arv$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$nodes.show(uuid) +#' @param uuid +#' @return Node object. +#' @name nodes.show +NULL + +#' nodes.destroy is a method defined in Arvados class. +#' +#' @usage arv$nodes.destroy(uuid) +#' @param uuid +#' @return Node object. +#' @name nodes.destroy +NULL + +#' repositories.get is a method defined in Arvados class. +#' +#' @usage arv$repositories.get(uuid) +#' @param uuid The UUID of the Repository in question. +#' @return Repository object. +#' @name repositories.get +NULL + +#' repositories.index is a method defined in Arvados class. +#' +#' @usage arv$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$repositories.create(repository, +#' ensure_unique_name = "false") +#' @param repository Repository object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Repository object. +#' @name repositories.create +NULL + +#' repositories.update is a method defined in Arvados class. +#' +#' @usage arv$repositories.update(repository, +#' uuid) +#' @param repository Repository object. +#' @param uuid The UUID of the Repository in question. +#' @return Repository object. +#' @name repositories.update +NULL + +#' repositories.delete is a method defined in Arvados class. +#' +#' @usage arv$repositories.delete(uuid) +#' @param uuid The UUID of the Repository in question. +#' @return Repository object. +#' @name repositories.delete +NULL + +#' repositories.get_all_permissions is a method defined in Arvados class. +#' +#' @usage arv$repositories.get_all_permissions(NULL) +#' @return Repository object. +#' @name repositories.get_all_permissions +NULL + +#' repositories.list is a method defined in Arvados class. +#' +#' @usage arv$repositories.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return RepositoryList object. +#' @name repositories.list +NULL + +#' repositories.show is a method defined in Arvados class. +#' +#' @usage arv$repositories.show(uuid) +#' @param uuid +#' @return Repository object. +#' @name repositories.show +NULL + +#' repositories.destroy is a method defined in Arvados class. +#' +#' @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) +#' @param uuid The UUID of the Specimen in question. +#' @return Specimen object. +#' @name specimens.get +NULL + +#' specimens.index is a method defined in Arvados class. +#' +#' @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, +#' ensure_unique_name = "false") +#' @param specimen Specimen object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Specimen object. +#' @name specimens.create +NULL + +#' specimens.update is a method defined in Arvados class. +#' +#' @usage arv$specimens.update(specimen, +#' uuid) +#' @param specimen Specimen object. +#' @param uuid The UUID of the Specimen in question. +#' @return Specimen object. +#' @name specimens.update +NULL + +#' specimens.delete is a method defined in Arvados class. +#' +#' @usage arv$specimens.delete(uuid) +#' @param uuid The UUID of the Specimen in question. +#' @return Specimen object. +#' @name specimens.delete +NULL + +#' specimens.list is a method defined in Arvados class. +#' +#' @usage arv$specimens.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return SpecimenList object. +#' @name specimens.list +NULL + +#' specimens.show is a method defined in Arvados class. +#' +#' @usage arv$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) +#' @param uuid The UUID of the Log in question. +#' @return Log object. +#' @name logs.get +NULL + +#' logs.index is a method defined in Arvados class. +#' +#' @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") +#' @param log Log object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Log object. +#' @name logs.create +NULL + +#' logs.update is a method defined in Arvados class. +#' +#' @usage arv$logs.update(log, uuid) +#' @param log Log object. +#' @param uuid The UUID of the Log in question. +#' @return Log object. +#' @name logs.update +NULL + +#' logs.delete is a method defined in Arvados class. +#' +#' @usage arv$logs.delete(uuid) +#' @param uuid The UUID of the Log in question. +#' @return Log object. +#' @name logs.delete +NULL + +#' logs.list is a method defined in Arvados class. +#' +#' @usage arv$logs.list(filters = NULL, where = NULL, +#' order = NULL, select = NULL, distinct = NULL, +#' limit = "100", offset = "0", count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return LogList object. +#' @name logs.list +NULL + +#' logs.show is a method defined in Arvados class. +#' +#' @usage arv$logs.show(uuid) +#' @param uuid +#' @return Log object. +#' @name logs.show +NULL + +#' logs.destroy is a method defined in Arvados class. +#' +#' @usage arv$logs.destroy(uuid) +#' @param uuid +#' @return Log object. +#' @name logs.destroy +NULL + +#' traits.get is a method defined in Arvados class. +#' +#' @usage arv$traits.get(uuid) +#' @param uuid The UUID of the Trait in question. +#' @return Trait object. +#' @name traits.get +NULL + +#' traits.index is a method defined in Arvados class. +#' +#' @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") +#' @param trait Trait object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Trait object. +#' @name traits.create +NULL + +#' traits.update is a method defined in Arvados class. +#' +#' @usage arv$traits.update(trait, uuid) +#' @param trait Trait object. +#' @param uuid The UUID of the Trait in question. +#' @return Trait object. +#' @name traits.update +NULL + +#' traits.delete is a method defined in Arvados class. +#' +#' @usage arv$traits.delete(uuid) +#' @param uuid The UUID of the Trait in question. +#' @return Trait object. +#' @name traits.delete +NULL + +#' traits.list is a method defined in Arvados class. +#' +#' @usage arv$traits.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return TraitList object. +#' @name traits.list +NULL + +#' traits.show is a method defined in Arvados class. +#' +#' @usage arv$traits.show(uuid) +#' @param uuid +#' @return Trait object. +#' @name traits.show +NULL + +#' traits.destroy is a method defined in Arvados class. +#' +#' @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) +#' @param uuid The UUID of the VirtualMachine in question. +#' @return VirtualMachine object. +#' @name virtual_machines.get +NULL + +#' virtual_machines.index is a method defined in Arvados class. +#' +#' @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, +#' ensure_unique_name = "false") +#' @param virtualMachine VirtualMachine object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return VirtualMachine object. +#' @name virtual_machines.create +NULL + +#' virtual_machines.update is a method defined in Arvados class. +#' +#' @usage arv$virtual_machines.update(virtualmachine, +#' uuid) +#' @param virtualMachine VirtualMachine object. +#' @param uuid The UUID of the VirtualMachine in question. +#' @return VirtualMachine object. +#' @name virtual_machines.update +NULL + +#' virtual_machines.delete is a method defined in Arvados class. +#' +#' @usage arv$virtual_machines.delete(uuid) +#' @param uuid The UUID of the VirtualMachine in question. +#' @return VirtualMachine object. +#' @name virtual_machines.delete +NULL + +#' virtual_machines.logins is a method defined in Arvados class. +#' +#' @usage arv$virtual_machines.logins(uuid) +#' @param uuid +#' @return VirtualMachine object. +#' @name virtual_machines.logins +NULL + +#' virtual_machines.get_all_logins is a method defined in Arvados class. +#' +#' @usage arv$virtual_machines.get_all_logins(NULL) +#' @return VirtualMachine object. +#' @name virtual_machines.get_all_logins +NULL + +#' virtual_machines.list is a method defined in Arvados class. +#' +#' @usage arv$virtual_machines.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return VirtualMachineList object. +#' @name virtual_machines.list +NULL + +#' virtual_machines.show is a method defined in Arvados class. +#' +#' @usage arv$virtual_machines.show(uuid) +#' @param uuid +#' @return VirtualMachine object. +#' @name virtual_machines.show +NULL + +#' virtual_machines.destroy is a method defined in Arvados class. +#' +#' @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) +#' @param uuid The UUID of the Workflow in question. +#' @return Workflow object. +#' @name workflows.get +NULL + +#' workflows.index is a method defined in Arvados class. +#' +#' @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, +#' ensure_unique_name = "false") +#' @param workflow Workflow object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return Workflow object. +#' @name workflows.create +NULL + +#' workflows.update is a method defined in Arvados class. +#' +#' @usage arv$workflows.update(workflow, +#' uuid) +#' @param workflow Workflow object. +#' @param uuid The UUID of the Workflow in question. +#' @return Workflow object. +#' @name workflows.update +NULL + +#' workflows.delete is a method defined in Arvados class. +#' +#' @usage arv$workflows.delete(uuid) +#' @param uuid The UUID of the Workflow in question. +#' @return Workflow object. +#' @name workflows.delete +NULL + +#' workflows.list is a method defined in Arvados class. +#' +#' @usage arv$workflows.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return WorkflowList object. +#' @name workflows.list +NULL + +#' workflows.show is a method defined in Arvados class. +#' +#' @usage arv$workflows.show(uuid) +#' @param uuid +#' @return Workflow object. +#' @name workflows.show +NULL + +#' workflows.destroy is a method defined in Arvados class. +#' +#' @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) +#' @param uuid The UUID of the Group in question. +#' @return Group object. +#' @name groups.get +NULL + +#' groups.index is a method defined in Arvados class. +#' +#' @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") +#' @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 groups.create +NULL + +#' groups.update is a method defined in Arvados class. +#' +#' @usage arv$groups.update(group, uuid) +#' @param group Group object. +#' @param uuid The UUID of the Group in question. +#' @return Group object. +#' @name groups.update +NULL + +#' groups.delete is a method defined in Arvados class. +#' +#' @usage arv$groups.delete(uuid) +#' @param uuid The UUID of the Group in question. +#' @return Group object. +#' @name groups.delete +NULL + +#' groups.contents is a method defined in Arvados class. +#' +#' @usage arv$groups.contents(filters = NULL, +#' where = NULL, order = NULL, distinct = NULL, +#' limit = "100", offset = "0", count = "exact", +#' include_trash = NULL, uuid = NULL, recursive = NULL) +#' @param filters +#' @param where +#' @param order +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @param include_trash Include items whose is_trashed attribute is true. +#' @param uuid +#' @param recursive Include contents from child groups recursively. +#' @return Group object. +#' @name groups.contents +NULL + +#' groups.trash is a method defined in Arvados class. +#' +#' @usage arv$groups.trash(uuid) +#' @param uuid +#' @return Group object. +#' @name groups.trash +NULL + +#' groups.untrash is a method defined in Arvados class. +#' +#' @usage arv$groups.untrash(uuid) +#' @param uuid +#' @return Group object. +#' @name groups.untrash +NULL + +#' groups.list is a method defined in Arvados class. +#' +#' @usage arv$groups.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact", include_trash = NULL) +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @param include_trash Include items whose is_trashed attribute is true. +#' @return GroupList object. +#' @name groups.list +NULL + +#' groups.show is a method defined in Arvados class. +#' +#' @usage arv$groups.show(uuid) +#' @param uuid +#' @return Group object. +#' @name groups.show +NULL + +#' groups.destroy is a method defined in Arvados class. +#' +#' @usage arv$groups.destroy(uuid) +#' @param uuid +#' @return Group object. +#' @name groups.destroy +NULL + +#' user_agreements.get is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.get(uuid) +#' @param uuid The UUID of the UserAgreement in question. +#' @return UserAgreement object. +#' @name user_agreements.get +NULL + +#' user_agreements.index is a method defined in Arvados class. +#' +#' @usage arv$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$user_agreements.create(useragreement, +#' ensure_unique_name = "false") +#' @param userAgreement UserAgreement object. +#' @param ensure_unique_name Adjust name to ensure uniqueness instead of returning an error on (owner_uuid, name) collision. +#' @return UserAgreement object. +#' @name user_agreements.create +NULL + +#' user_agreements.update is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.update(useragreement, +#' uuid) +#' @param userAgreement UserAgreement object. +#' @param uuid The UUID of the UserAgreement in question. +#' @return UserAgreement object. +#' @name user_agreements.update +NULL + +#' user_agreements.delete is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.delete(uuid) +#' @param uuid The UUID of the UserAgreement in question. +#' @return UserAgreement object. +#' @name user_agreements.delete +NULL + +#' user_agreements.signatures is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.signatures(NULL) +#' @return UserAgreement object. +#' @name user_agreements.signatures +NULL + +#' user_agreements.sign is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.sign(NULL) +#' @return UserAgreement object. +#' @name user_agreements.sign +NULL + +#' user_agreements.list is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.list(filters = NULL, +#' where = NULL, order = NULL, select = NULL, +#' distinct = NULL, limit = "100", offset = "0", +#' count = "exact") +#' @param filters +#' @param where +#' @param order +#' @param select +#' @param distinct +#' @param limit +#' @param offset +#' @param count +#' @return UserAgreementList object. +#' @name user_agreements.list +NULL + +#' user_agreements.new is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.new(NULL) +#' @return UserAgreement object. +#' @name user_agreements.new +NULL + +#' user_agreements.show is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.show(uuid) +#' @param uuid +#' @return UserAgreement object. +#' @name user_agreements.show +NULL + +#' user_agreements.destroy is a method defined in Arvados class. +#' +#' @usage arv$user_agreements.destroy(uuid) +#' @param uuid +#' @return UserAgreement object. +#' @name user_agreements.destroy +NULL + #' @export Arvados <- R6::R6Class( @@ -30,13 +2443,46 @@ Arvados <- R6::R6Class( }, + project.get = function(uuid) + { + self$groups.get(uuid) + }, + + project.create = function(group, ensure_unique_name = "false") + { + group <- c("group_class" = "project", group) + self$groups.create(group, ensure_unique_name) + }, + + project.update = function(group, uuid) + { + group <- c("group_class" = "project", group) + self$groups.update(group, uuid) + }, + + project.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact", + include_trash = NULL) + { + filters[[length(filters) + 1]] <- list("group_class", "=", "project") + self$groups.list(filters, where, order, select, distinct, + limit, offset, count, include_trash) + }, + + project.delete = function(uuid) + { + self$groups.delete(uuid) + }, + users.get = function(uuid) { endPoint <- stringr::str_interp("users/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -46,32 +2492,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, - users.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + 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) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -81,11 +2516,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, users.create = function(user, ensure_unique_name = "false") @@ -95,7 +2526,12 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- user$toJSON() + + 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) @@ -104,17 +2540,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.update = function(user, uuid) @@ -123,8 +2549,13 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- user$toJSON() + queryArgs <- NULL + + if(length(user) > 0) + body <- jsonlite::toJSON(list(user = user), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -133,17 +2564,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.delete = function(uuid) @@ -152,7 +2573,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -162,17 +2584,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.current = function() @@ -182,6 +2594,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -191,17 +2604,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.system = function() @@ -211,6 +2614,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -220,17 +2624,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.activate = function(uuid) @@ -239,7 +2633,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -249,31 +2644,20 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, - users.setup = function( - user = NULL, openid_prefix = NULL, repo_name = NULL, - vm_uuid = NULL, send_notification_email = "false") + users.setup = function(user = NULL, openid_prefix = NULL, + repo_name = NULL, vm_uuid = NULL, send_notification_email = "false") { endPoint <- stringr::str_interp("users/setup") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - user = user, openid_prefix = openid_prefix, - repo_name = repo_name, vm_uuid = vm_uuid, - send_notification_email = send_notification_email) + queryArgs <- list(user = user, openid_prefix = openid_prefix, + repo_name = repo_name, vm_uuid = vm_uuid, + send_notification_email = send_notification_email) + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -283,17 +2667,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.unsetup = function(uuid) @@ -302,7 +2676,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -312,17 +2687,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.update_uuid = function(uuid, new_uuid) @@ -331,7 +2696,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid, new_uuid = new_uuid) + queryArgs <- list(new_uuid = new_uuid) + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -341,32 +2707,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, - users.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + 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) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -376,11 +2731,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, users.show = function(uuid) @@ -389,7 +2740,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -399,17 +2751,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, users.destroy = function(uuid) @@ -418,7 +2760,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -428,17 +2771,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - User$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, email = resource$email, - first_name = resource$first_name, last_name = resource$last_name, - identity_url = resource$identity_url, is_admin = resource$is_admin, - prefs = resource$prefs, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - is_active = resource$is_active, username = resource$username) + resource }, api_client_authorizations.get = function(uuid) @@ -447,7 +2780,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -457,30 +2791,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, - api_client_authorizations.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + api_client_authorizations.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("api_client_authorizations") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -490,22 +2816,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorizationList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - api_client_authorizations.create = function( - api_client_authorization, ensure_unique_name = "false") + api_client_authorizations.create = function(apiclientauthorization, + ensure_unique_name = "false") { endPoint <- stringr::str_interp("api_client_authorizations") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- api_client_authorization$toJSON() + + 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) @@ -514,25 +2841,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, - api_client_authorizations.update = function(api_client_authorization, uuid) + 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$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- api_client_authorization$toJSON() + 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) @@ -541,15 +2865,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, api_client_authorizations.delete = function(uuid) @@ -558,7 +2874,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -568,15 +2885,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, api_client_authorizations.create_system_auth = function(api_client_id = NULL, scopes = NULL) @@ -585,8 +2894,9 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - api_client_id = api_client_id, scopes = scopes) + queryArgs <- list(api_client_id = api_client_id, + scopes = scopes) + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -596,15 +2906,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, api_client_authorizations.current = function() @@ -614,6 +2916,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -623,30 +2926,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, - api_client_authorizations.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + 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) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -656,11 +2951,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorizationList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, api_client_authorizations.show = function(uuid) @@ -669,7 +2960,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -679,15 +2971,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, api_client_authorizations.destroy = function(uuid) @@ -696,7 +2980,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -706,24 +2991,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientAuthorization$new( - uuid = resource$uuid, etag = resource$etag, - api_token = resource$api_token, api_client_id = resource$api_client_id, - user_id = resource$user_id, created_by_ip_address = resource$created_by_ip_address, - last_used_by_ip_address = resource$last_used_by_ip_address, - last_used_at = resource$last_used_at, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at, - default_owner_uuid = resource$default_owner_uuid, - scopes = resource$scopes) + resource }, - api_clients.get = function(uuid) + containers.get = function(uuid) { - endPoint <- stringr::str_interp("api_clients/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -733,28 +3011,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClient$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - url_prefix = resource$url_prefix, created_at = resource$created_at, - updated_at = resource$updated_at, is_trusted = resource$is_trusted) + resource }, - api_clients.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + containers.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("api_clients") + endPoint <- stringr::str_interp("containers") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -764,21 +3036,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - api_clients.create = function(api_client, ensure_unique_name = "false") + containers.create = function(container, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("api_clients") + endPoint <- stringr::str_interp("containers") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- api_client$toJSON() + + if(length(container) > 0) + body <- jsonlite::toJSON(list(container = container), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -787,23 +3060,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClient$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - url_prefix = resource$url_prefix, created_at = resource$created_at, - updated_at = resource$updated_at, is_trusted = resource$is_trusted) + resource }, - api_clients.update = function(api_client, uuid) + containers.update = function(container, uuid) { - endPoint <- stringr::str_interp("api_clients/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- api_client$toJSON() + queryArgs <- NULL + + if(length(container) > 0) + body <- jsonlite::toJSON(list(container = container), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -812,22 +3084,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClient$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - url_prefix = resource$url_prefix, created_at = resource$created_at, - updated_at = resource$updated_at, is_trusted = resource$is_trusted) + resource }, - api_clients.delete = function(uuid) + containers.delete = function(uuid) { - endPoint <- stringr::str_interp("api_clients/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -837,28 +3104,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClient$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - url_prefix = resource$url_prefix, created_at = resource$created_at, - updated_at = resource$updated_at, is_trusted = resource$is_trusted) + resource }, - api_clients.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + containers.auth = function(uuid) { - endPoint <- stringr::str_interp("api_clients") + endPoint <- stringr::str_interp("containers/${uuid}/auth") url <- paste0(private$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, @@ -868,70 +3124,57 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ApiClientList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - api_clients.show = function(uuid) + containers.lock = function(uuid) { - endPoint <- stringr::str_interp("api_clients/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}/lock") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClient$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - url_prefix = resource$url_prefix, created_at = resource$created_at, - updated_at = resource$updated_at, is_trusted = resource$is_trusted) + resource }, - api_clients.destroy = function(uuid) + containers.unlock = function(uuid) { - endPoint <- stringr::str_interp("api_clients/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}/unlock") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("DELETE", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ApiClient$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - url_prefix = resource$url_prefix, created_at = resource$created_at, - updated_at = resource$updated_at, is_trusted = resource$is_trusted) + resource }, - container_requests.get = function(uuid) + containers.secret_mounts = function(uuid) { - endPoint <- stringr::str_interp("container_requests/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}/secret_mounts") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -941,41 +3184,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequest$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - properties = resource$properties, state = resource$state, - requesting_container_uuid = resource$requesting_container_uuid, - container_uuid = resource$container_uuid, - container_count_max = resource$container_count_max, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - container_image = resource$container_image, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - priority = resource$priority, expires_at = resource$expires_at, - filters = resource$filters, updated_at = resource$updated_at, - container_count = resource$container_count, - use_existing = resource$use_existing, scheduling_parameters = resource$scheduling_parameters, - output_uuid = resource$output_uuid, log_uuid = resource$log_uuid, - output_name = resource$output_name, output_ttl = resource$output_ttl) + resource }, - container_requests.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + containers.current = function() { - endPoint <- stringr::str_interp("container_requests") + endPoint <- stringr::str_interp("containers/current") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -985,97 +3204,62 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequestList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - container_requests.create = function( - container_request, ensure_unique_name = "false") + containers.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("container_requests") + endPoint <- stringr::str_interp("containers") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- container_request$toJSON() + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - response <- private$REST$http$exec("POST", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequest$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - properties = resource$properties, state = resource$state, - requesting_container_uuid = resource$requesting_container_uuid, - container_uuid = resource$container_uuid, - container_count_max = resource$container_count_max, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - container_image = resource$container_image, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - priority = resource$priority, expires_at = resource$expires_at, - filters = resource$filters, updated_at = resource$updated_at, - container_count = resource$container_count, - use_existing = resource$use_existing, scheduling_parameters = resource$scheduling_parameters, - output_uuid = resource$output_uuid, log_uuid = resource$log_uuid, - output_name = resource$output_name, output_ttl = resource$output_ttl) + resource }, - container_requests.update = function(container_request, uuid) + containers.show = function(uuid) { - endPoint <- stringr::str_interp("container_requests/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- container_request$toJSON() + queryArgs <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequest$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - properties = resource$properties, state = resource$state, - requesting_container_uuid = resource$requesting_container_uuid, - container_uuid = resource$container_uuid, - container_count_max = resource$container_count_max, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - container_image = resource$container_image, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - priority = resource$priority, expires_at = resource$expires_at, - filters = resource$filters, updated_at = resource$updated_at, - container_count = resource$container_count, - use_existing = resource$use_existing, scheduling_parameters = resource$scheduling_parameters, - output_uuid = resource$output_uuid, log_uuid = resource$log_uuid, - output_name = resource$output_name, output_ttl = resource$output_ttl) + resource }, - container_requests.delete = function(uuid) + containers.destroy = function(uuid) { - endPoint <- stringr::str_interp("container_requests/${uuid}") + endPoint <- stringr::str_interp("containers/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -1085,41 +3269,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequest$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - properties = resource$properties, state = resource$state, - requesting_container_uuid = resource$requesting_container_uuid, - container_uuid = resource$container_uuid, - container_count_max = resource$container_count_max, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - container_image = resource$container_image, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - priority = resource$priority, expires_at = resource$expires_at, - filters = resource$filters, updated_at = resource$updated_at, - container_count = resource$container_count, - use_existing = resource$use_existing, scheduling_parameters = resource$scheduling_parameters, - output_uuid = resource$output_uuid, log_uuid = resource$log_uuid, - output_name = resource$output_name, output_ttl = resource$output_ttl) + resource }, - container_requests.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + api_clients.get = function(uuid) { - endPoint <- stringr::str_interp("container_requests") + endPoint <- stringr::str_interp("api_clients/${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$exec("GET", url, headers, body, @@ -1129,20 +3289,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequestList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - container_requests.show = function(uuid) + api_clients.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("container_requests/${uuid}") + endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1152,181 +3314,130 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequest$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - properties = resource$properties, state = resource$state, - requesting_container_uuid = resource$requesting_container_uuid, - container_uuid = resource$container_uuid, - container_count_max = resource$container_count_max, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - container_image = resource$container_image, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - priority = resource$priority, expires_at = resource$expires_at, - filters = resource$filters, updated_at = resource$updated_at, - container_count = resource$container_count, - use_existing = resource$use_existing, scheduling_parameters = resource$scheduling_parameters, - output_uuid = resource$output_uuid, log_uuid = resource$log_uuid, - output_name = resource$output_name, output_ttl = resource$output_ttl) + resource }, - container_requests.destroy = function(uuid) + api_clients.create = function(apiclient, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("container_requests/${uuid}") + endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - response <- private$REST$http$exec("DELETE", url, headers, body, + if(length(apiclient) > 0) + body <- jsonlite::toJSON(list(apiclient = apiclient), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - ContainerRequest$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - properties = resource$properties, state = resource$state, - requesting_container_uuid = resource$requesting_container_uuid, - container_uuid = resource$container_uuid, - container_count_max = resource$container_count_max, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - container_image = resource$container_image, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - priority = resource$priority, expires_at = resource$expires_at, - filters = resource$filters, updated_at = resource$updated_at, - container_count = resource$container_count, - use_existing = resource$use_existing, scheduling_parameters = resource$scheduling_parameters, - output_uuid = resource$output_uuid, log_uuid = resource$log_uuid, - output_name = resource$output_name, output_ttl = resource$output_ttl) + resource }, - authorized_keys.get = function(uuid) + api_clients.update = function(apiclient, uuid) { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") + endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + 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$errors) - AuthorizedKey$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - key_type = resource$key_type, authorized_user_uuid = resource$authorized_user_uuid, - public_key = resource$public_key, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - authorized_keys.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + api_clients.delete = function(uuid) { - endPoint <- stringr::str_interp("authorized_keys") + endPoint <- stringr::str_interp("api_clients/${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) if(!is.null(resource$errors)) stop(resource$errors) - AuthorizedKeyList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - authorized_keys.create = function( - authorized_key, ensure_unique_name = "false") + api_clients.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("authorized_keys") + endPoint <- stringr::str_interp("api_clients") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- authorized_key$toJSON() + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - response <- private$REST$http$exec("POST", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - AuthorizedKey$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - key_type = resource$key_type, authorized_user_uuid = resource$authorized_user_uuid, - public_key = resource$public_key, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - authorized_keys.update = function(authorized_key, uuid) + api_clients.show = function(uuid) { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") + endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- authorized_key$toJSON() + queryArgs <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + 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$errors) - AuthorizedKey$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - key_type = resource$key_type, authorized_user_uuid = resource$authorized_user_uuid, - public_key = resource$public_key, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - authorized_keys.delete = function(uuid) + api_clients.destroy = function(uuid) { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") + endPoint <- stringr::str_interp("api_clients/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -1336,29 +3447,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - AuthorizedKey$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - key_type = resource$key_type, authorized_user_uuid = resource$authorized_user_uuid, - public_key = resource$public_key, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - authorized_keys.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + authorized_keys.get = function(uuid) { - endPoint <- stringr::str_interp("authorized_keys") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1368,20 +3467,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - AuthorizedKeyList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - authorized_keys.show = function(uuid) + authorized_keys.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") + endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1391,183 +3492,131 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - AuthorizedKey$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - key_type = resource$key_type, authorized_user_uuid = resource$authorized_user_uuid, - public_key = resource$public_key, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - authorized_keys.destroy = function(uuid) + authorized_keys.create = function(authorizedkey, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("authorized_keys/${uuid}") + endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) - response <- private$REST$http$exec("DELETE", url, headers, body, + if(length(authorizedkey) > 0) + body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - AuthorizedKey$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - key_type = resource$key_type, authorized_user_uuid = resource$authorized_user_uuid, - public_key = resource$public_key, expires_at = resource$expires_at, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - collections.get = function(uuid) + authorized_keys.update = function(authorizedkey, uuid) { - endPoint <- stringr::str_interp("collections/${uuid}") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + if(length(authorizedkey) > 0) + body <- jsonlite::toJSON(list(authorizedkey = authorizedkey), + auto_unbox = TRUE) + else + body <- NULL + + response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact", include_trash = NULL) + authorized_keys.delete = function(uuid) { - endPoint <- stringr::str_interp("collections") + endPoint <- stringr::str_interp("authorized_keys/${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, include_trash = include_trash) + 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) if(!is.null(resource$errors)) stop(resource$errors) - CollectionList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - collections.create = function(collection, ensure_unique_name = "false") + authorized_keys.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("collections") + endPoint <- stringr::str_interp("authorized_keys") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- collection$toJSON() + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) - response <- private$REST$http$exec("POST", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.update = function(collection, uuid) + authorized_keys.show = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- collection$toJSON() + queryArgs <- NULL - response <- private$REST$http$exec("PUT", url, headers, body, + body <- NULL + + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.delete = function(uuid) + authorized_keys.destroy = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}") + endPoint <- stringr::str_interp("authorized_keys/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -1577,32 +3626,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.provenance = function(uuid) + container_requests.get = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}/provenance") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1612,32 +3646,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.used_by = function(uuid) + container_requests.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("collections/${uuid}/used_by") + endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1647,33 +3671,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.trash = function(uuid) + container_requests.create = function(containerrequest, + ensure_unique_name = "false") { - endPoint <- stringr::str_interp("collections/${uuid}/trash") + endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- NULL + queryArgs <- list(ensure_unique_name = ensure_unique_name) + + if(length(containerrequest) > 0) + body <- jsonlite::toJSON(list(containerrequest = containerrequest), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -1682,73 +3696,66 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + 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) - collection$setRESTService(private$REST) - collection + resource }, - collections.untrash = function(uuid) + container_requests.delete = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}/untrash") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- 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) if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact", include_trash = NULL) + container_requests.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { - endPoint <- stringr::str_interp("collections") + endPoint <- stringr::str_interp("container_requests") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count, include_trash = include_trash) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1758,20 +3765,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - CollectionList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - collections.show = function(uuid) + container_requests.show = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1781,32 +3785,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - collections.destroy = function(uuid) + container_requests.destroy = function(uuid) { - endPoint <- stringr::str_interp("collections/${uuid}") + endPoint <- stringr::str_interp("container_requests/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -1816,32 +3805,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - collection <- Collection$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) - - collection$setRESTService(private$REST) - collection + resource }, - containers.get = function(uuid) + collections.get = function(uuid) { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1851,36 +3825,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + collections.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact", include_trash = NULL) { - endPoint <- stringr::str_interp("containers") + endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count, + include_trash = include_trash) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -1890,21 +3851,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - containers.create = function(container, ensure_unique_name = "false") + collections.create = function(collection, ensure_unique_name = "false") { - endPoint <- stringr::str_interp("containers") + endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- container$toJSON() + + 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) @@ -1913,31 +3875,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.update = function(container, uuid) + collections.update = function(collection, uuid) { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- container$toJSON() + 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) @@ -1946,30 +3899,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.delete = function(uuid) + collections.delete = function(uuid) { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -1979,30 +3919,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.auth = function(uuid) + collections.provenance = function(uuid) { - endPoint <- stringr::str_interp("containers/${uuid}/auth") + endPoint <- stringr::str_interp("collections/${uuid}/provenance") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2012,63 +3939,37 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.lock = function(uuid) + collections.used_by = function(uuid) { - endPoint <- stringr::str_interp("containers/${uuid}/lock") + endPoint <- stringr::str_interp("collections/${uuid}/used_by") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("POST", url, headers, body, + response <- private$REST$http$exec("GET", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.unlock = function(uuid) + collections.trash = function(uuid) { - endPoint <- stringr::str_interp("containers/${uuid}/unlock") + endPoint <- stringr::str_interp("collections/${uuid}/trash") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -2078,69 +3979,43 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.current = function() + collections.untrash = function(uuid) { - endPoint <- stringr::str_interp("containers/current") + endPoint <- stringr::str_interp("collections/${uuid}/untrash") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL - response <- private$REST$http$exec("GET", url, headers, body, + response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) resource <- private$REST$httpParser$parseJSONResponse(response) if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + 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("containers") + endPoint <- stringr::str_interp("collections") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + 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$exec("GET", url, headers, body, @@ -2150,20 +4025,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - ContainerList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - containers.show = function(uuid) + collections.show = function(uuid) { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2173,30 +4045,17 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, - containers.destroy = function(uuid) + collections.destroy = function(uuid) { - endPoint <- stringr::str_interp("containers/${uuid}") + endPoint <- stringr::str_interp("collections/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -2206,21 +4065,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Container$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - state = resource$state, started_at = resource$started_at, - finished_at = resource$finished_at, log = resource$log, - environment = resource$environment, cwd = resource$cwd, - command = resource$command, output_path = resource$output_path, - mounts = resource$mounts, runtime_constraints = resource$runtime_constraints, - output = resource$output, container_image = resource$container_image, - progress = resource$progress, priority = resource$priority, - updated_at = resource$updated_at, exit_code = resource$exit_code, - auth_uuid = resource$auth_uuid, locked_by_uuid = resource$locked_by_uuid, - scheduling_parameters = resource$scheduling_parameters) + resource }, humans.get = function(uuid) @@ -2229,7 +4074,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2239,27 +4085,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Human$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, properties = resource$properties, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - humans.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + humans.index = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { endPoint <- stringr::str_interp("humans") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2269,11 +4109,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - HumanList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, humans.create = function(human, ensure_unique_name = "false") @@ -2283,7 +4119,12 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- human$toJSON() + + if(length(human) > 0) + body <- jsonlite::toJSON(list(human = human), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -2292,12 +4133,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Human$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, properties = resource$properties, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, humans.update = function(human, uuid) @@ -2306,8 +4142,13 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- human$toJSON() + queryArgs <- NULL + + if(length(human) > 0) + body <- jsonlite::toJSON(list(human = human), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -2316,12 +4157,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Human$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, properties = resource$properties, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, humans.delete = function(uuid) @@ -2330,7 +4166,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -2340,27 +4177,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Human$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, properties = resource$properties, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - humans.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + humans.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { endPoint <- stringr::str_interp("humans") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2370,11 +4201,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - HumanList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, humans.show = function(uuid) @@ -2383,7 +4210,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2393,12 +4221,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Human$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, properties = resource$properties, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, humans.destroy = function(uuid) @@ -2407,7 +4230,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -2417,12 +4241,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Human$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, properties = resource$properties, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, job_tasks.get = function(uuid) @@ -2431,7 +4250,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2441,32 +4261,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - JobTask$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, job_uuid = resource$job_uuid, - sequence = resource$sequence, parameters = resource$parameters, - output = resource$output, progress = resource$progress, - success = resource$success, created_at = resource$created_at, - updated_at = resource$updated_at, created_by_job_task_uuid = resource$created_by_job_task_uuid, - qsequence = resource$qsequence, started_at = resource$started_at, - finished_at = resource$finished_at) + resource }, - job_tasks.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + job_tasks.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("job_tasks") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2476,21 +4286,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - JobTaskList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - job_tasks.create = function(job_task, ensure_unique_name = "false") + job_tasks.create = function(jobtask, ensure_unique_name = "false") { endPoint <- stringr::str_interp("job_tasks") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- job_task$toJSON() + + if(length(jobtask) > 0) + body <- jsonlite::toJSON(list(jobtask = jobtask), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -2499,27 +4310,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - JobTask$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, job_uuid = resource$job_uuid, - sequence = resource$sequence, parameters = resource$parameters, - output = resource$output, progress = resource$progress, - success = resource$success, created_at = resource$created_at, - updated_at = resource$updated_at, created_by_job_task_uuid = resource$created_by_job_task_uuid, - qsequence = resource$qsequence, started_at = resource$started_at, - finished_at = resource$finished_at) + resource }, - job_tasks.update = function(job_task, uuid) + job_tasks.update = function(jobtask, uuid) { endPoint <- stringr::str_interp("job_tasks/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- job_task$toJSON() + queryArgs <- NULL + + if(length(jobtask) > 0) + body <- jsonlite::toJSON(list(jobtask = jobtask), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -2528,17 +4334,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - JobTask$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, job_uuid = resource$job_uuid, - sequence = resource$sequence, parameters = resource$parameters, - output = resource$output, progress = resource$progress, - success = resource$success, created_at = resource$created_at, - updated_at = resource$updated_at, created_by_job_task_uuid = resource$created_by_job_task_uuid, - qsequence = resource$qsequence, started_at = resource$started_at, - finished_at = resource$finished_at) + resource }, job_tasks.delete = function(uuid) @@ -2547,7 +4343,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -2557,32 +4354,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - JobTask$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, job_uuid = resource$job_uuid, - sequence = resource$sequence, parameters = resource$parameters, - output = resource$output, progress = resource$progress, - success = resource$success, created_at = resource$created_at, - updated_at = resource$updated_at, created_by_job_task_uuid = resource$created_by_job_task_uuid, - qsequence = resource$qsequence, started_at = resource$started_at, - finished_at = resource$finished_at) + resource }, - job_tasks.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + job_tasks.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { 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) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2592,11 +4379,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - JobTaskList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, job_tasks.show = function(uuid) @@ -2605,7 +4388,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2615,17 +4399,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - JobTask$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, job_uuid = resource$job_uuid, - sequence = resource$sequence, parameters = resource$parameters, - output = resource$output, progress = resource$progress, - success = resource$success, created_at = resource$created_at, - updated_at = resource$updated_at, created_by_job_task_uuid = resource$created_by_job_task_uuid, - qsequence = resource$qsequence, started_at = resource$started_at, - finished_at = resource$finished_at) + resource }, job_tasks.destroy = function(uuid) @@ -2634,7 +4408,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -2644,17 +4419,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - JobTask$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, job_uuid = resource$job_uuid, - sequence = resource$sequence, parameters = resource$parameters, - output = resource$output, progress = resource$progress, - success = resource$success, created_at = resource$created_at, - updated_at = resource$updated_at, created_by_job_task_uuid = resource$created_by_job_task_uuid, - qsequence = resource$qsequence, started_at = resource$started_at, - finished_at = resource$finished_at) + resource }, links.get = function(uuid) @@ -2663,7 +4428,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2673,30 +4439,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Link$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, tail_uuid = resource$tail_uuid, - link_class = resource$link_class, name = resource$name, - head_uuid = resource$head_uuid, properties = resource$properties, - updated_at = resource$updated_at) + resource }, - links.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + links.index = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { endPoint <- stringr::str_interp("links") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2706,11 +4463,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - LinkList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, links.create = function(link, ensure_unique_name = "false") @@ -2720,7 +4473,12 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- link$toJSON() + + if(length(link) > 0) + body <- jsonlite::toJSON(list(link = link), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -2729,15 +4487,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Link$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, tail_uuid = resource$tail_uuid, - link_class = resource$link_class, name = resource$name, - head_uuid = resource$head_uuid, properties = resource$properties, - updated_at = resource$updated_at) + resource }, links.update = function(link, uuid) @@ -2746,8 +4496,13 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- link$toJSON() + queryArgs <- NULL + + if(length(link) > 0) + body <- jsonlite::toJSON(list(link = link), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -2756,15 +4511,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Link$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, tail_uuid = resource$tail_uuid, - link_class = resource$link_class, name = resource$name, - head_uuid = resource$head_uuid, properties = resource$properties, - updated_at = resource$updated_at) + resource }, links.delete = function(uuid) @@ -2773,7 +4520,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -2783,30 +4531,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Link$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, tail_uuid = resource$tail_uuid, - link_class = resource$link_class, name = resource$name, - head_uuid = resource$head_uuid, properties = resource$properties, - updated_at = resource$updated_at) + resource }, - links.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + links.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { endPoint <- stringr::str_interp("links") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2816,11 +4555,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - LinkList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, links.show = function(uuid) @@ -2829,7 +4564,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2839,15 +4575,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Link$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, tail_uuid = resource$tail_uuid, - link_class = resource$link_class, name = resource$name, - head_uuid = resource$head_uuid, properties = resource$properties, - updated_at = resource$updated_at) + resource }, links.destroy = function(uuid) @@ -2856,7 +4584,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -2866,15 +4595,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Link$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, tail_uuid = resource$tail_uuid, - link_class = resource$link_class, name = resource$name, - head_uuid = resource$head_uuid, properties = resource$properties, - updated_at = resource$updated_at) + resource }, links.get_permissions = function(uuid) @@ -2883,7 +4604,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2893,15 +4615,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Link$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, tail_uuid = resource$tail_uuid, - link_class = resource$link_class, name = resource$name, - head_uuid = resource$head_uuid, properties = resource$properties, - updated_at = resource$updated_at) + resource }, jobs.get = function(uuid) @@ -2910,7 +4624,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2920,43 +4635,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) + resource }, - jobs.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + jobs.index = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { endPoint <- stringr::str_interp("jobs") 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(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -2966,28 +4659,27 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - JobList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - jobs.create = function( - job, ensure_unique_name = "false", find_or_create = "false", - filters = NULL, minimum_script_version = NULL, - exclude_script_versions = NULL) + 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("jobs") 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) - body <- job$toJSON() + queryArgs <- list(ensure_unique_name = ensure_unique_name, + find_or_create = find_or_create, filters = filters, + minimum_script_version = minimum_script_version, + exclude_script_versions = exclude_script_versions) + + if(length(job) > 0) + body <- jsonlite::toJSON(list(job = job), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -2996,28 +4688,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) + resource }, jobs.update = function(job, uuid) @@ -3026,8 +4697,13 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- job$toJSON() + queryArgs <- NULL + + if(length(job) > 0) + body <- jsonlite::toJSON(list(job = job), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -3036,28 +4712,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) + resource }, jobs.delete = function(uuid) @@ -3066,7 +4721,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -3076,43 +4732,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) + resource }, - jobs.queue = 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("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) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3122,28 +4756,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) + resource }, jobs.queue_size = function() @@ -3153,6 +4766,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3162,28 +4776,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) + resource }, jobs.cancel = function(uuid) @@ -3192,7 +4785,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -3202,28 +4796,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) + resource }, jobs.lock = function(uuid) @@ -3232,7 +4805,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -3242,43 +4816,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) + resource }, - jobs.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + jobs.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { endPoint <- stringr::str_interp("jobs") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3288,11 +4840,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - JobList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, jobs.show = function(uuid) @@ -3301,7 +4849,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3311,28 +4860,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) + resource }, jobs.destroy = function(uuid) @@ -3341,7 +4869,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -3351,28 +4880,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Job$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, submit_id = resource$submit_id, - script = resource$script, script_version = resource$script_version, - script_parameters = resource$script_parameters, - cancelled_by_client_uuid = resource$cancelled_by_client_uuid, - cancelled_by_user_uuid = resource$cancelled_by_user_uuid, - cancelled_at = resource$cancelled_at, started_at = resource$started_at, - finished_at = resource$finished_at, running = resource$running, - success = resource$success, output = resource$output, - created_at = resource$created_at, updated_at = resource$updated_at, - is_locked_by_uuid = resource$is_locked_by_uuid, - log = resource$log, tasks_summary = resource$tasks_summary, - runtime_constraints = resource$runtime_constraints, - nondeterministic = resource$nondeterministic, - repository = resource$repository, supplied_script_version = resource$supplied_script_version, - docker_image_locator = resource$docker_image_locator, - priority = resource$priority, description = resource$description, - state = resource$state, arvados_sdk_version = resource$arvados_sdk_version, - components = resource$components, script_parameters_digest = resource$script_parameters_digest) + resource }, keep_disks.get = function(uuid) @@ -3381,7 +4889,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3391,32 +4900,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepDisk$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, ping_secret = resource$ping_secret, - node_uuid = resource$node_uuid, filesystem_uuid = resource$filesystem_uuid, - bytes_total = resource$bytes_total, bytes_free = resource$bytes_free, - is_readable = resource$is_readable, is_writable = resource$is_writable, - last_read_at = resource$last_read_at, last_write_at = resource$last_write_at, - last_ping_at = resource$last_ping_at, created_at = resource$created_at, - updated_at = resource$updated_at, keep_service_uuid = resource$keep_service_uuid) + resource }, - keep_disks.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + keep_disks.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { 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(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3426,21 +4925,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepDiskList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - keep_disks.create = function(keep_disk, ensure_unique_name = "false") + keep_disks.create = function(keepdisk, ensure_unique_name = "false") { endPoint <- stringr::str_interp("keep_disks") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- keep_disk$toJSON() + + if(length(keepdisk) > 0) + body <- jsonlite::toJSON(list(keepdisk = keepdisk), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -3449,27 +4949,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepDisk$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, ping_secret = resource$ping_secret, - node_uuid = resource$node_uuid, filesystem_uuid = resource$filesystem_uuid, - bytes_total = resource$bytes_total, bytes_free = resource$bytes_free, - is_readable = resource$is_readable, is_writable = resource$is_writable, - last_read_at = resource$last_read_at, last_write_at = resource$last_write_at, - last_ping_at = resource$last_ping_at, created_at = resource$created_at, - updated_at = resource$updated_at, keep_service_uuid = resource$keep_service_uuid) + resource }, - keep_disks.update = function(keep_disk, uuid) + keep_disks.update = function(keepdisk, uuid) { endPoint <- stringr::str_interp("keep_disks/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- keep_disk$toJSON() + queryArgs <- NULL + + if(length(keepdisk) > 0) + body <- jsonlite::toJSON(list(keepdisk = keepdisk), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -3478,17 +4973,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepDisk$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, ping_secret = resource$ping_secret, - node_uuid = resource$node_uuid, filesystem_uuid = resource$filesystem_uuid, - bytes_total = resource$bytes_total, bytes_free = resource$bytes_free, - is_readable = resource$is_readable, is_writable = resource$is_writable, - last_read_at = resource$last_read_at, last_write_at = resource$last_write_at, - last_ping_at = resource$last_ping_at, created_at = resource$created_at, - updated_at = resource$updated_at, keep_service_uuid = resource$keep_service_uuid) + resource }, keep_disks.delete = function(uuid) @@ -3497,7 +4982,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -3507,32 +4993,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepDisk$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, ping_secret = resource$ping_secret, - node_uuid = resource$node_uuid, filesystem_uuid = resource$filesystem_uuid, - bytes_total = resource$bytes_total, bytes_free = resource$bytes_free, - is_readable = resource$is_readable, is_writable = resource$is_writable, - last_read_at = resource$last_read_at, last_write_at = resource$last_write_at, - last_ping_at = resource$last_ping_at, created_at = resource$created_at, - updated_at = resource$updated_at, keep_service_uuid = resource$keep_service_uuid) + resource }, - keep_disks.ping = function( - uuid = NULL, ping_secret, node_uuid = NULL, - filesystem_uuid = NULL, service_host = NULL, - service_port, service_ssl_flag) + 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("keep_disks/ping") 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(uuid = uuid, ping_secret = ping_secret, + node_uuid = node_uuid, filesystem_uuid = filesystem_uuid, + service_host = service_host, service_port = service_port, + service_ssl_flag = service_ssl_flag) + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -3542,32 +5018,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepDisk$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, ping_secret = resource$ping_secret, - node_uuid = resource$node_uuid, filesystem_uuid = resource$filesystem_uuid, - bytes_total = resource$bytes_total, bytes_free = resource$bytes_free, - is_readable = resource$is_readable, is_writable = resource$is_writable, - last_read_at = resource$last_read_at, last_write_at = resource$last_write_at, - last_ping_at = resource$last_ping_at, created_at = resource$created_at, - updated_at = resource$updated_at, keep_service_uuid = resource$keep_service_uuid) + resource }, - keep_disks.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + keep_disks.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("keep_disks") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3577,11 +5043,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepDiskList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, keep_disks.show = function(uuid) @@ -3590,7 +5052,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3600,17 +5063,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepDisk$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, ping_secret = resource$ping_secret, - node_uuid = resource$node_uuid, filesystem_uuid = resource$filesystem_uuid, - bytes_total = resource$bytes_total, bytes_free = resource$bytes_free, - is_readable = resource$is_readable, is_writable = resource$is_writable, - last_read_at = resource$last_read_at, last_write_at = resource$last_write_at, - last_ping_at = resource$last_ping_at, created_at = resource$created_at, - updated_at = resource$updated_at, keep_service_uuid = resource$keep_service_uuid) + resource }, keep_disks.destroy = function(uuid) @@ -3619,7 +5072,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -3629,17 +5083,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepDisk$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, ping_secret = resource$ping_secret, - node_uuid = resource$node_uuid, filesystem_uuid = resource$filesystem_uuid, - bytes_total = resource$bytes_total, bytes_free = resource$bytes_free, - is_readable = resource$is_readable, is_writable = resource$is_writable, - last_read_at = resource$last_read_at, last_write_at = resource$last_write_at, - last_ping_at = resource$last_ping_at, created_at = resource$created_at, - updated_at = resource$updated_at, keep_service_uuid = resource$keep_service_uuid) + resource }, keep_services.get = function(uuid) @@ -3648,7 +5092,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3658,29 +5103,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepService$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, service_host = resource$service_host, - service_port = resource$service_port, service_ssl_flag = resource$service_ssl_flag, - service_type = resource$service_type, created_at = resource$created_at, - updated_at = resource$updated_at, read_only = resource$read_only) + resource }, - keep_services.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + keep_services.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("keep_services") 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(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3690,22 +5128,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepServiceList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - keep_services.create = function( - keep_service, ensure_unique_name = "false") + keep_services.create = function(keepservice, + ensure_unique_name = "false") { endPoint <- stringr::str_interp("keep_services") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- keep_service$toJSON() + + if(length(keepservice) > 0) + body <- jsonlite::toJSON(list(keepservice = keepservice), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -3714,24 +5153,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepService$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, service_host = resource$service_host, - service_port = resource$service_port, service_ssl_flag = resource$service_ssl_flag, - service_type = resource$service_type, created_at = resource$created_at, - updated_at = resource$updated_at, read_only = resource$read_only) + resource }, - keep_services.update = function(keep_service, uuid) + keep_services.update = function(keepservice, uuid) { endPoint <- stringr::str_interp("keep_services/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- keep_service$toJSON() + queryArgs <- NULL + + if(length(keepservice) > 0) + body <- jsonlite::toJSON(list(keepservice = keepservice), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -3740,14 +5177,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepService$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, service_host = resource$service_host, - service_port = resource$service_port, service_ssl_flag = resource$service_ssl_flag, - service_type = resource$service_type, created_at = resource$created_at, - updated_at = resource$updated_at, read_only = resource$read_only) + resource }, keep_services.delete = function(uuid) @@ -3756,7 +5186,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -3766,14 +5197,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepService$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, service_host = resource$service_host, - service_port = resource$service_port, service_ssl_flag = resource$service_ssl_flag, - service_type = resource$service_type, created_at = resource$created_at, - updated_at = resource$updated_at, read_only = resource$read_only) + resource }, keep_services.accessible = function() @@ -3783,6 +5207,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3792,29 +5217,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepService$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, service_host = resource$service_host, - service_port = resource$service_port, service_ssl_flag = resource$service_ssl_flag, - service_type = resource$service_type, created_at = resource$created_at, - updated_at = resource$updated_at, read_only = resource$read_only) + resource }, - keep_services.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + keep_services.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("keep_services") 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(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3824,11 +5242,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepServiceList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, keep_services.show = function(uuid) @@ -3837,7 +5251,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3847,14 +5262,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepService$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, service_host = resource$service_host, - service_port = resource$service_port, service_ssl_flag = resource$service_ssl_flag, - service_type = resource$service_type, created_at = resource$created_at, - updated_at = resource$updated_at, read_only = resource$read_only) + resource }, keep_services.destroy = function(uuid) @@ -3863,7 +5271,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -3873,14 +5282,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - KeepService$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, service_host = resource$service_host, - service_port = resource$service_port, service_ssl_flag = resource$service_ssl_flag, - service_type = resource$service_type, created_at = resource$created_at, - updated_at = resource$updated_at, read_only = resource$read_only) + resource }, pipeline_templates.get = function(uuid) @@ -3889,7 +5291,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3899,29 +5302,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineTemplate$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - components = resource$components, updated_at = resource$updated_at, - description = resource$description) + resource }, - pipeline_templates.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + pipeline_templates.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("pipeline_templates") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -3931,22 +5327,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineTemplateList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - pipeline_templates.create = function( - pipeline_template, ensure_unique_name = "false") + pipeline_templates.create = function(pipelinetemplate, + ensure_unique_name = "false") { endPoint <- stringr::str_interp("pipeline_templates") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- pipeline_template$toJSON() + + 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) @@ -3955,24 +5352,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineTemplate$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - components = resource$components, updated_at = resource$updated_at, - description = resource$description) + resource }, - pipeline_templates.update = function(pipeline_template, uuid) + pipeline_templates.update = function(pipelinetemplate, uuid) { endPoint <- stringr::str_interp("pipeline_templates/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- pipeline_template$toJSON() + queryArgs <- NULL + + if(length(pipelinetemplate) > 0) + body <- jsonlite::toJSON(list(pipelinetemplate = pipelinetemplate), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -3981,14 +5376,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineTemplate$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - components = resource$components, updated_at = resource$updated_at, - description = resource$description) + resource }, pipeline_templates.delete = function(uuid) @@ -3997,7 +5385,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -4007,29 +5396,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineTemplate$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - components = resource$components, updated_at = resource$updated_at, - description = resource$description) + resource }, - pipeline_templates.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + pipeline_templates.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("pipeline_templates") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4039,11 +5421,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineTemplateList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, pipeline_templates.show = function(uuid) @@ -4052,7 +5430,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4062,14 +5441,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineTemplate$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - components = resource$components, updated_at = resource$updated_at, - description = resource$description) + resource }, pipeline_templates.destroy = function(uuid) @@ -4078,7 +5450,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -4088,14 +5461,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineTemplate$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - components = resource$components, updated_at = resource$updated_at, - description = resource$description) + resource }, pipeline_instances.get = function(uuid) @@ -4104,7 +5470,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4114,32 +5481,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstance$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, pipeline_template_uuid = resource$pipeline_template_uuid, - name = resource$name, components = resource$components, - updated_at = resource$updated_at, properties = resource$properties, - state = resource$state, components_summary = resource$components_summary, - started_at = resource$started_at, finished_at = resource$finished_at, - description = resource$description) + resource }, - pipeline_instances.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + pipeline_instances.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("pipeline_instances") 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(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4149,22 +5506,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstanceList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - pipeline_instances.create = function( - pipeline_instance, ensure_unique_name = "false") + pipeline_instances.create = function(pipelineinstance, + ensure_unique_name = "false") { 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) - body <- pipeline_instance$toJSON() + + if(length(pipelineinstance) > 0) + body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -4173,27 +5531,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstance$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, pipeline_template_uuid = resource$pipeline_template_uuid, - name = resource$name, components = resource$components, - updated_at = resource$updated_at, properties = resource$properties, - state = resource$state, components_summary = resource$components_summary, - started_at = resource$started_at, finished_at = resource$finished_at, - description = resource$description) + resource }, - pipeline_instances.update = function(pipeline_instance, uuid) + pipeline_instances.update = function(pipelineinstance, uuid) { endPoint <- stringr::str_interp("pipeline_instances/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- pipeline_instance$toJSON() + queryArgs <- NULL + + if(length(pipelineinstance) > 0) + body <- jsonlite::toJSON(list(pipelineinstance = pipelineinstance), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -4202,17 +5555,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstance$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, pipeline_template_uuid = resource$pipeline_template_uuid, - name = resource$name, components = resource$components, - updated_at = resource$updated_at, properties = resource$properties, - state = resource$state, components_summary = resource$components_summary, - started_at = resource$started_at, finished_at = resource$finished_at, - description = resource$description) + resource }, pipeline_instances.delete = function(uuid) @@ -4221,7 +5564,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -4231,17 +5575,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstance$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, pipeline_template_uuid = resource$pipeline_template_uuid, - name = resource$name, components = resource$components, - updated_at = resource$updated_at, properties = resource$properties, - state = resource$state, components_summary = resource$components_summary, - started_at = resource$started_at, finished_at = resource$finished_at, - description = resource$description) + resource }, pipeline_instances.cancel = function(uuid) @@ -4250,7 +5584,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -4260,32 +5595,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstance$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, pipeline_template_uuid = resource$pipeline_template_uuid, - name = resource$name, components = resource$components, - updated_at = resource$updated_at, properties = resource$properties, - state = resource$state, components_summary = resource$components_summary, - started_at = resource$started_at, finished_at = resource$finished_at, - description = resource$description) + resource }, - pipeline_instances.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + pipeline_instances.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("pipeline_instances") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4295,11 +5620,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstanceList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, pipeline_instances.show = function(uuid) @@ -4308,7 +5629,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4318,17 +5640,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstance$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, pipeline_template_uuid = resource$pipeline_template_uuid, - name = resource$name, components = resource$components, - updated_at = resource$updated_at, properties = resource$properties, - state = resource$state, components_summary = resource$components_summary, - started_at = resource$started_at, finished_at = resource$finished_at, - description = resource$description) + resource }, pipeline_instances.destroy = function(uuid) @@ -4337,7 +5649,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -4347,17 +5660,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - PipelineInstance$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, pipeline_template_uuid = resource$pipeline_template_uuid, - name = resource$name, components = resource$components, - updated_at = resource$updated_at, properties = resource$properties, - state = resource$state, components_summary = resource$components_summary, - started_at = resource$started_at, finished_at = resource$finished_at, - description = resource$description) + resource }, nodes.get = function(uuid) @@ -4366,7 +5669,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4376,32 +5680,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Node$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, slot_number = resource$slot_number, - hostname = resource$hostname, domain = resource$domain, - ip_address = resource$ip_address, first_ping_at = resource$first_ping_at, - last_ping_at = resource$last_ping_at, info = resource$info, - updated_at = resource$updated_at, properties = resource$properties, - job_uuid = resource$job_uuid) + resource }, - nodes.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + nodes.index = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { 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) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4411,24 +5704,24 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - NodeList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - nodes.create = function( - node, ensure_unique_name = "false", assign_slot = NULL) + 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) - body <- node$toJSON() + queryArgs <- list(ensure_unique_name = ensure_unique_name, + assign_slot = assign_slot) + + if(length(node) > 0) + body <- jsonlite::toJSON(list(node = node), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -4437,17 +5730,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Node$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, slot_number = resource$slot_number, - hostname = resource$hostname, domain = resource$domain, - ip_address = resource$ip_address, first_ping_at = resource$first_ping_at, - last_ping_at = resource$last_ping_at, info = resource$info, - updated_at = resource$updated_at, properties = resource$properties, - job_uuid = resource$job_uuid) + resource }, nodes.update = function(node, uuid, assign_slot = NULL) @@ -4456,8 +5739,13 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid, assign_slot = assign_slot) - body <- node$toJSON() + queryArgs <- list(assign_slot = assign_slot) + + if(length(node) > 0) + body <- jsonlite::toJSON(list(node = node), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -4466,17 +5754,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Node$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, slot_number = resource$slot_number, - hostname = resource$hostname, domain = resource$domain, - ip_address = resource$ip_address, first_ping_at = resource$first_ping_at, - last_ping_at = resource$last_ping_at, info = resource$info, - updated_at = resource$updated_at, properties = resource$properties, - job_uuid = resource$job_uuid) + resource }, nodes.delete = function(uuid) @@ -4485,7 +5763,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -4495,17 +5774,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Node$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, slot_number = resource$slot_number, - hostname = resource$hostname, domain = resource$domain, - ip_address = resource$ip_address, first_ping_at = resource$first_ping_at, - last_ping_at = resource$last_ping_at, info = resource$info, - updated_at = resource$updated_at, properties = resource$properties, - job_uuid = resource$job_uuid) + resource }, nodes.ping = function(uuid, ping_secret) @@ -4514,7 +5783,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid, ping_secret = ping_secret) + queryArgs <- list(ping_secret = ping_secret) + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -4524,32 +5794,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Node$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, slot_number = resource$slot_number, - hostname = resource$hostname, domain = resource$domain, - ip_address = resource$ip_address, first_ping_at = resource$first_ping_at, - last_ping_at = resource$last_ping_at, info = resource$info, - updated_at = resource$updated_at, properties = resource$properties, - job_uuid = resource$job_uuid) + resource }, - nodes.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("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) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4559,11 +5818,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - NodeList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, nodes.show = function(uuid) @@ -4572,7 +5827,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4582,17 +5838,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Node$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, slot_number = resource$slot_number, - hostname = resource$hostname, domain = resource$domain, - ip_address = resource$ip_address, first_ping_at = resource$first_ping_at, - last_ping_at = resource$last_ping_at, info = resource$info, - updated_at = resource$updated_at, properties = resource$properties, - job_uuid = resource$job_uuid) + resource }, nodes.destroy = function(uuid) @@ -4601,7 +5847,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -4611,17 +5858,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Node$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, slot_number = resource$slot_number, - hostname = resource$hostname, domain = resource$domain, - ip_address = resource$ip_address, first_ping_at = resource$first_ping_at, - last_ping_at = resource$last_ping_at, info = resource$info, - updated_at = resource$updated_at, properties = resource$properties, - job_uuid = resource$job_uuid) + resource }, repositories.get = function(uuid) @@ -4630,7 +5867,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4640,27 +5878,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Repository$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - repositories.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + repositories.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("repositories") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4670,11 +5903,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - RepositoryList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, repositories.create = function(repository, ensure_unique_name = "false") @@ -4684,7 +5913,12 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- repository$toJSON() + + if(length(repository) > 0) + body <- jsonlite::toJSON(list(repository = repository), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -4693,12 +5927,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Repository$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, repositories.update = function(repository, uuid) @@ -4707,8 +5936,13 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- repository$toJSON() + queryArgs <- NULL + + if(length(repository) > 0) + body <- jsonlite::toJSON(list(repository = repository), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -4717,12 +5951,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Repository$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, repositories.delete = function(uuid) @@ -4731,7 +5960,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -4741,12 +5971,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Repository$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, repositories.get_all_permissions = function() @@ -4756,6 +5981,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4765,27 +5991,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Repository$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - repositories.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + repositories.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("repositories") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4795,11 +6016,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - RepositoryList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, repositories.show = function(uuid) @@ -4808,7 +6025,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4818,12 +6036,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Repository$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, repositories.destroy = function(uuid) @@ -4832,7 +6045,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -4842,12 +6056,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Repository$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, specimens.get = function(uuid) @@ -4856,7 +6065,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4866,28 +6076,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Specimen$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, material = resource$material, - updated_at = resource$updated_at, properties = resource$properties) + resource }, - specimens.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + specimens.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("specimens") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -4897,11 +6101,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - SpecimenList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, specimens.create = function(specimen, ensure_unique_name = "false") @@ -4911,7 +6111,12 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- specimen$toJSON() + + if(length(specimen) > 0) + body <- jsonlite::toJSON(list(specimen = specimen), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -4920,13 +6125,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Specimen$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, material = resource$material, - updated_at = resource$updated_at, properties = resource$properties) + resource }, specimens.update = function(specimen, uuid) @@ -4935,8 +6134,13 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- specimen$toJSON() + queryArgs <- NULL + + if(length(specimen) > 0) + body <- jsonlite::toJSON(list(specimen = specimen), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -4945,13 +6149,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Specimen$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, material = resource$material, - updated_at = resource$updated_at, properties = resource$properties) + resource }, specimens.delete = function(uuid) @@ -4960,7 +6158,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -4970,28 +6169,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Specimen$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, material = resource$material, - updated_at = resource$updated_at, properties = resource$properties) + resource }, - specimens.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("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) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5001,11 +6194,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - SpecimenList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, specimens.show = function(uuid) @@ -5014,7 +6203,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5024,13 +6214,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Specimen$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, material = resource$material, - updated_at = resource$updated_at, properties = resource$properties) + resource }, specimens.destroy = function(uuid) @@ -5039,7 +6223,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -5049,13 +6234,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Specimen$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, material = resource$material, - updated_at = resource$updated_at, properties = resource$properties) + resource }, logs.get = function(uuid) @@ -5064,7 +6243,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5074,30 +6254,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Log$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - object_uuid = resource$object_uuid, event_at = resource$event_at, - event_type = resource$event_type, summary = resource$summary, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at, modified_at = resource$modified_at, - object_owner_uuid = resource$object_owner_uuid) + resource }, - logs.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + logs.index = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { endPoint <- stringr::str_interp("logs") 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(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5107,11 +6278,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - LogList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, logs.create = function(log, ensure_unique_name = "false") @@ -5121,7 +6288,12 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- log$toJSON() + + if(length(log) > 0) + body <- jsonlite::toJSON(list(log = log), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -5130,15 +6302,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Log$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - object_uuid = resource$object_uuid, event_at = resource$event_at, - event_type = resource$event_type, summary = resource$summary, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at, modified_at = resource$modified_at, - object_owner_uuid = resource$object_owner_uuid) + resource }, logs.update = function(log, uuid) @@ -5147,8 +6311,13 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- log$toJSON() + queryArgs <- NULL + + if(length(log) > 0) + body <- jsonlite::toJSON(list(log = log), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -5157,15 +6326,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Log$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - object_uuid = resource$object_uuid, event_at = resource$event_at, - event_type = resource$event_type, summary = resource$summary, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at, modified_at = resource$modified_at, - object_owner_uuid = resource$object_owner_uuid) + resource }, logs.delete = function(uuid) @@ -5174,7 +6335,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -5184,30 +6346,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Log$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - object_uuid = resource$object_uuid, event_at = resource$event_at, - event_type = resource$event_type, summary = resource$summary, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at, modified_at = resource$modified_at, - object_owner_uuid = resource$object_owner_uuid) + resource }, - logs.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + logs.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { endPoint <- stringr::str_interp("logs") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5217,11 +6370,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - LogList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, logs.show = function(uuid) @@ -5230,7 +6379,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5240,15 +6390,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Log$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - object_uuid = resource$object_uuid, event_at = resource$event_at, - event_type = resource$event_type, summary = resource$summary, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at, modified_at = resource$modified_at, - object_owner_uuid = resource$object_owner_uuid) + resource }, logs.destroy = function(uuid) @@ -5257,7 +6399,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -5267,15 +6410,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Log$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - object_uuid = resource$object_uuid, event_at = resource$event_at, - event_type = resource$event_type, summary = resource$summary, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at, modified_at = resource$modified_at, - object_owner_uuid = resource$object_owner_uuid) + resource }, traits.get = function(uuid) @@ -5284,7 +6419,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5294,28 +6430,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Trait$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at) + resource }, - traits.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + traits.index = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { endPoint <- stringr::str_interp("traits") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5325,11 +6454,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - TraitList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, traits.create = function(trait, ensure_unique_name = "false") @@ -5339,7 +6464,12 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- trait$toJSON() + + if(length(trait) > 0) + body <- jsonlite::toJSON(list(trait = trait), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -5348,13 +6478,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Trait$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at) + resource }, traits.update = function(trait, uuid) @@ -5363,8 +6487,13 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- trait$toJSON() + queryArgs <- NULL + + if(length(trait) > 0) + body <- jsonlite::toJSON(list(trait = trait), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -5373,13 +6502,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Trait$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at) + resource }, traits.delete = function(uuid) @@ -5388,7 +6511,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -5398,28 +6522,21 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Trait$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at) + resource }, - traits.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + traits.list = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact") { 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(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5429,11 +6546,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - TraitList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, traits.show = function(uuid) @@ -5442,7 +6555,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5452,13 +6566,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Trait$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at) + resource }, traits.destroy = function(uuid) @@ -5467,7 +6575,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -5477,13 +6586,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Trait$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - properties = resource$properties, created_at = resource$created_at, - updated_at = resource$updated_at) + resource }, virtual_machines.get = function(uuid) @@ -5492,7 +6595,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5502,27 +6606,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - virtual_machines.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + virtual_machines.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("virtual_machines") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5532,22 +6631,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachineList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - virtual_machines.create = function( - virtual_machine, ensure_unique_name = "false") + virtual_machines.create = function(virtualmachine, + ensure_unique_name = "false") { endPoint <- stringr::str_interp("virtual_machines") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- virtual_machine$toJSON() + + if(length(virtualmachine) > 0) + body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -5556,22 +6656,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - virtual_machines.update = function(virtual_machine, uuid) + virtual_machines.update = function(virtualmachine, uuid) { endPoint <- stringr::str_interp("virtual_machines/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- virtual_machine$toJSON() + queryArgs <- NULL + + if(length(virtualmachine) > 0) + body <- jsonlite::toJSON(list(virtualmachine = virtualmachine), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -5580,12 +6680,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, virtual_machines.delete = function(uuid) @@ -5594,7 +6689,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -5604,12 +6700,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, virtual_machines.logins = function(uuid) @@ -5618,7 +6709,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5628,12 +6720,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, virtual_machines.get_all_logins = function() @@ -5643,6 +6730,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5652,27 +6740,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, - virtual_machines.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + virtual_machines.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("virtual_machines") 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(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5682,11 +6765,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachineList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, virtual_machines.show = function(uuid) @@ -5695,7 +6774,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5705,12 +6785,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, virtual_machines.destroy = function(uuid) @@ -5719,7 +6794,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -5729,12 +6805,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - VirtualMachine$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, hostname = resource$hostname, - created_at = resource$created_at, updated_at = resource$updated_at) + resource }, workflows.get = function(uuid) @@ -5743,7 +6814,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5753,28 +6825,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Workflow$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - definition = resource$definition, updated_at = resource$updated_at) + resource }, - workflows.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + workflows.index = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("workflows") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5784,11 +6850,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - WorkflowList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, workflows.create = function(workflow, ensure_unique_name = "false") @@ -5798,7 +6860,12 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- workflow$toJSON() + + if(length(workflow) > 0) + body <- jsonlite::toJSON(list(workflow = workflow), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -5807,13 +6874,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Workflow$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - definition = resource$definition, updated_at = resource$updated_at) + resource }, workflows.update = function(workflow, uuid) @@ -5822,8 +6883,13 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- workflow$toJSON() + queryArgs <- NULL + + if(length(workflow) > 0) + body <- jsonlite::toJSON(list(workflow = workflow), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -5832,13 +6898,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Workflow$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - definition = resource$definition, updated_at = resource$updated_at) + resource }, workflows.delete = function(uuid) @@ -5847,7 +6907,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -5857,28 +6918,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Workflow$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - definition = resource$definition, updated_at = resource$updated_at) + resource }, - workflows.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + workflows.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("workflows") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5888,11 +6943,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - WorkflowList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, workflows.show = function(uuid) @@ -5901,7 +6952,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5911,13 +6963,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Workflow$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - definition = resource$definition, updated_at = resource$updated_at) + resource }, workflows.destroy = function(uuid) @@ -5926,7 +6972,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -5936,13 +6983,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Workflow$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_at = resource$modified_at, modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - name = resource$name, description = resource$description, - definition = resource$definition, updated_at = resource$updated_at) + resource }, groups.get = function(uuid) @@ -5951,7 +6992,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5961,30 +7003,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, - groups.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact", include_trash = NULL) + groups.index = function(filters = NULL, where = NULL, + order = NULL, select = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact", + include_trash = NULL) { endPoint <- stringr::str_interp("groups") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count, include_trash = include_trash) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count, + include_trash = include_trash) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -5994,11 +7029,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - GroupList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, groups.create = function(group, ensure_unique_name = "false") @@ -6008,7 +7039,12 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- group$toJSON() + + if(length(group) > 0) + body <- jsonlite::toJSON(list(group = group), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -6017,15 +7053,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, groups.update = function(group, uuid) @@ -6034,8 +7062,13 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- group$toJSON() + queryArgs <- NULL + + if(length(group) > 0) + body <- jsonlite::toJSON(list(group = group), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -6044,15 +7077,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, groups.delete = function(uuid) @@ -6061,7 +7086,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -6071,32 +7097,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, - groups.contents = function( - filters = NULL, where = NULL, order = NULL, - distinct = NULL, limit = "100", offset = "0", - count = "exact", include_trash = NULL, uuid = NULL, - recursive = NULL) + groups.contents = function(filters = NULL, + where = NULL, order = NULL, distinct = NULL, + limit = "100", offset = "0", count = "exact", + include_trash = NULL, uuid = NULL, recursive = NULL) { endPoint <- stringr::str_interp("groups/contents") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$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) + queryArgs <- list(filters = filters, where = where, + order = order, distinct = distinct, limit = limit, + offset = offset, count = count, include_trash = include_trash, + uuid = uuid, recursive = recursive) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -6106,15 +7123,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, groups.trash = function(uuid) @@ -6123,7 +7132,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -6133,15 +7143,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, groups.untrash = function(uuid) @@ -6150,7 +7152,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -6160,30 +7163,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, - groups.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact", include_trash = NULL) + groups.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("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) + 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$exec("GET", url, headers, body, @@ -6193,11 +7189,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - GroupList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, groups.show = function(uuid) @@ -6206,7 +7198,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -6216,15 +7209,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, groups.destroy = function(uuid) @@ -6233,7 +7218,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -6243,15 +7229,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - Group$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, name = resource$name, - description = resource$description, updated_at = resource$updated_at, - group_class = resource$group_class, trash_at = resource$trash_at, - is_trashed = resource$is_trashed, delete_at = resource$delete_at) + resource }, user_agreements.get = function(uuid) @@ -6260,7 +7238,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -6270,35 +7249,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, - user_agreements.index = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + 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) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -6308,22 +7274,23 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreementList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, - user_agreements.create = function( - user_agreement, ensure_unique_name = "false") + user_agreements.create = function(useragreement, + ensure_unique_name = "false") { endPoint <- stringr::str_interp("user_agreements") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- list(ensure_unique_name = ensure_unique_name) - body <- user_agreement$toJSON() + + if(length(useragreement) > 0) + body <- jsonlite::toJSON(list(useragreement = useragreement), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, queryArgs, private$numRetries) @@ -6332,30 +7299,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, - user_agreements.update = function(user_agreement, uuid) + user_agreements.update = function(useragreement, uuid) { endPoint <- stringr::str_interp("user_agreements/${uuid}") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) - body <- user_agreement$toJSON() + queryArgs <- NULL + + if(length(useragreement) > 0) + body <- jsonlite::toJSON(list(useragreement = useragreement), + auto_unbox = TRUE) + else + body <- NULL response <- private$REST$http$exec("PUT", url, headers, body, queryArgs, private$numRetries) @@ -6364,20 +7323,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, user_agreements.delete = function(uuid) @@ -6386,7 +7332,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -6396,20 +7343,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, user_agreements.signatures = function() @@ -6419,6 +7353,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -6428,20 +7363,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, user_agreements.sign = function() @@ -6451,6 +7373,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("POST", url, headers, body, @@ -6460,35 +7383,22 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, - user_agreements.list = function( - filters = NULL, where = NULL, order = NULL, - select = NULL, distinct = NULL, limit = "100", - offset = "0", count = "exact") + user_agreements.list = function(filters = NULL, + where = NULL, order = NULL, select = NULL, + distinct = NULL, limit = "100", offset = "0", + count = "exact") { endPoint <- stringr::str_interp("user_agreements") url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list( - filters = filters, where = where, order = order, - select = select, distinct = distinct, limit = limit, - offset = offset, count = count) + queryArgs <- list(filters = filters, where = where, + order = order, select = select, distinct = distinct, + limit = limit, offset = offset, count = count) + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -6498,11 +7408,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreementList$new( - kind = resource$kind, etag = resource$etag, - items = resource$items, next_link = resource$next_link, - next_page_token = resource$next_page_token, - selfLink = resource$selfLink) + resource }, user_agreements.new = function() @@ -6512,6 +7418,7 @@ Arvados <- R6::R6Class( headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -6521,20 +7428,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, user_agreements.show = function(uuid) @@ -6543,7 +7437,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("GET", url, headers, body, @@ -6553,20 +7448,7 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, user_agreements.destroy = function(uuid) @@ -6575,7 +7457,8 @@ Arvados <- R6::R6Class( url <- paste0(private$host, endPoint) headers <- list(Authorization = paste("OAuth2", private$token), "Content-Type" = "application/json") - queryArgs <- list(uuid = uuid) + queryArgs <- NULL + body <- NULL response <- private$REST$http$exec("DELETE", url, headers, body, @@ -6585,25 +7468,13 @@ Arvados <- R6::R6Class( if(!is.null(resource$errors)) stop(resource$errors) - UserAgreement$new( - uuid = resource$uuid, etag = resource$etag, - owner_uuid = resource$owner_uuid, created_at = resource$created_at, - modified_by_client_uuid = resource$modified_by_client_uuid, - modified_by_user_uuid = resource$modified_by_user_uuid, - modified_at = resource$modified_at, portable_data_hash = resource$portable_data_hash, - replication_desired = resource$replication_desired, - replication_confirmed_at = resource$replication_confirmed_at, - replication_confirmed = resource$replication_confirmed, - updated_at = resource$updated_at, manifest_text = resource$manifest_text, - name = resource$name, description = resource$description, - properties = resource$properties, delete_at = resource$delete_at, - file_names = resource$file_names, trash_at = resource$trash_at, - is_trashed = resource$is_trashed) + resource }, getHostName = function() private$host, getToken = function() private$token, - setRESTService = function(newREST) private$REST <- newREST + setRESTService = function(newREST) private$REST <- newREST, + getRESTService = function() private$REST ), private = list(